Re: [Freesurfer] Group Analysis - 4 groups 3 covariates

On 11/29/2023 2:16 PM, Tejaswi D. Sudhakar wrote: External Email - Use Caution Hi, I would like to run a group analysis on 4 groups (patientM, patientF, controlM, controlF) with 3 covariates (age, cogscore1, cogscore2). I am running with dods - so I would have 16 total

[Freesurfer] Group Analysis - 4 groups 3 covariates

External Email - Use Caution Hi, I would like to run a group analysis on 4 groups (patientM, patientF, controlM, controlF) with 3 covariates (age, cogscore1, cogscore2). I am running with dods - so I would have 16 total regressors. How would I create contrast matrices for

Re: [Freesurfer] Group analysis question

So you are trying to predict the neuropsych battery from brain measurement? This is not how mri_glmfit is usually used, but it is just a GLM so it is possible. You'd have to set up a table for the --table input. You can try running asegstats2table to get an example table, then you'd just set

[Freesurfer] Group analysis question

External Email - Use Caution Hello, I am working on a project using FreeSurfer, and I am trying to set up a whole brain group analysis. However, I am not sure how to set up the FSDG files, etc., as my dependent variable is not a cortical measurement. My dependent variable is a

Re: [Freesurfer] Group Analysis - glmfit results

] Group Analysis - glmfit results [*CAUTION:* Non-UBC Email] Since this is longitudinal, I'm assuming that your contrast is actually something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might both be less than 0

Re: [Freesurfer] Group Analysis - glmfit results

, 2022 12:45:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Group Analysis - glmfit results [CAUTION: Non-UBC Email] Since this is longitudinal, I'm assuming that your contrast is actually something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the the time points

Re: [Freesurfer] Group Analysis - glmfit results

Since this is longitudinal, I'm assuming that your contrast is actually something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might both be less than 0, but if INT is less negative than CON, then C will be

[Freesurfer] Group Analysis - glmfit results

External Email - Use Caution Hello Freesurfer Team, I recently ran analysis to compare change in cortical thickness between an Intervention and Control group longitudinally. The contrast is set up as INT-CON, and therefore I would interpret a positive change as the intervention

Re: [Freesurfer] Group Analysis - FSGD and Contrast

yes, that is the correct interpretation On 7/16/2022 1:00 PM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Dear experts, I am conducting a group analysis and wanted to confirm that the set up below accurately addresses our research question. Thanks for your help,

Re: [Freesurfer] Group Analysis - FSGD and Contrast

External Email - Use Caution Hi there, Just following up on this Thanks, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health

[Freesurfer] Group Analysis - FSGD and Contrast

External Email - Use Caution Dear experts, I am conducting a group analysis and wanted to confirm that the set up below accurately addresses our research question. Thanks for your help, much appreciated! Background: * We have two groups (intervention vs control) and two

Re: [Freesurfer] Group Analysis

Can you send the log file for the 2nd mris_preproc command? On 2/8/2021 4:52 PM, Larissa Bechtle wrote: External Email - Use Caution Hi everybody, I ran the following commands which worked out fine for my Group Analysis. Just like in the wiki-Tutorial available I focused on the

[Freesurfer] Group Analysis

External Email - Use CautionHi everybody,   I ran the following commands which worked out fine for my Group Analysis. Just like in the wiki-Tutorial available I focused on the thickness of my probands brains at first.     setenv FREESURFER_HOME /Applications/freesurfer

Re: [Freesurfer] Group Analysis Question

I think that contrast computes Female-Male regressing out Dx and age. If you want HC vs MS, then use -0.5 -0.5 0.5 0.5 On 12/29/2020 4:52 PM, Swanson,Clayton wrote: External Email - Use Caution Hi Freesurfer Team, I am performing an analysis on 23 HC and 26 people with MS and I would

[Freesurfer] Group Analysis Question

External Email - Use Caution Hi Freesurfer Team, I am performing an analysis on 23 HC and 26 people with MS and I would like to perform the stats appropriately. I would like to control for (or regress out) age and sex. Therefore, I created my FSGD file which has 4 classes

