[Freesurfer] fsgd

Dear FreeSurfer experts, I am trying to start mris_preproc, but unfortunately it doesn't find my created fsgd file. I saved it in the foulder where you can find all subjects data. Shall I save it somewhere else? Thanks for your help, best Marie ___ Fre

[Freesurfer] FSGD

Hello, I am getting the following error when I try to load an FSGD file in tksurfer. The stats were processed using a custom design matrix without error and I am able to view the results. FSGD file doesn't contain a PlotFile entry. Error loading GDF /scratch/freesurfer/subjects/adina/descic39_all

Re: [Freesurfer] fsgd

Hi Marie, you have to pass it as a command-line option with --fsgd doug On 6/6/12 4:19 AM, Marie Schneider wrote: Dear FreeSurfer experts, I am trying to start mris_preproc, but unfortunately it doesn't find my created fsgd file. I saved it in the foulder where you can find all subjects data.

Re: [Freesurfer] fsgd

I exactly tried that. I typed: mris_preproc --fsgd \ --cache in thickness.fwhm.10.fsaverage \ --target fsaverage \ --hemi lh \ --out .mgh everytime I am running this it says that my fsgd file cannot be found. So I wonder where I have to save it so that FreeSurfer can find it. Thanks for any he

Re: [Freesurfer] fsgd

Did you pass it the full path to the fsgd file, not just it's name? If so, please send the full command line. Also, run it with ---debug and send me the full terminal output. doug On 6/7/12 9:39 AM, Marie Schneider wrote: I exactly tried that. I typed: mris_preproc --fsgd \ --cache in thick

[Freesurfer] fsgd file

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scor

[Freesurfer] FSGD-File

External Email - Use CautionHi everybody,   I am currently trying to run mris_prepoc. However FreeSurfer keeps telling me that there are no subjects specified. Thus, I think that the fsgd-file I created is the problem. I already checked it several times but still don’t know wha

[Freesurfer] Fsgd-File

External Email - Use Caution Hi freesurfer-experts, I am currently trying to run mris_prepoc. However FreeSurfer keeps telling me that there are no subjects specified. Thus, I think that the fsgd-file I created is the problem. I already checked it several times but still don’t

[Freesurfer] FSGD File

External Email - Use CautionHi everyone,   thank you very much for answering! Originally I created the FSGD File with excel, saved it as a tab delimited text file and used the tr-command afterwards (tr ’\r’ ’\n’ < FSGD_2.fsgd.txt > FSGD_2.fsgd).  After having read your message

[Freesurfer] FSGD file

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. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx

[Freesurfer] fsgd creation

External Email - Use Caution Hi Freesurfer developers, My question is related to creation of an fsgd file for glm analysis. I have approximately 500 subjects and 10 variables. I was wondering whats the most time efficient way of creating an fsgd file given my data currently reside

[Freesurfer] FSGD file

External Email - Use Caution Hello FreeSurfer Developers, I would like to know what I put in the FSGD file for patients who don't have data for a variable. In my case, I want to analyze CU (cognitively unimpaired) patients versus CI (cognitively impaired) patients, controlling

[Freesurfer] --fsgd file

Hi everyone, I was wondering if it is possible to flag missing entries in the covariates corresponding to subjects, in the construction of the file passed through --fsgd to mri_glmfit ? Not all my subjects completed all the tasks, and i need to code them in the file, somehow.

Re: [Freesurfer] FSGD

Jerry, Your .fsgd file is probably missing a PlotFile line. Add this before the DesignMatFile line: PlotFile /path/to/my/y.mgh where the y.mgh file is the one containing the concatenation of your input data (in qdec, its automatically generated and called y.mgh). The fsgdPlot.tcl problem is (w

Re: [Freesurfer] FSGD

Thanks for such a prompt reply, Nick! I realize now that the root issue is probably that I did not use the --fsgd flag when I ran mri_glmfit (because it conflicted with the --X flag, which I used to specify a custom design matrix). So, the y.fsgd file was not created in the glmdir. The y.fsgd file

