User Manual for Scribe 3.0
Contents
1. Finger Tapping Rest or Word Generation Experiments An experiment is the result of comparing two or more conditions Each experiment name should indicate which conditions were contrasted In the preceding example the experiment would be named Finger Tapping Rest The names used here should be entered on the Experiments panel Experiments should be listed here and in the order in which they were published Do not enter conditions that do not result in activations or were not used in experiments But please document in the Feedback panel that there were in fact conditions or experiments that did not fit the BrainMap coding criteria and why i e no reported coordinates experiments were ROI seeded Most information needed for the sections can be found directly from the original article Do not include any bias or personal input if information is not found in the text Findings should strictly reflect the author s work opinions Because the hypothesis is not always clearly stated in an article this header can be omitted if the author does not explicitly state the expectations The sessions header should only be included if multiple scanning sessions were done otherwise it can be omitted as well Scribe User Manual page 8 The PURPOSE section is usually taken directly from the Introduction and the majority of the time you can find it in the last paragraph Define any abbreviations used The main poin2. Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Describe umr cuhiart rniimne 4 8 0 0 Edit Subjects Healthy Controls Heal Enter a brief name for your subject group Healthy Controis S O Provide Diagnosis Normals a ICD code If applicable please provide concurrent diagnosis ln hd Provide Short Description 5 men 4 women Total subjects l9 Min Age Gender Mixed Max Age Handedness Unknown Mean Age 33 Native Language Unknown Cancel Ok hift Up oOo ChiDowm O Name of Subject Group Provide a brief name for the subject group Normal subjects groups should be referred to as Healthy Controls In the case of subgroups used from a larger group population please enter the subgroup in the following matter Subgroup of Main Group unique feature of the subgroup e g Subgroup of Healthy Controls Males Only Provide Diagnosis Select from the list any medical or psychological conditions ICD Code Most diseases are listed in the International Classification of Diseases ICD If the ICD number is not known usually the case then leave this blank Provide Short Description Enter the ratio of male to female subjects e g 4 women 5 men Also enter the ratio of right handed and left handed subjects e g 6 right handed 4 left handed Include inclusion or ex
3. Braille Reading Classical Conditioning Counting Calculation Cued Explicit Recall Deductive Reasoning Delayed Match To Sample Divided Auditory Attention Drawing Eating Encoding Episodic Recall Face Monitor Discrimination Film Viewing Finger Tapping Fixation Flanker Task Flashing Checkerboard Flexion Extension Free Word List Recall Go No Go Imaninad Maun mant Select Other Remove Experiment Not Saved Close Save Paradigm Class Paradigm Class refers to those experimental paradigms that have been used repeatedly by different researchers Some have become widely known and accepted by brain imagers and have acquired informal or formal names This list is not intended to include a fitting description of every experimental paradigm imaginable but evolves with the field Please refer to the BrainMap Lex available on Brainmap org for more details Select only the Paradigm Class that fits the Activation condition For example if the Activation condition is the Stroop task and the Control condition is Fixation then for Activation Control select Stroop only not Stroop AND Fixation Scribe User Manual page 34 Experiments Behavioral Domain AAO BrainMap Scribe Adler_AA_97 ent 009e Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domair Locations Select the behavioral
4. or talking in the background and 4 human bodies same as for 2 but for human bodies and reduce rating if only part of the body e g torso is visible disregard faces alone CONDITIONS Condition 1 Color Subjects rated color intensity by means of a button push Condition 2 Faces Subjects indicated the degree to which they saw and looked at faces by means of a button push Condition 3 Language Subjects indicated the degree to which they heard read or listened to language by means of a button push Condition 4 Human Bodies Subjects indicated the degree to which they saw and looked at human bodies by means of a button push Condition 5 Rest Subjects fixated on a black screen when it appeared EXPERIMENTS Experiment 1 Color gt Rest Experiment 2 Faces gt Rest Experiment 3 Language gt Rest Experiment 4 Human Bodies gt Rest Scribe User Manual page 10 Just_CC 07 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Enter your prose description here see the Scribe User s Manual PURPOSE The brain activation of a group of high functioning autistic participants was measured using functional magnetic resonance imaging fMRI during the performance of a Tower of London TOL task in comparison with a control group matched with respect to intelligent quotient age and gender HYPOTHESIS This study measured the size of the various segments of the corpus callosu
5. Close Save Check if entering individual subject s data Check this box if the coordinates entered are for individual subjects as opposed to group means Hemisphere Adhere to the standard that left is negative Inspect your table carefully to be sure that all coordinates listed from the left hemisphere have x values that are negative and those from the right hemisphere are positive If not switch the signs of your x values before entering them into the table X mm Y mm Z mm Enter the x y and z values as printed in the table with the exception as noted above SPI Value Enter the SPI value statistic reported in the paper for example z t or r The z score or t statistic can be the mean or the maximum value for the cluster SPI Unit Indicate the variable z t r entered in the SPI Value column Do not enter voxel wise P values in the SPI columns Scribe User Manual page 36 Extent mm Report the extent also referred to as volume or size of the activation recorded in cubic millimeters This number usually ranges from the low hundreds to 1000 or 2000 Do not record the number of voxels not in units of mm e dml 1cc 1cm 1000 mm e 1ul 1mm For other conversions please see http www onlineconversion com volume htm Scribe User Manual page 37 Results Synopsis Just_CC O ent 4 Prose Descr Subjects Conditions Sessions Brain Template Exp
6. Stimulus Response and Instructions Edit Condition Selection Money EITT EE External Variable Verify and Close Provide a Name for this Condition Selection Money Stimulus Choose Stimulus None Visual Shapes responses square i Modality Visual Shapes a 2 color wheel cir Choose Stimulus Type None Up Provide Short Down Description Add Stimulus Remove Stimulus Response Choose Response Modality None Hand Button Press right hand 2 button Choose Response Type None Up Provide Short Description Down Add Response o Remove Response Instruction Choose Instructions None Discriminate Subjects chose between the up Provide Short Description Down Add Instruction Remove Instruction There were 3 different wheels presented 1 10 chance of winning 7 and 90 chance of winning 1 high risk high reward 2 30 chance of winning 2 and 70 chance of winning 1 moderate risk moderate reward 3 two 50 chances of winning 2 equal risk Provide a Name for this Condition Use the same naming system as defined in the prose description Again try to keep the naming convention of the paper but use your best judgment Sometimes authors can be confusing and will invent a very long condition name for a simple task If in the interest of brevity it is necessary to formulate your own condition names then do so