Re: [Freesurfer] group analysis

For starters, you need to have four classes, HC-Male, HC-Female, CMT-Male, CMT-Female and not use gender as a variable. Try that. I would also normalize the age and thickness On 11/24/2020 12:04 PM, Ambulatorio SNA FEDERICO II wrote: External Email - Use Caution Dear Freesurfer team,

Re: [Freesurfer] Group Analysis

arvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Group Analysis External Email - Use Caution Hi Freesurfer experts, I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it si

Re: [Freesurfer] Group Analysis

Make sure that --meas volume was passed to mris_preproc was passed (this is the usual way you would do this) in which case it makes a jacobian correction. The only other thing to do would be to correct for intra-cranial volume. If you have 7.X, you can just add --etiv to mris_preproc On

[Freesurfer] group analysis

External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness, age and sex. My FSGD file is: GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender

Re: [Freesurfer] Group Analysis {Disarmed}

Just use --meas volume instead of --meas area From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sara Lyn Sent: Thursday, November 19, 2020 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Group Analysis {Disarmed} External Email

Re: [Freesurfer] Group Analysis {Disarmed}

Sorry, meant to say instead of --meas thickness From: Greve, Douglas N.,Ph.D. Sent: Thursday, November 19, 2020 1:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] Group Analysis {Disarmed} Just use --meas volume instead of --meas area

Re: [Freesurfer] Group Analysis {Disarmed}

..@nmr.mgh.harvard.edu> on behalf of Sara Lyn < > saralyn...@gmail.com> > *Sent:* Wednesday, November 18, 2020 6:37 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Group Analysis > > > External Email - Use Caution > > Hi Freesurfer expe

Re: [Freesurfer] Group Analysis

://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table?highlight=%28asegstats%29 Best, Jocelyn From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sara Lyn Sent: Wednesday, November 18, 2020 6:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Group Analysis

[Freesurfer] Group Analysis

External Email - Use Caution Hi Freesurfer experts, I was looking to run the three steps of group analysis-mris preproc, mri surf2surf using the measure volume and unsure of how to go about it since the wiki page talks about thickness only. I would appreciate any help. Best,

Re: [Freesurfer] Group Analysis: Comparing four groups

Yes, that is all correct. I only have a few comments. One is that 15mm is a lot of smoothing; this is not wrong, just more than the 5-10 that I usually use. Second, you might want to use permutation instead of MCZ; the threshold of 4 should make MCZ control the false positives adequately, but

[Freesurfer] Group Analysis: Comparing four groups

External Email - Use Caution Dear Freesurfer experts, This is the first time I perform group analysis in Freesurfer. My aim is to compare the cortical thickness in four groups matched in age, sex and years of education using the Monte Carlo multiple comparisons correction. I

Re: [Freesurfer] Group Analysis Covariates

mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200521/f046db37/attachment-0001.html

Re: [Freesurfer] Group Analysis Covariates

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Re: [Freesurfer] Group Analysis Covariates

Typo yhat = X(:,[1 2 3])*beta([1 2 3],:) On 5/21/2020 2:12 PM, Hua, Jessica wrote: External Email - Use Caution I apologize for resending all of this info, but my email is acting up and every time I try to respond to the other email, my Outlook freezes. Here is info from our

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution I apologize for resending all of this info, but my email is acting up and every time I try to respond to the other email, my Outlook freezes. Here is info from our thread. I modified it to include the analysis in which I found significant clusters

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Attached are the fsgd and Xg.dat files. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri GroupComparison_AllMRI.AgeSexICV.fsgd Description: GroupComparison_AllMRI.AgeSexICV.fsgd

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution I was not sure how to modify the last line in your code in order to calculate adjusted values accounting for age, sex, and ICV for each participant (this is a three group design). Your code: There is not an easy way to do it, but you can do it in

Re: [Freesurfer] Group Analysis Covariates

And what is your new question? On 5/17/20 12:10 PM, Hua, Jessica wrote: External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Sure, attached are the files again and here is our previous correspondence: Original question: After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters.