[Freesurfer] FSGD Error

External Email - Use Caution Hello there, I am attempting to run the runGLMs.sh script and I am receiving the error message: ERROR: gdfRead: reading is not formatted properly. The first string is ‘GroupDescriptorFile’, should be ‘GroupDescriptorFile’ It looks like the .fsgd fi

[Freesurfer] fsgd contrast question

Dear experts, I've been reading through the tutorial for group analysis, but I am still a little confused about the contrasts and want to make sure that my contrast is set properly for what I'm interested in looking for. I've made my fsgd file, which contains three groups: ADdiagnosisGroup1, AD

[Freesurfer] Fsgd file format

I have a clarifying question about fsgd file format. We have 40 participants, and a large battery of individual difference measures (egg., vocabulary, phonological skill, etc.) We applied a PCA to the battery and found 4 components, corresponding to WMC, processing speed, comprehension ability, and

[Freesurfer] FSGD Format Error

Hi all, I have been struggling with my .fsgd file. Its header is the following (a total of 119 subjects): GroupDescriptorFile1 TitlePatients_vs_Controls MeasurementNamethickness ClassPxMale ClassPxFemale ClassConMale ClassConFemale ClassPxMPRAGE ClassPxSPGR Cla

Re: [Freesurfer] FSGD-File

That looks ok. How did you create the FSGD file? Sometimes it can be a little finicky about white space, and a file that looks ok might not work (eg, if you made the file in windows). Can you send the actual FSGD file as an attachement? On 11/22/2018 09:09 AM, Larissa Bechtle wrote: > >    

Re: [Freesurfer] FSGD File

If you want to use the --cache-in option, you need to have run recon-all with the -qcache option. If you take away the -cache-in option, then mris_preproc should run correctly On 11/28/2018 12:45 PM, Larissa Bechtle wrote: > > External Email - Use Caution > > Hi everyone, > thank you ver

Re: [Freesurfer] FSGD file

The contrast is not correct for your design. Your design matrix will have 3 columns, one for HC, one for CMT, and one for rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a DOSS kind of way. If you want to test for a difference in thickness-meylin slopes between the two groups

Re: [Freesurfer] FSGD file

External Email - Use Caution Thanks a lot. Sorry if I bother you again: If I want to remove thickness, age and gender as nuisance variables; My FSGD file should be: GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF

Re: [Freesurfer] FSGD file

yes, that is the right contrast On 1/5/19 7:30 AM, Raffaele Dubbioso wrote: External Email - Use Caution Thanks a lot. Sorry if I bother you again: If I want to remove thickness, age and gender as nuisance variables; My FSGD file should be: GroupDescriptorFile 1 Title Func Class HC Clas

Re: [Freesurfer] FSGD file

External Email - Use Caution Thanks, but I got the following error message: RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous va

[Freesurfer] fsgd and contrasts

External Email - Use Caution Hi, I realize this is fairly straightforward for most of you, but I am relatively new to freesurfer and want to make sure I'm proceeding correctly with group analysis. We have ~35 TBI subjects and a similar number of age- and sex-matched controls, a

Re: [Freesurfer] fsgd creation

I'm not an excel expert, so there might be a way to get excel to create the fsgd file for you. I would probably export it as a text or csv file, then use matlab or shell scripts to create the fsgd file. On 4/19/2019 5:49 PM, Amrita Bedi wrote: External Email - Use Caution Hi Freesurfer

[Freesurfer] FSGD file error

Dear free surfer developers, When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underlying languages, since it appears to occur both when I create a plain txt file or when I adjust the tutorials gender_age.fsgd and ad

Re: [Freesurfer] FSGD file

There is no way to model a missing cell in the FSGD. You'd have to figure out a value (eg, using imputation) or exclude those subjects On 11/30/2021 2:59 PM, Laura Willers de Souza wrote: External Email - Use Caution Hello FreeSurfer Developers, I would like to know what I put in the

Re: [Freesurfer] --fsgd file

No, there's no way to do that, sorry. Siddharth Srivastava wrote: Hi everyone, I was wondering if it is possible to flag missing entries in the covariates corresponding to subjects, in the construction of the file passed through --fsgd to mri_glmfit ? Not all my subjects c