7. enter in all the information for the first experiment EXCEPT for the coordinates Then save the experiment duplicate it and edit the duplication s for the additional experiment s The final step is to go back and enter in the coordinates for all the experiments once they have been created Scribe User Manual page 25 Experiments Context BrainMap Scribe Adler_AA_97 ent Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Locations Provide a brief name for the experiment It should indicate the source of contrast in the image e g Read vs Rest see Submit User s Manual Painful vs Warm Deactivations Select contexts appropriate for your experiment Age Effects Normal Mapping Disease Effects Drug Effects Experimental Design Effects Gender Effects Handedness Effects Learning Linguistic Effects Meta Analysis Norma Mapping Treatment Effects Select Other d Remove Experiment Saved Close Save Provide a brief name for the experiment The names entered here must be the same as those used in the Prose Panel Abbreviations are acceptable but the first use must be defined then the subsequent references can just be entered in the abbreviated form Select contexts appropriate for the experiment Context refers to the broadest category to which an experiment belongs to within the realm of brain imaging Most frequently the context of D
8. files which allows each type of submission to be easily identified Regardless of the type of submission the first panel of the BrainMap Scribe interface is entitled Citation and the last is entitled Feedback The interface is designed to enter data from the left to right Some entry panels will not accept information until previous panels have been completed Furthermore all panels except Experiment require paper level information Some fields provide drop down menus and some provide windows for free form entry The words from the drop down menus are all keywords that users may use to conduct searches using BrainMap Sleuth www brainmap org sleuth Save BrainMap Database Submission It is a good idea to save your changes to file after completing each major panel To do so click on the top left program menu File gt Save As This saves the information in an ent file or a vom file depending on your choice Enter the file name in the following format Author Journal Year ent If you are on a PC be sure and type in file extension Journal names should be abbreviated if they are more than one word and years listed as the last two digits of the published year for example Lee HBM_02 ent or Lee _Neurolmage 02 vbm Please save the PDF file this way as well when submitting Scribe User Manual page 3 Functional or Structural Database Submissions When Scribe is launched you will see the following dialo
9. i e centers of mass of sites of activation are extracted from the SPls and are entered into the database Initially the BrainMap database archived only functional neuroimaging experiments In 2007 the BrainMap team initiated efforts to expand into archiving structural neuroimaging data Specifically voxel based morphometry VBM which is a statistical analysis for investigating structural differences between two groups of subjects e g areas of increased gray matter density for patients vs healthy controls had also achieved community standardization such that results reported in the form of stereotactic coordinates in the same form as for functional neuroimaging data had become the norm Formal integration by meta analyses on structural neuroimaging findings thus become possible Following multiple years of data entry as well as database servlet and software programming and development the BrainMap VBM database was released to the public in June 2011 The Scribe software application is used to code data and meta data from a functional or structural paper so that this information can be submitted and inserted into the BrainMap database When Scribe is launched a dialog window asks users to select which type of paper they wish to code functional or structural Following this the main application window is configured to match the user s selection Functional submissions are created as ent files while the structural database archives vbm
10. patients have been experiencing symptoms specify days months years Medication If subjects are medicated provide all of the names of the medications Specify the number of subjects taking each medication in the short description Native Language Choose the native language or languages of the subjects or add a new language to the list by choosing Other and typing into the window that appears Min Age Fill in Min Age if reported Only integers are allowed Max Age Fill in Max Age if reported Only integers are allowed Mean Age Fill in Mean Age if reported Only integers are allowed Age Matched Controls Select Yes if the non control patient group and control group have the same similar mean age External Assessments This menu is primarily intended for studies wherein an external assessment Test Score Physical Characteristic etc was correlated with brain morphometry If an experiment correlated an external assessment with the volume of brain matter and provided x y z locations enter it here After selecting the desired option from the menu click the Select button If the exact external assessment from your paper is not in the list provided try your best to fit it into one of the provided categories and then provide the exact test name characteristic etc in the short description Do not add your own external assessment other to the list unless absolutely
11. to be processed simultaneously and identify regions whose activity correlates with the perception of specific features HYPOTHESIS AIMS Researchers expected that there would be correspondingly little correlation in activity between the distinct areas specialized to process these features At the same time because different observers agreed in their intensity rating for the same feature they expected activity in corresponding areas in different observers to be comparably high METHODS Eight normal subjects viewed the first 22 min of the James Bond movie Tomorrow Never Dies on a translucent back projection screen via an angled mirror The movie was interrupted every 2 5 or 3 min for 30 sec with a black screen with no sound rest Five normal human observers were asked to view the same movie clip four times each and rate the intensity of the subjective experience in one of four attributes in each viewing During each of the four viewings each observer indicated by key presses the perceived intensity of one of the four attributes Four keys were available 1 no percept 2 moderate 3 medium 4 intense percept The attributes and instructions were as follows 1 color rate color according to the intensity with which it is perceived 2 faces indicate the degree to which you see and look at faces on the screen 3 language indicate the degree to which you hear read and listen to language reduce rates for reduced intelligibility e g Chinese
12. BrainMap Scribe 3 0 http brainmap org ys r Copyright 2003 2015 Research Imaging Institute University of Texas Health Science Center at San Antonio User Manual for Scribe 3 0 Research Imaging Institute UT Health Science Center San Antonio BrainMap Development Team Peter T Fox M D Angela R Laird Ph D Simon B Eickhoff M D Jack L Lancaster Ph D Mick Fox Programmer Analyst Angela M Uecker Programmer Analyst Michaela Robertson Research Scientist Iliana Sanchez Research Assistant Updated February 2015 Scribe User Manual page 2 Introduction BrainMap has been in step wise development since 1988 and actively in use since 1992 Its purpose is to facilitate the retrieval and understanding of the literature on functional mapping of the human brain and to enable meta analysis of this literature The structure of BrainMap data entry involves three levels of information paper experiment and locations coordinates Paper level information contains fields such as authors year of publication and subject demographics In the BrainMap database experiments are defined as the comparison of two or more imaged conditions that result in a statistical parametric image SPI Papers containing multiple experiments require information for each experiment to be entered separately this includes fields such as the paradigm class and behavioral domain At the location level Talairach or MNI x y z coordinates