Re: [Freesurfer] Group Analysis Covariates

Sorry, can you include previous correspondence so that I have context? On 5/16/2020 1:55 PM, Hua, Jessica wrote: External Email - Use Caution Sure, attached is the FSGD file. In case helpful, I have also attached the Xg.dat file. --- Jessica Hua, M.A. Cognitive and Emotional

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Sure, attached is the FSGD file. In case helpful, I have also attached the Xg.dat file. --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri GroupComparison_AllMRI.AgeSexICV.fsgd

Re: [Freesurfer] Group Analysis Covariates

There is not an easy way to do it, but you can do it in matlab cd glmdir X = load('Xg.dat'); y = load('perm.th30.abs.y.ocn.dat'); beta = inv(X'*X)*X'*y; yhat = X(:,[i j k ...]*beta([i j k ...]) where i j k ... indicate the factors you want keep in your data. Each factor gets a column in the

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters. The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values

Re: [Freesurfer] Group Analysis Covariates

That is how you would compute a partial model fit, though I'm not sure which part of the model you are trying to fit. In what you have, it will remove the main effect of group (but not interactions). On 5/14/2020 1:30 PM, Hua, Jessica wrote: External Email - Use Caution Hi

[Freesurfer] Group Analysis Covariates

External Email - Use Caution Hi FreeSurfer Experts, I am trying to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates in my permutation analysis. This is a 3 group analysis with 3 covariates (age, sex, and ICV).

Re: [Freesurfer] group analysis of large data sets

e a version of mri_glmfit code without limits? Thank you very much. Xin -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfe

Re: [Freesurfer] group analysis of large data sets

vard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] group analysis of large data sets I don't think there is a maximum size. You would do the big analysis the same way as the small. On 03/26/20

Re: [Freesurfer] Group analysis

External Email - Use Caution I meant the latter. Thank you very much for responding to my questions. I have one more question: Can we do non-parametric approaches by Freesurfer? On Sat, Mar 14, 2020 at 2:13 AM Douglas N. Greve wrote: > Are you asking how to do subcortical

Re: [Freesurfer] Group analysis

Are you asking how to do subcortical analysis or are you asking how to account for subcortical analysis during correction for multiple corrections? For the latter, use --3spaces On 3/12/2020 2:03 PM, Hengameh Marzbani wrote: External Email - Use Caution thank you for your detailed

Re: [Freesurfer] Group analysis

External Email - Use Caution thank you for your detailed and helpful explanation. question 3: I mean just left and right. But what should I do if I want to consider subcortical as well as left and right? Best Regards Hengameh On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve

Re: [Freesurfer] Group analysis

On 3/11/2020 4:21 PM, Hengameh Marzbani wrote: External Email - Use Caution Thank you for the quick response. question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I can see the clusters by tksurfer. But, Can I have a text file included all clusters? You can,

Re: [Freesurfer] Group analysis

External Email - Use Caution Thank you for the quick response. question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I can see the clusters by tksurfer. But, Can I have a text file included all clusters? question 3: I want to do the analyse by considering

Re: [Freesurfer] Group analysis with qdec: qcache change this?

It will NOT affect any of the other files On 3/10/2020 10:46 AM, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Dear freesurfer experts, Before running group analysis in qdec is necessary run the qcache command over all subjects but, does this command change some

[Freesurfer] Group analysis with qdec: qcache change this?