Re: [Freesurfer] --fsgd file

Hi Jurgen, Thanks for the response. Seems like a feasible idea. I can do it for my "Normals", but the atypicals have a large variability in the measure. And only the atypicals have missing data. Thanks for the idea though... sid. On Thu, Jan 29, 2009 at 11:02 AM, Jürgen Hänggi < j.h

[Freesurfer] fsgd file creation

Dear All, I am new to freesurfer, i am sorry i am confused so i am posting this message. I have two groups i want to compare cortical thickness values in all the areas reported in aparc.stats file between these two groups. So i started creating my fsgd file the problem i have is with the contr

[Freesurfer] FSGD file problems

Dear Freesurfers, I recently tried to correlate age in a group of subjects with their cortical thickness. After having set up an FSDG file and my contrasts, I ran mris_preproc and mri_surf2surf, and finally mri_glmfit. This, however, did not work and I got this errormessage: gdfReadHeader: re

[Freesurfer] fsgd plots > 2 Class

Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but I

[Freesurfer] FSGD File Formatting Error

Hi Freesurfers, I'm having some issues running mri_glmfit using a simple custom GLM file. I've double checked to make sure the subject session file passed to isxconcat-sess is the same as the fsgd file and also checked the formatting corresponds with what is posted online however I keep getting th

Re: [Freesurfer] fsgd contrast question

Hi Meghan, you will need to use an F-contrast. Choose any two of those contrasts and put them in a single file with two lines. Before you do that, you should look for an interaction between your groups and your covariate with another F-contrast: 0 0 0 1 0 -1 0 0 0 1 -1 0 with the DODS model.

[Freesurfer] FSGD file FS-FAST

Hi list,please could you suggest me the group.effect.mtx and the file.mtx relative to Null Hypothesis for 4 Groups (1 Factor, 4 Levels), Zero Covariates. DODS or DOSS.ThanksStefano___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.n

Re: [Freesurfer] Fsgd file format

If you want to test for interactions among nuisance variables, then you have to create a new regressor where you multiply them together. doug On 3/30/14 4:20 PM, Clint Johns wrote: I have a clarifying question about fsgd file format. We have 40 participants, and a large battery of individual

Re: [Freesurfer] Fsgd file format

I'm not sure I understand (sorry for being obtuse!) We don't want to check for interactions among nuisance variables (inasmuch as we only have the one, the average thickness). Rather, we want to check for interactions among the four factors revealed by our PCA, controlling for the nuisance variable

Re: [Freesurfer] Fsgd file format

Sorry, that should have been interaction among continuous (not necessarily nuisance) variables. You will need to create new variables that are products of your variables of interest in order to test for interactions. doug On 3/30/14 9:20 PM, Clint Johns wrote: I'm not sure I understand (so

Re: [Freesurfer] Fsgd file format

I understand, I think! So our matrix should be something like this, which includes each of the 4 components we are using as variables, all possible interactions, and the covariate of mean cortical thickness? group - Var1 - Var2 - Var3 - Var4 - 1x2 - 1x3 - 1x4 - 2x3 - 2x4 - 3x4 - 1x2x3 - 1x2x4 - 1x

Re: [Freesurfer] Fsgd file format

That all looks right. Your final contrast matrix that you have a question about tests whether Var1+Var2=0 doug On 03/31/2014 08:33 AM, Clint Johns wrote: > I understand, I think! So our matrix should be something like this, > which includes each of the 4 components we are using as variables, all

Re: [Freesurfer] FSGD Format Error

Each subject can only have one class. So, if you have males and females who are conotrols and ADs, then you would have 4 classes, and each subject could only belong to one class On 10/9/14 11:55 AM, Retzepi, Kallirroi wrote: Hi all, I have been struggling with my .fsgd file. Its header is th

Re: [Freesurfer] fsgd and contrasts

On 2/14/19 1:04 PM, John Absher wrote: > > External Email - Use Caution > > Hi, I realize this is fairly straightforward for most of you, but I am > relatively new to freesurfer and want to make sure I’m proceeding > correctly with group analysis. > > We have ~35 TBI subjects and a sim