13. BrainVOX FSL Human Brain Atlas In House LIPSIA MedxX SPM2 SPM4 SPM5 MNI SPM5 None MNI 3 0 T 1x1xil Scribe User Manual page 22 Results Synopsis Feedback Double click on the software package used and make sure it appears on the right sided panel Select the brain template transform reference and MRI field strength from the drop down menus VBM Software Double click on the software list provided and choose the software used to analyze VBM data Brain Template Click on the drop down menu provided and choose the brain template used to report the stereotactic coordinates Transform If the aligned data was transformed to another coordinate space record the transform used here Reference Space Select the standard coordinate space used when reporting the paper s coordinates MRI Field Strength Click on the drop down menu provided and choose the strength of the MRI magnet used to acquire data in Tesla Resolution mm Scribe User Manual page 23 Provide the final voxel size resolution in mm e g 1x1x1 If this parameter is not provided in the paper provide the Field of View FOV and the slice thickness in mm Smoothing Kernel mm Provide the Gaussian smoothing kernel used in mm If anything is unclear or information is missing please enter it in the short description box If MNI coordinates are reported in Talairach form and the transform is not s
14. Choose a Stimulus Modality Choose the sensory mechanism through which the subject was stimulated That is what was used to stimulate one of their five senses while they were in the scanner Choose Stimulus Type Select the specific stimulus from the drop down menu If these choices do not match the stimulus exactly choose Other then click the Add button Scribe User Manual page 16 Provide Short Description Fill in any additional details about the stimulus that are necessary for a firm understanding of the paper or that add interest to the study This might include information about the exact type of stimulus not apparent from the Stimulus Type selected for example Letter Strings or Spanish Nouns Don t forget to click on Add Choose Overt Response Modality Enter measurable responses only for example imagined movement and silent verb generation are covert responses and should not be entered If the response was a button press choose Hand for the modality Choose Overt Response Type Select the appropriate response type Use the Overt Response Type Ocular for saccades or eye movement only not for simply looking at something Don t forget to click on Add Provide Short Description Fill in any additional details about the response that are truly necessary for a firm understanding of the study Choose Instructions Choose the instruction that best describes those u
15. Healthy Controls Provide Diagnosis Select from the list any medical or psychological conditions Age of Onset Provide the age in years when patients began to experience symptoms of disease condition Only integers are allowed Treatment Status Select the treatment Medicated or Unmedicated from the pull down list If Mixed provide the number of subjects unmedicated and medicated in the short description Total Number of Subjects Enter the number of subjects studied into the space provided Only integers are allowed Handedness Choose one option from the menu to describe the handedness of the subject group Use the Mixed option if the subjects had different handedness Right Handed Left Handed Ratio Provide the number of right handed and left handed people ex 5 5 Scribe User Manual page 42 Gender Select the gender from the pull down menu If Mixed gender is selected indicate the number of male and female subjects in the short description Male Female Provide the number of males and females ex 5 5 Sex Matched Controls Select Yes if the non control patient group and control group have the same similar ratio of males to females ICD Code Most diseases are listed in the International Classification of Diseases ICD If the ICD number is unknown usually the case then leave this blank Duration of Illness Provide the mean amount of time the
16. X 78229 3900 Enter the requested information about the submitter you Check the appropriate box if you are an author on the paper By clicking the Save as Defaults button you can save your submitter information so that you will not have to re type it on subsequent submissions Scribe User Manual page 7 Prose Description When entering a paper into BrainMap special care should be taken when writing the Prose Description The new format for prose entry differs from what has been previously documented in previous versions of Scribe The prose description should e Describe only the purpose of the study as well as the experimental design no background results or discussion should be included e Be illustrative but as succinct as possible e Be written in third person past tense format e Include sufficient specific information for each condition and experiment so that a reader will fully understand the experimental design of the study The prose section should be broken down into the following sections PURPOSE HYPOTHESIS SESSIONS METHODS CONDITIONS EXPERIMENTS According to BrainMap s system of describing a paper functional studies are broken down into Conditions and Experiments Conditions Subjects perform tasks under certain conditions and these conditions are contrasted in an experiment Each condition used in a BrainMap defined experiment should be briefly described and named by simple terms such as Read
17. ap coding scheme Brain Template Experiments Results Synopsis Feedback 1SO H20 PET 18f fdg pet 18f fluorodeoxyglucose positron er Abercrombie H C Abler B Abplanalp B Abrahams S Up Down Upon opening a saved ent file a dialog may appear displaying the most recent changes to the BrainMap Coding scheme Each line will begin with whether or not the following attribute was added or removed from the Coding Scheme Scribe User Manual page 40 Voxel Based Morphometry Neuroimaging Submissions The interface for VBM submissions is very similar to that for functional submissions Here we highlight the differences Due to the reduced complexity of VBM papers there is no Prose Description Instead we ask that you paste in the published abstract for your submission The Subjects panel has a few minor modifications based on the details for the subject groups e Anew panel VBM Analysis has been added for VBM submissions The Experiments panel is greatly simplified in comparison to functional submissions Schmidt Wilcke_Ceph_08 vbm Submitter Abstract Subjects Sessions VBM Analysis Experiments Feedback Title Subtle grey matter changes between migraine patients and healthy controls Journal Institution Cephalalgia B l University of Regensburg B Date City Jan B 2008 B Regensburg B Medline Num Volume Country Germany B 17986275 28 Page From Pa