External Email - Use Caution Dear freesurfer experts, Before running group analysis in qdec is necessary run the qcache command over all subjects but, does this command change some segmentation file (eg. rh/lh Pial or white surface) or other importants file? We would also like to

Re: [Freesurfer] Group analysis

On 3/9/20 5:53 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Hello Freesurfer developers, > 1- I want to extract the uncorrected clusters from the uncorrected > significance maps obtained from mri_glmfit for structural data (to illustrate > cluster, size, location,

[Freesurfer] Group analysis

External Email - Use Caution Hello Freesurfer developers, 1- I want to extract the uncorrected clusters from the uncorrected significance maps obtained from mri_glmfit for structural data (to illustrate cluster, size, location, and significance) like abs.sig.cluster.summary

Re: [Freesurfer] group analysis for same group in 2 conditions

What quantity do you want to compare across subjects/goggle condition? Sorry for the delay, I have not worked much with the retinotopy code in a while and don't have it at my fingertips On 3/2/2020 9:08 AM, Marco Ninghetto wrote: External Email - Use Caution Since that each subject

Re: [Freesurfer] group analysis for same group in 2 conditions

External Email - Use Caution Since that each subject undergoes to both conditions and functional images are in 2 different folders, I modify my folder structure and put functional folders together. It means that now I have a main functional folder (pRFs_functionals) in which I

Re: [Freesurfer] group analysis for same group in 2 conditions

External Email - Use Caution Thanks for your support. Here my "mkanalysis-sess" command: mkanalysis-sess -a rtopy.self.?h.ng -surface self ?h -paradigm rtopy.par > -retinotopy 41 -TR 2.5 -fsd bold -fwhm 5 -per-run I run this command for both no goggles condition

Re: [Freesurfer] group analysis for same group in 2 conditions

What quantity from the retinotopy analysis do you want to compare across subjects? Eg, the phase? Can you send your mkanalysis-sess command? On 2/28/2020 8:17 AM, Marco Ninghetto wrote: External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which

[Freesurfer] group analysis for same group in 2 conditions

External Email - Use Caution Dear experts, I'm performing a study on visual pathways, in which each participant undergoes to 2 different conditions. One in normal sight (NG, i.e.: No Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes Goggles). I'd like to

Re: [Freesurfer] Group analysis with gray matter volume in FS 6.0

When you say "gray matter volume", does it mean you are trying to do a VBM-style analysis? You can't do VBM with FS. You can do an analysis of cortical GM volume in a similar way. When you run mris_preproc, specify "volume" as the --meas On 12/12/19 12:58 PM, Marisa Cathryn Ross wrote: > >

Re: [Freesurfer] Group analysis

On 3/4/19 10:11 AM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Hi Freesurfers, > > I want to do group analysis on four groups and use the volume values > in aseg,stats. > 1- Is it correct that each subcortical segmentation is based on a > "volumetric segmentation

[Freesurfer] Group analysis

External Email - Use Caution Hi Freesurfers, I want to do group analysis on four groups and use the volume values in aseg,stats. 1- Is it correct that each subcortical segmentation is based on a "volumetric segmentation atlas" created by Freesurfer? 2- Are the volume values

Re: [Freesurfer] Group Analysis Covariates

sorry for the delay. There is not a super easy way to do this, but it is possible in matlab. cd into the glmdir folder and start matlab, then X = load('Xg.dat'); beta = MRIread('beta.mgh'); betamat = fast_vol2mat(beta); yhatmat = X(:,[i j k m n])*betamat([i j k m n],:); yhat = beta;

Re: [Freesurfer] Group Analysis Covariates

External Email - Use Caution Hi FreeSurfer experts, Just bringing this question back up to the top: I analyzed my data following the guidelines on the FreeSurfer Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the

Re: [Freesurfer] Group Analysis Covariates

The value in the ocn.dat file totally depends on what you used as input (--y) to mri_glmfit. If you used thickness, then it is thickness. That mri_segstats command is almost correct. You will need to add --accumulate so that it gives you the total volume rather than the average On 06/13/2018

Re: [Freesurfer] Group Analysis Covariates

On 06/11/2018 11:07 PM, Hua, Jessica wrote: > > > Dear Freesurfer Experts: > > > I analyzed my data following the guidelines on the FSL Tutorial/Group > Analysis page . I am trying to plot the adjusted values (covariates: > age, sex, and ICV) for the significant clusters for each of my >

[Freesurfer] Group Analysis Covariates

External Email - Use Caution Dear Freesurfer Experts: I analyzed my data following the guidelines on the FSL Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. I set