18. clusion criteria as well as any relevant subject group specific information Total Subjects Enter a number into the space provided Only integers are allowed Scribe User Manual page 13 Gender Select the gender from the pull down menu If Mixed gender is selected indicate the number of male and female subjects in the short description Handedness Choose one option from the menu to describe the handedness of the subject group Use the Mixed option if the subjects had different handedness Native Language Choose the native language or languages of the subjects or add a new language to the list by choosing Other and typing into the window that appears Ages of Subjects Fill in Min Age Max Age and Mean Age if reported Only integers are allowed Scribe User Manual page 14 Conditions e080 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Each stimulation or control state would be considered a condition Please provide the names of your conditions Enter only conditions used in the experiments including the control conditions e g Rest or Baseline To change the order listed to better reflect the order used in the experiment click the Shift Up or Shift Down button at the bottom of the window Scribe User Manual page 15 Condition Properties
19. curacy positively correlating with activation Clinical Dementia Rating negatively correlating with activation Experience Dependent Change Experimental results could have been affected by experience Example learning order priming repetition training Group Conditions of an experiment are identical but were endured by two different subject groups Example PTSD Patients vs Healthy Controls Session Conditions of an experiment were identical and were endured by only one group but during more than one session Example Post Treatment Session vs Baseline PTSD Patients Example 1 For the Contrast field you have the opportunity to indicate which aspects of the conditions differed in a specific experiment For instance an experiment might involve the following Condition 1 the subject focused on a fixation point while a checkerboard wedge stimulated one part of the visual field There was no response Condition 2 the subject focused on a fixation point while a checkerboard wedge stimulated a more peripheral part of the visual field There was no response You notice that both are described as Stimulus Modality Visual Response Modality None Response Type None Instruction Attend The point of interest of this experiment is the different areas stimulated by the checkerboard In this experiment the choice of contrast selected would be Stimulus Type because it was the stimulus that differed between conditions All other fi
20. domain s Possible Behavioral Domain s Selected Behavioral Domain s L Cognition Perception Somesthesis Pain L Emotion Pharmacology L Perception L Interoception Action Pharmacology Remove Experiment Not Saved Close Save Behavioral Domain The categories on the left provide several subcategories as drop down menus Double click on the categories to see the related subcategories These categories and subcategories classify the mental operations likely to be isolated by the experimental contrast Select only the Behavioral Domain that fits the Activation condition For example if the Activation condition is semantic in nature and the Control condition is phonological in nature then for Activation Control select Semantics only not Semantics AND Phonology Use both Behavioral Domains of Cognition Language Speech and Action Execution Speech with overt speech production but with covert speech production use only the Behavioral Domain of Cognition Language Speech Scribe User Manual page 35 Experiments Locations AMO BrainMap Scribe Adler_AA_97 ent 009 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast Paradigm Class Behavioral Domain Check if entering individual subject s data Hemisphere Xmm Ymm zmm vae Pon eem 10 68 20 3 0 z Left Add Row Remove Row Experiment Not Saved
21. e 19 Conditions Verify and Close Edit Condition Warm l Condition Properties External Variable When you are finished with editing click Verify and Close to verify information and update the paper or Cancel to close this dialog Cancel and Close Verify and Close this dialog Once all condition information has been entered click on the Verify and Close this dialog button To discard the changes select Cancel and Close Scribe User Manual page 20 Sessions 08 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Session refers to the period of time between the scanning recording set up and the release of the subject Single Session v Multiple Sessions Placebo Injection Add Session Fentanyl Injection Edit Session J Remove Session J Sessions refers to the period of time between the scanning recording set up and the release of a subject Most studies occur during only one session If a subject is set up released and then set up again the second set up marks the beginning of a second session Before and after treatment studies and before and after practice studies would involve multiple sessions e For one session studies no entries are required on this panel e For multiple sessions check on Multiple Sessions and click the Add Session button A m
22. elds would remain unchecked Example 2 If the experiment involved Condition 1 subject viewed nouns on a screen and was asked to generate verbs aloud which pertain to the nouns on the screen and Condition 2 subject viewed nouns on a screen and was asked to read the words aloud the only difference here is in the instructions For both conditions the stimulus is visual words and the response is speech In this case the instructions for Condition 1 would be Generate and the instructions for Condition 2 would be Read It is implied that during Condition 1 the subject had to read the nouns first in order to generate verbs Therefore the contrast between the conditions is only in Instructions All other fields would remain unchecked Example 3 If the experiment involved Condition 1 subject listened to nouns presented aurally one ata time with instructions to generate verbs which pertain to the nouns and Condition 2 subject listened to nouns presented one at a time and was instructed to generate words that rhyme with the nouns then in this case all three fields stimulus response instructions would be entered identically for the two conditions However the generation performed in each condition was indeed different Therefore enter again the contrast as Instructions All other fields would remain unchecked Example 4 Group Contrast If the conditions of an experiment are identical but were endured by two different gro
23. er the published x y z coordinates were extracted from the Center of Mass or Peak Voxel of the observed cluster Description If relevant specify the external assessment as you did in the Subjects panel If corrected for multiple comparisons include the method of correction e g Family wise Error Correction etc here Save VBM BrainMap Database Submission After all information has been entered save the BrainMap database submission by clicking on the top left program menu File gt Save As This saves the information in a vbm file Enter the file name in the following format Author Journal Year Journal names should be abbreviated and years listed as the last two digits of the published year for example Lee HBM_02 vbm Upon completion email your vbm file and a pdf of the original article to submissions brainmap org for review and insertion into the database It is recommended that 1 2 articles be sent first for review to receive feedback rather than sending many ineligible or miscoded files at the same time Scribe User Manual page 46 Troubleshooting Scribe says that I m missing an essential file Data file missing Unable to find an essential file SearchList xml Try checking your internet connection or Z configuring your proxy server settings under Options This can indicate one of two things First the BrainMap web server may be down for maintenance In this ca
24. eriments Results Synopsis Feedback Enter in a brief prose explaining the results synopsis of the paper The 2 groups generally activated the same cortical areas to similar degrees However there were 3 indications of underconnectivity in the group with autism First the degree of synchronization i e the functional connectivity or the correlation of the time series of the activation between the frontal and parietal areas of activation was lower for the autistic than the control participants Second relevant parts of the corpus callosum through which many of the bilaterally activated cortical areas communicate were smaller in cross sectional area in the autistic participants Third within the autism group but not within the control group the size of the genu of the corpus callosum was correlated with frontal parietal functional connectivity These findings suggest that the neural basis of altered cognition in autism entails a lower degree of integration of information across certain cortical areas resulting from reduced intracortical connectivity The results add support to a new theory of cortical underconnectivity in autism which posits a deficit in integration of information at the neural and cognitive levels To enter the results synopsis of a paper copy the published abstract from Medline or PubMed Delete the first sentences that deal with the introduction methods and design of the study and leave only the sentences concerning the r
25. essage box will then appear prompting you to enter at least two sessions e lf your paper includes multiple sessions be sure to include this design in the prose description Scribe User Manual page 21 Sessions Session Name BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Session refers to the period of time between the scanning recording set up and the release of the subject C Single Session V Masisinta ennmi i 009A Edit Session Fentanyl Injection Placebo Injection Shadi eban Session Name Fentanyl Injection Description Subjects were injected with fentany just prior to scanning Give the session a brief name for example Before Treatment or After Therapy Description of this Session Describe the session including sufficient detail to distinguish this session from other sessions and to give a firm understanding of the study Please use a complete sentence to describe the session Analysis Citation Submitter Software Packages Double click to select one or more software packages Template Brain If Talairach 1967 Choose Origin Transform Reference Space MRI Field Strength Resolution e g 1x1x1 mm or FOV and Slice Thickness Smoothing Kernel mm Provide Short Description Prose Descr Subjects Conditions Sessions Experiments AFNI AIR Brain Voyager BRAINS
26. esults and conclusions DO NOT edit the synopsis to include your own interpretation of the study Only change verbiage to reflect a third person past tense view Scribe User Manual page 38 Feedback Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis This paper is missing information usually required for BrainMap inclusion This paper contains both structural and functional experiments Please use this window to record any questions or comments you may have on the paper Also if you feel like the BrainMap Coding scheme did not allow for your paper to be easily coded please check the box and explain your reasoning in the comment box The comments in the feedback section will not be reflected in the database and will only be viewed internally by the BrainMap team Document whether conditions or experiments were excluded due to not being used in analysis or not being whole brain Also indicate if the paper contains a functional structural study that needs to be coded separately Upon completion email your ent file and a pdf of the original article to submissions brainmap org for review and insertion into the database It is recommended that 1 2 articles be sent first for review to receive feedback prior to sending large batches BrainMap Coding Scheme Changes Scribe User Manual page 39 Toyomura_Nl_11 ent File Options Help Submitter Prose Descr Sub
27. g window BrainMap Paper Type Please choose which type of paper to code Functional ent or Structural vbm Structural Functional Selecting Structural takes you to the interface for a VBM submission while selecting Functional will take you to the interface for an ENT submission In this manual we will first describe how to generate a submission for the BrainMap functional neuroimaging database On page 40 we address the modifications necessary to generate a BrainMap voxel based morphometry submission You can find an additional manual online for our sparse method of coding used in functional studies that do not make use of the behavioral domain Functional Neuroimaging Submissions Citation Title Prose Descr Subjects Conditions Sessions Scribe User Manual page 4 Analysis Experiments Results Synopsis Feedback The balance between feeling and knowing affective and cognitive empathy are reflected in the brain s intrinsic functional dynamics Journal Institution Social Cognitive and Affective Neuroscience NYU Langone Medical Center Date City Aug 2012 New York Pubmed ID Volume Country 21896497 0 United States Page From Page To 727 737 Citation Keywords Authors limbic structures Select affectve empathy Aasen I Select Cox CL 150 H20 PET cognitive empathy Abbott D F Uddin L Q 18f fdg pet pense fMRI Abdallah S A Martino A D 18f fluorodeoxyglucose p
28. ge To 1 4 Citation Keywords Ch E 18F FDG PET 22q11 22q11 2 deletion syndrome 22qD 5 HT 5 HT 1A receptor S HT2A receptor 5 HTT Q DC WAY100635 18F FDG PET la MTrp brain trapping Abstinence cingulate cortex imaging migraine voxel based morphometry Authors Aasen Abbott D F Abe M Abe O Abele M Aberg L E Absinta M Acker J D Acosta Cabronero J Acton P D Adali T Aarsland D 0 a v Schmidt Wilcke T Gansbauer S Neuner T Bogdahn U Maya Scribe User Manual page 41 Subjects Subject Group Edit Subjects Migraine Patients Subject Description _ ipti External Assessments Enter a brief name for your subject group Migraine Patients Provide Diagnosis Migraines B ICD code Age of Onset 0 Duration of Illness Treatment Status Mixed B Medication NSAID Total Number of Subjects 35 Native Language Unknown B Handedness Unknown Ages of Subjects Right Handed Left Handed Ratio Min Age 18 Gender Mixed B Max Age 49 Male Female Ratio 3 32 Mean Age 32 Sex Matched Controls O Yes No O Unknown Age Matched Controls Oira Mio sy Provide Short Description 35 migraine patients 3 male 32 female 19 patients with menstrual migraine 16 patients without menstrual migraine SEEE Cancel EEE Name of Subject Group Provide a brief name for the subject group for example
29. he Up Down buttons to reorganize the keywords as needed If the appropriate keywords used in your paper are not included in the list provided click the Other button and type in the keyword in the window provided e Enter the exact keyword listed for example fMRI and functional MRI are two different keywords e Do not use capital letters except for proper names nouns e Enter only the keywords published with the paper If there are no keywords listed leave this field blank Authors Enter all authors listed on the paper e Format should be last name followed by first name initials with no punctuation included e Do not add another version of an author s name that already appears in the database e g Friston K and Friston K J e List authors in the order of appearance on the paper e Do not hyphenate first names of authors Example Marie Claude Antoinette should be entered as Antoinette M C not as Antoinette M C Submitter Citation PET aaa Prose Descr Subjects Conditions Sessions Scribe User Manual page 6 Analysis Experiments Results Synopsis Feedback Check if you are an author Name Iliana Sanchez Email sancheziS uthscsa edu Phone 210 567 8215 Position Research Assistant Staff Save As Defaults Coding Author Institution and Address The University of Texas Health Science Center at San Antonio Research Imaging Center 7703 Floyd Curl Drive MC 6240 San Antonio T