Re: [Freesurfer] Group Analysis Contrast (Follow-up)

You need to put in age, weight, AND age*weight. If you have two classes and use DODS, then the contrast would be 0 0 0 0 0 0 0.5 0.5 On 4/13/18 8:02 PM, David S Lee wrote: Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1

[Freesurfer] Group Analysis Contrast (Follow-up)

Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous variable (age X weight). My fsgd looks like this: *GroupDescriptorFile 1* *Title Cortical Thickness Interaction between Age and Weight* *Class class1 plus blue* *Class

Re: [Freesurfer] Group Analysis Design Matrix

If you want to test for an interaction between Age and Weight, you need to create a new covariate which is Age*Weight, then test the sig of this covariate. I would demean Age and Weight for both the inidvidual covaraite and before computing the product. On 04/12/2018 12:35 PM, David S Lee

[Freesurfer] Group Analysis Design Matrix

Hi FreeSurfer Experts, I have two groups (Male and Female) and two covariates (Age and Weight). I want to test change of cortical thickness with age and weight, after removing effects of Group. In other words, is there an interaction between age and weight, regressing out the effects of groups.

Re: [Freesurfer] group analysis on thickness/mask

Pass it with --mask, not --label On 09/11/2017 09:42 PM, Xianwei Che wrote: > Dear Doug, > > After some trial and error I am still not able to run group analysis > in ROI manner. > > Here is my understanding: I need to define a label (mri_binarize ?) in > which my ROIs should be labeled as 1

Re: [Freesurfer] group analysis on thickness/mask

Dear Doug, After some trial and error I am still not able to run group analysis in ROI manner. Here is my understanding: I need to define a label (mri_binarize ?) in which my ROIs should be labeled as 1 with other regions being 0. Then I can take this label to glm with --lable and then run

Re: [Freesurfer] group analysis on thickness/mask

Dear Doug, Thank you for the answer. I will try it out. Regards *-* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia On 12 September 2017 at

Re: [Freesurfer] group analysis on thickness/mask

On 09/10/2017 04:02 AM, Xianwei Che wrote: > Dear experts, > > I am going to run a group analysis on thickness but limit the results > to certain regions, say prefrontal cortex. l did find this thread but > failed to make it work on my data >

[Freesurfer] group analysis on thickness/mask

Dear experts, I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). I know I could extract the

Re: [Freesurfer] group analysis of large data sets

e these the maximum? The mri_glmfit is written in C. Could you send me a > version of mri_glmfit code without limits? > Thank you very much. > > Xin > > -Original Message- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Monday, March 27, 2017 1:47 PM

Re: [Freesurfer] group analysis of large data sets

age- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 27, 2017 1:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] group analysis of large data sets I don't think there is a maximum size. You would do the big analysis the same way as the small. On

Re: [Freesurfer] group analysis of large data sets

I don't think there is a maximum size. You would do the big analysis the same way as the small. On 03/26/2017 07:54 PM, Wang, Xin wrote: > > Hello, FreeSurfer Group, > > What is the maximal matrix size for glm_fit process? > > How to use FreeSurfer for group analyses of more than 2000 subjects,

[Freesurfer] group analysis of large data sets

Hello, FreeSurfer Group, What is the maximal matrix size for glm_fit process? How to use FreeSurfer for group analyses of more than 2000 subjects, 128 variables, and 128 Classes? Thank you. Xin ___ Freesurfer mailing list

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

Hello Bruce, Thank you so much. I will try later. Xiuyi On 2 March 2017 at 17:11, Douglas N Greve wrote: > Click the button that says to show the annotation in outline (since you > could not load it in outline mode > > > On 03/02/2017 11:50 AM, Xiuyi Wang wrote: >

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

when you say it stops, you mean it crashes and returns control to the command line? Or that the GUI stays up but is unresponsive? On 03/02/2017 11:29 AM, Xiuyi Wang wrote: > Hello Bruce, > > The program stops after displaying this message. > > So I guess your solution is to use FreeSurfer 6 and

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

Hello Bruce, Thank you for your reply. I have tried to delete “:annot_outline=1: before and the command lines are: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