30. iments Subjects O 0 0 Adler_AA_97 ent Context Functional Imaging S i s 4 Conditions Sessions Contrast ParadigmClass Behavioral Domain Locations _ Select subject group s for this experiment Possible oo Group s Selected oe Group s Experiment Saved This panel contains the list of groups entered on the previous Subjects panel Click on the group used for the experiment you are presently entering and then click Select Scribe User Manual page 28 Experiments Conditions BrainMap Scribe Adler_AA_97 ent Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects onditions Sessions Contrast Paradigm Class Behavioral Domain Locations Activations Deactivations High Level Control Low Level Control Select conditions used in this experiment Possible Conditions Selected Conditions Warm Painful Painful Warm Select Remove Experiment Saved Save Check the box to indicate whether this experiment reports activations increases or deactivations decreases and whether a high or low level of control was used to contrast with the activation condition Only select Low Level Control for rest or fixation control conditions Select Conditions This panel contains the names of the conditions you provided previously on the Conditions panel Choose the conditions included in this experiment After selecting a condition fro
31. isease Effects will be selected if there is solely a patient group or a comparison between a patient group and healthy controls Normal Mapping will only be selected if the subject group s included in the respective experiment were only healthy controls If Drug Effects is selected you must also select the appropriate pharmacology class in order to save the experiment Experimental Design Effects is ONLY selected for studies in which a technical aspect of the paradigm is being manipulated such as when comparing the effect of the rate of presentation of the stimuli Self Paced n back vs Fixed Paced n back or Slow Words vs Fast Words This is NOT the appropriate context when simply contrasting two or more conditions within healthy subjects that is Normal Mapping Scribe User Manual page 26 Experiments Functional Imaging Select the functional modality from the pull down menu Please provide the magnet strength if available along with any other imaging relevant information Enter New Experiment EEC Subjects Conditions Sessions Contrast ParadigmClass Behavioral Domain Locations Select the functional imaging modality fMRI a Provide a short description Participants were scanned using a Siemens Erlangen Germany Magnetom Vision 1 5T scanner at the University Hospital Basel Experiment Not Saved Close Save Scribe User Manual page 27 Exper
32. jects Conditions Title Effect Journal This paper was last edited 2013 02 01 14 23 42 The following options are the most recent changes to the BrainMap coding scheme Neu added Lancaster Transform SPM8 to Brain Template Brain Template Date added Neuroticism to Conditions External Variable added Response Consistency to Conditions External Variable Aug added Choose to Conditions Instruction Medlin added Predict to Conditions Instruction added Animation human to Conditions Stimulus Response 2162 added Playing Cards to Conditions Stimulus Response jadded Tools to Conditions Stimulus Response Page Fl added Affective Pictures to Experiment Paradigm Class 1507 added Cued Speech to Experiment Paradigm Class added Driving to Experiment Paradigm Class jadded Emotion Induction to Experiment Paradigm Class added Estimation to Experiment Paradigm Class Citatig added Fluency Induction to Experiment Paradigm Class added Gambling Task to Experiment Paradigm Class limbi added Lexical Decision to Experiment Paradigm Class l hz added Multi Tasking to Experiment Paradigm Class 5 htt added Reasoning to Experiment Paradigm Class 6 18 added Self Reflection to Experiment Paradigm Class 7t added Visual Object Identification to Experiment Paradigm Class 99mt added Autism Spectrum Disorders to Subjects Diagnosis removed Autism Spectrum Disorder from Subjects Diagnosis Sessions Recent changes to BrainM
33. m of each participant in the functional imaging study hypothesizing that the sizes of key areas would be smaller in the autistic participants following similar previous findings in purely morphometric studies The secondary hypothesis was that in the participants with autism there would be a positive correlation because the size of the corpus callosum is constraining the functional connectivity In the control group there should be no correlation because there is no constraint on information processing imposed by the size of their corpus callosum and their neural connectivity METHODS In the TOL task the subject must rearrange the positions of 3 distinctive balls in 3 suspended pool pockets until they match a specified goal configuration The standard TOL task was modified for use in the scanner such that the participants did not move any physical ball but indicated in a forced choice response how many moves the optimal solution would require The left side of the display showed the initial state and the right side showed the goal state On each trial the subject is asked to work out how the balls could be rearranged in a sequence of moves such that the configuration on the right comes to be the same as the configuration on the left in the minimum number of moves The rules governing the movements of the balls are only one ball can be moved at a time a ball cannot be moved out of a pocket if another ball is on top of it and a ball must be moved t
34. m the menu click the Select button Scribe User Manual page 29 Experiments Sessions 000 BrainMap Scribe Adler_AA_97 ent 009 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Contrast Paradigm Class Behavioral Domain Locations Select sessions used in this experiment Possible Sessions Selected Sessions Placebo Injection Placebo Injection Fentanyl Injection Fentanyl Injection Experiment Saved F Select Sessions This panel contains the names of the sessions previously provided on the Sessions panel If the paper included more than one session choose the session used in this experiment If not ignore this panel Scribe User Manual page 30 Experiments Contrast Context Functional Imaging Subjects Conditions Sessions Paradigm Class Behavioral Domain Locations Contrast refers to any and all possible sources of activation in a functional image comparing scans from two conditions between levels of a parametric design effect of correlating a regressor or the main effects and interactions in a factorial design V Stimulus Modality External Variable V Stimulus Type Experience Dependent Change Response Modality v Group Response Type Session Instruction Provide a short description Stimulus modality visual and auditory vs none Stimulus type ear symbol picture and music vs none Group pianists vs non musicians Experime
35. necessary Click Ok when complete with the subjects panel to save your information Scribe User Manual page 43 Experiments PR vb Citation Submitter Abstract Subjects Sessions VBM Analysis Feedback An experiment is anything that produces an SPi Statistical Parametric Image Please enter your experiment s PTSD Patients lt Healthy Controls Gray Matter Volume New Experiment Edit Experiment Remove Experiment Duplicate Experiment Shift Up Shift Down In the Experiments panel the options for Context Imaging Modality Subjects Sessions and Locations are the same as for functional submissions A new panel for VBM Analysis has been added Due to the simplicity of VBM protocols there is no panel for Conditions Paradigm Class or Behavioral Domain When naming experiments please specify if the locations are Grey Matter or White Matter increases or decreases Scribe User Manual page 44 Experiments VBM Analysis Context Imaging Modality Subjects Sessions Locations Contrast Gray Matter White Matter CSF Unknown External Assessment None None Double click to select one or more external assessments that pertain to this experiment Threshold P value lt 0 05 Thresholding e Voxel wise Cluster wise Unknown Corrected for Multiple Comparisons Yes i Optimized Yes Observed Changes Controls gt Patients Coordinates Center of Mass Peak Voxel Unknown Description FWE corrected Ex
36. ng Rate Syllable Rate Tammpoarnatiirna Accuracy Select Other Remove Provide Short Description Performance during syncopation and synchronization sessions average and standard deviation of the relative phase with respect to the metronome beat was measured Values were used to analyze variance and interpret results but were not mapped or correlated with activations This menu is primarily intended for studies wherein an external variable was correlated with brain activity If a correlation included an external variable enter the variable here After selecting the desired option from the menu click the Select button The external variable is any measurement taken during the scan e g eye movement heart rate accuracy temperature etc In order to be listed here the external variable must be specifically stated in the study When there is no external variable select None Many studies record accuracy and response time Do not forget to include these external variables Provide Short Description In most instances one of the following scenarios will pertain 1 EV was measured but not in fact used i e often EEG measured to ensure activation is task related 2 EV was measured and used to drive analysis i e correlating performance response rate etc with an image 3 EV was measured and used to clarify results i e behavioral analysis used to clarify neuroimaging findings Scribe User Manual pag
37. nstructions If the description CAN be classified as one of the three components then enter the desired information into one of the short description fields listed above Also making a mental note of the differences in various conditions of your paper during entry will assist in identifying the contrast when entering experiment information later on Scribe User Manual page 17 Before exiting this panel make sure that the way this condition differs from the other condition s in your paper can be determined by looking at the Conditions panel i e don t duplicate conditions To edit existing conditions simply double click on the selected field entry This will populate the condition information back into the drop down menus so that you may edit the details If necessary use the Up Down buttons to organize the condition information to reference time dependent stimuli responses or instructions stimuli presented first listed first while stimuli presented later listed second Scribe User Manual page 18 Conditions External Variable dit Conditi Condition Properties Verify and Close Choose External Variables non imaging variables that are correlated with imaging results Possible External Variables Selected External Variables Civity Grip Force Heart Rate Neuroticism Pain Rating Penile Tumescence Respiratory Data Response Consistency Response Time ROI Activity Skin Conductance Stutteri
38. nt Not Saved Close Save The purpose of the contrast panel is to identify the key aspect of the study In a given experiment the contrast field indicates how the conditions being compared in an experiment are different Multiple selections can be made To choose the source of contrast in the experiment click on the box to the left of the description Make as many choices as appropriate for each experiment Use the blank window in the lower half of this panel to summarize and clarify the contrast of a given experiment A description is required for each contrast selected Stimulus Modality Conditions vary in method of delivery Example Visual vs Auditory Galvanic Stimulation vs No Stimulus Stimulus Type Types of stimulus per modality Example Pictures of Faces vs Fixation Cross Words vs Numbers Response Modality Response varies in method Example Finger Response vs No Response Visual Response vs Hand Response Response Type Types of responses per response modality Example Finger Tapping vs No Response Visual Tracking vs Joystick Control Instruction Directions per condition differ Example Press button only upon presentation of odd numbers vs Press button only upon presentation of even numbers Scribe User Manual page 31 External Variable Non imaging variable correlated with brain activity where this external variable is the means or purpose for cultivating the brain image Example Ac
39. nt indicates which conditions were used in each experiment See Thierry _HBM_03 ent for an example Abbreviations are acceptable but the first use must be defined then the subsequent references can just be entered in the abbreviated form Do not include region of interest ROI experiments but document this in the feedback panel Avoid use of the word task in the condition and experiment name For example Finger Tapping Task should be named Finger Tapping If Rest is used as a control condition list it last The conditions Rest and Fixation do not require a description Some papers report increases and decreases in activation Be sure to inspect the coordinate tables carefully as authors frequently present each in the same table Increases and decreases should be coded and named as separate experiments For example a study may investigate motor function and acquire data on two conditions Finger Tapping and Rest The coordinate table may be titled Increases and Decreases and the paper should be coded with two experiments not one Scribe User Manual page 9 Citation Submitter Piges eee Subjects Conditions Sessions Analysis Experiments Results Synopsis Feedback Enter your prose description here see the Scribe User s Manual PURPOSE Researchers wanted to learn whether functional segregation is maintained during more natural complex and dynamic conditions when many features have
40. o the lowest unoccupied location in the destination pocket The participant indicates the minimum number of moves required by pressing the appropriate button in the response panel and the next problem is presented CONDITIONS 1 Tower of London TOL Task 2 Fixation EXPERIMENTS 1 Tower of Londton TOL Task gt Fixation High Functioning Autism Patients 2 TOL gt Fixation Healthy Controls _ Scribe User Manual page 11 Subjects 0090 Adler_AA_97 ent File Options Help Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback Describe your subject groups Add Group Edit Group Remove Group Duplicate Group Shift Down Click the Add Group button to enter subject information in the Subjects panel that appears as a blank window To enter several similar subject groups enter the first set of data and then click on the group name Next click the Duplicate Group button Data entered for the first group will be copied into a new subject group window Rename the duplicate subject group and change the data as appropriate If coordinates reported are for individual subjects as opposed to group mean data enter each subject s information as an individual group Scribe User Manual page 12 Subjects Subject Group Adler_AA _97 ent File Options Help Citation Submitter Prose Descr
41. ositron er resting state functional connec Abe J Castellanos F X 1 hz social cognition Abel K M Milham M P S htt Other Abelson J L Other Kelly C 5 hydroxytryptamine Abe N 6 18F fluoro L dopa FDOPA PE Abend N S 7t Abercrombie H C 99mtc ecd single photon emission Abler B 99mtc hexamethylpyleneamine ox Abplanalp B 99mtc hmpao spect Abraham A Up Down Abrahams S Up Down Title Capitalize the initial word and those used to capitalize proper names use lowercase for all other words Also capitalize the first letter after a colon Do not leave a period at the end of the title Journal Select the journal name from the pull down menu provided If the journal name does not appear choose Other and enter the journal name without abbreviations Do not list sections Institution List the name of the institution where the data was acquired Enter the university name not the department e Enter Institute of Psychiatry King s College of London as University of London e Enter Wellcome Department of Cognitive Neurology as University College London Medline Num The Medline Number can be located at the PubMed or Medline website If a paper is not archived in PubMed leave this field blank Citation Keywords Scribe User Manual page 5 Click on the desired keywords from the list published with the paper and then click the Select button The chosen keyword will appear in the box to the right Use t