Hello Bruce, The program stops after displaying this message. So I guess your solution is to use FreeSurfer 6 and I am not able to view the data using FreeSurfer 5.3. Thanks. Xiuyi On 2 March 2017 at 16:26, Douglas N Greve wrote: > That is not an error, the

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

That is not an error, the program should have run normally after that. This has been fixed in v6. On 03/02/2017 11:23 AM, Xiuyi Wang wrote: > Hello Bruce, > > Thank you for your reply. > > I have tried to delete “:annot_outline=1: before andthe command lines are: > > freeview -f >

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

You can use that command, just remove annot_outline=1: On 03/02/2017 07:18 AM, Xiuyi Wang wrote: > Hi, > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system. > > I followed the detailed instruction on the tutorial website. > >

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

Hi, I am learning Group Analysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis These are the commands that I typed: freeview

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

The outline only works on 6.0 On 2/10/17 11:57 AM, Xiuyi Wang wrote: Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

[Freesurfer] Fwd: FreeSurfer group analysis visualize data

Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis But I got an error message when running this command to visualize uncorrected significance

Re: [Freesurfer] Group analysis Cortical Thickness

Check out the group analysis tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 10/26/16 7:11 AM, Dev vasu wrote: Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the

[Freesurfer] Group analysis Cortical Thickness

Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the changes in cortical thickness between 2 groups, could you please kindly inform me some methods that i should adapt to perform the analysis. Thanks

[Freesurfer] Group analysis in repeated measures anova

Dear Freesurfer users I am trying to examine differences between 3 groups in surface thickness and volume over three time periods (pre-intervention, post-intervention, and 6-month followup). Previously, when only the first 2 time points were available, I followed the instructions for paired

Re: [Freesurfer] group analysis

Both contrasts are right. You might want to change the value from 0.5 to 1/6, but that won't affect the actual p-values (only the gamma values). The 2nd contrast is correct, but it maybe difficult to interpret if the first contrast has an effect. Technically, you should verify that there is

Re: [Freesurfer] group analysis

Dear Douglas and Trisanna, Thank you very much for your explanations. I just would like to be sure of what I am doing since there is no example on the wiki as complex as mine. If I have the following classes : Diagnosis : Patient or Control Gender : Male or Female Site : Site1 or Site2 or

Re: [Freesurfer] group analysis

This is a straightforward extension to the FSGD examples. You have 3 discrete factors (2 diagnosis, 2 gender, 6 centers), this yields 2*2*6=24 classes. With one covariate, you would have 24 covariate regressors (one for each class) for a total of 48. You would then need to create a contrast

Re: [Freesurfer] group analysis

there is a tutorial with similar variables available here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Oct 5, 2016 at 9:22 AM, charles laidi

[Freesurfer] group analysis

Dear FreeSurfers, I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

i_glmfit-sim after mri_mcsim. correct > Best, > Paul > > Sent from my BlackBerry 10 smartphone. >Original Message > From: Douglas N Greve > Sent: Friday, August 5, 2016 11:49 AM > To: freesurfer@nmr.mgh.harvard.edu > Reply To: Freesurfer support list > Subjec

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

: Friday, August 5, 2016 11:49 AM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach There are several things that need to be changed as I've indicated below On 08/01/2016 10:09 PM, miracle ozzoude wrote

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

There are several things that need to be changed as I've indicated below On 08/01/2016 10:09 PM, miracle ozzoude wrote: > Thanks doug. Also, Please can you verify if this are the right codes > for performing ROI surface based analysis using the command line. I > tried to reverse the whole brain

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

Thanks doug. Also, Please can you verify if this are the right codes for performing ROI surface based analysis using the command line. I tried to reverse the whole brain analysis tutorial with some of the previous threads i read. I'm trying to mask the entorhinal and MT and then perform ROI on

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

I think there is an example on the wiki in the ROI analysis section. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs

[Freesurfer] group analysis/ region of interest (ROI) approach

Hey FreeSurfer experts, Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. Best, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

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