42. pecified in the text please indicate this in the short description All MNI coordinates will be automatically converted to Talairach space using the icbm2tal transform Lancaster et al 2007 All MNI coordinates converted to Talairach space via the Brett transform in the original publication will be subject to 2 transforms 1 reverse Brett to convert back to MNI space and 2 icbm2tal for correct transformation from MNI to Talairach space Scribe User Manual page 24 Experiments 8080 BrainMap Scribe Adler_AA_97 ent Citation Submitter Prose Descr Subjects Conditions Sessions Brain Template Experiments Results Synopsis Feedback An experiment is anything that produces an SPi Statistical Parametric Image Please enter your experiment s Painful vs Warm Activations New Experiment Painful vs Warm Deactivations Fentanyl vs Placebo Activations Fentanyl vs Placebo Deactivations Edit Experiment Remove Experiment Duplicate Experiment Shift Up Shift Down b To enter several similar experiments enter the information for the first experiment and verify and close it Then click on its name and click the Duplicate Experiment button The experiment data will be copied into a new experiment Enter a new name for the new experiment making changes to the existing data as needed Shortcut Many experiments are very similar within a paper so it can save time if you
43. periment Not Saved Close Save Contrast Select the tissue contrast for the given experiment External Assessment This panel contains the names of the external assessments previously provided on the Subjects panel If the paper included more than one external assessment choose the one correlated in the given experiment If no external assessment was correlated then you should select None Threshold P value Provide the p value used for this experiment e g lt 0 01 lt 0 001 lt 0 05 etc Thresholding Select the method of thresholding If information not provided select Unknown Corrected for Multiple Comparisons Select the answer from the pull down menu Optimized State whether the authors used an optimized VBM protocol If the paper states they used the protocol described in Good et al 2001 or Asburner and Friston 2000 then this is optimized Also if images were modulated by the Jacobian determinant then this is also considered optimized Scribe User Manual page 45 Observed Changes If there is greater brain matter volume in controls Healthy Controls gt Patients then this would be Increases in Controls if great brain matter volume in patients Patients gt Healthy Controls then you would select Increases in Patients If the experiment contrasts two patient groups or two healthy control groups choose Neither Coordinates State wheth
44. se try restarting Scribe in an hour or so Alternatively there may be a firewall blocking communication to the BrainMap web server If a successful connection to BrainMap has been made previously then please contact BrainMap technical support to check the web server If you are behind a restrictive firewall and have a known proxy server Scribe can use it to access our BrainMap web server Under File Options there is a menu item called Proxy Settings You will need to know the IP and valid port of the proxy server O Scribe 1 2 Preferences Use HTTP Proxy Host 129 111 249 38 Port 3128
45. sed in the study If a subject was instructed to read words aloud choose Read as the instruction and Speech as the subject s response rather than choosing Speak as the instruction If the instructions were to attend and then press a button upon perceiving a target it is only necessary that you enter the instruction to Attend Button Press should be entered only as a response e Do not confuse detect and discriminate Detect is to discover the presence of i e does target exist While discriminate is to distinguish from another like object by discerning differences i e choosing a target e Do not use attend every time the subjects pay attention to the stimulus otherwise it will be coded in every paper Only use attend in studies where the subjects only instruction is to pay attention to the stimuli Provide Short Description Any additional details about instructions that are necessary for a firm understanding of the study should be entered in this field Please use a complete sentence to describe the instructions e g Subjects generated verbs in response to the presented nouns Also please use the past tense Don t forget to click on Add Short Description Bottom Window Use this space to enter any summary or clarifying information that pertains to the condition as a whole i e that cannot be broken into one of the three components stimulus response i
46. ts we want to capture in the METHODS section is the experimental design being used the response being observed if any and the instructions given to the subjects Any relevant or important details such as training or follow up information can also be included Details will vary per submission To keep the prose description as concise as possible do not repeat information in both the METHODS and CONDITIONS sections This can be done in one of two ways The CONDTIONS can be defined in the METHODS section then only listed under the CONDITIONS header or they can be stated in the METHODS then defined in more detail under the CONDITIONS header Describe the conditions in a chronological sense For example subjects viewed a series of letters after a delay subjects viewed a probe letter and recalled if the probe letter had been one of the encoded letters Capitalize the first letter in all words in the names of conditions and the names of experiments The names of experiments should be taken directly from the coordinate tables or figures in the papers Some experiment names explicitly state the conditions in them Finger Tapping Rest or Finger Tapping vs Rest or Finger Tapping gt Rest and some do not Motor Directed Attention or Conjunction Analysis Use the convention of naming adopted in the paper For conjunction and disjunction analyses normally all conditions are used in all experiments unless the experime
47. ups this would be considered a Group contrast In this case click the box to the left of Group and all other boxes would remain unchecked Example 5 Session Contrast If all of the conditions of an experiment were identical and were endured by only one group but during more than one session this would be considered a Session contrast Select the Session box and all other boxes would remain unchecked Example 6 External Variable Contrast If an experiment included an external variable with which to conduct a correlation with brain activity and this was the means for cultivating brain images choose the Scribe User Manual page 32 box for External Variable This contrast type must be selected for all experiments that investigated the accuracy of the responses Example 7 Experience Dependent Change If the experimental results could have been affected by experience for example learning order priming repetition or training select the box for Experience Dependent Change Scribe User Manual page 33 Experiments Paradigm Class AAO BrainMap Scribe Adler_AA_97 ent e080 Edit Experiment Painful vs Warm Deactivations Context Functional Imaging Subjects Conditions Sessions Contrast aradigm Class Behavioral Domain Locations Select classes appropriate for your experiment Possible Classes Selected Classes Action Observation Pain Monitor Discrimination Acupuncture Anti Saccades
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