Re: [Freesurfer] FSGD file error

please send the fsgd file. Also, send the full text output from mri_glmfit On 4/3/18 5:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote: Dear free surfer developers, When I try to run the mri_glmfit free surfer does not seem to recognise my FSGD file. I believe it has something to do with the underly

Re: [Freesurfer] FSGD file error

The problem is that you only have one subject for group haemorrhage. If you are going to include a covariate, then you need more than one subject On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrote: > Dear free surfer developers, > > When I try to run the mri_glmfit free surfer does not see

Re: [Freesurfer] FSGD file error

you should also demean your covariate On 04/03/2018 03:13 PM, Douglas N. Greve wrote: > The problem is that you only have one subject for group haemorrhage. If > you are going to include a covariate, then you need more than one subject > > > On 04/03/2018 05:49 AM, Dijkshoorn, A.B.C. (Aicha) wrot

Re: [Freesurfer] FSGD file error

Sorry, one more thing. I think that it should work if you demean your covariate, no need to have multiple subjects from that group On 04/03/2018 03:16 PM, Douglas N. Greve wrote: > you should also demean your covariate > > > On 04/03/2018 03:13 PM, Douglas N. Greve wrote: >> The problem is that

Re: [Freesurfer] FSGD file error

. Greve [dgr...@mgh.harvard.edu] Sent: Tuesday, April 03, 2018 9:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSGD file error Sorry, one more thing. I think that it should work if you demean your covariate, no need to have multiple subjects from that group On 04/03/2018 03:16 PM

[Freesurfer] fsgd file - glmfit error

External Email - Use Caution Dear Freesurfer experts, Hope this email finds you well. I am having some trouble with the fsgd file for glmfit and I'm confused why. This is the error I'm getting when running glmfit: iMac-Pro:BAP_complete ajobsaid$ mri_glmfit --y mrip.rh_volume_F7_B

[Freesurfer] FSGD Contrast Setup Question

Hi Freesurfers, I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1 Covariate analysis but just want to make sure I'm using the correct contrast option. For the first analyis, the two groups are Drug Pre and Drug Post, with folate-serum level as a covaraite. We want to keep

[Freesurfer] fsgd and contrast matrix

Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1

[Freesurfer] fsgd file from qdec

Dear All, I am new to freesurfer. I am wondering is it possible to save the fsgd created automatically by qdec. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.

Re: [Freesurfer] fsgd file creation

How are you going to do the test? I'm not sure what the stats file has to do with the fsgd file ... doug Rajagopalan, Venkateswaran wrote: > > Dear All, > > I am new to freesurfer, i am sorry i am confused so i am posting this > message. I have two groups i want to compare cortical thickness va

Re: [Freesurfer] fsgd file creation

. Thanks again, venkat From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Fri 5/7/2010 11:35 AM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsgd file creation How are you going to do the test? I'm not

Re: [Freesurfer] FSGD file problems

You should use "Variables" Note the "s". doug Theodor R?ber wrote: > Dear Freesurfers, > > I recently tried to correlate age in a group of subjects > with their cortical thickness. After having set up an FSDG > file and my contrasts, I ran mris_preproc and > mri_surf2surf, and finally mri_glmf

[Freesurfer] FSGD and design matrix

All- I am looking to run freesurfer group analysis on a longitudinal study, examining the changes between baseline and follow-up. I would like to set up a paired t-test, yet I am still in need of some assistance creating my FSGD file and my design matrix. I have read the GroupAnalysis wiki pa

[Freesurfer] FSGD file and constrast

External Email - Use Caution Dear FreeSurfer experts, I have MRI data of one group of subjects and would like to evaluate positive and negative correlations between cortical thickness and some biomarkers by excluding the potential effects of age and sex. I followed the FS tutorial

Re: [Freesurfer] fsgd plots > 2 Class

Hi Dan, I have not tried the FSGD plot in freeview yet. You can certainly do the matlab/python thing. The order is the same as in the fsgd file. doug On 03/03/2014 01:17 PM, dgw wrote: > Hi, > > What is the best way for me to either generate fsgd plots or at least > extract the data when I have

Re: [Freesurfer] FSGD File Formatting Error

looks like you created the fsgd file under windows? There are a bunch of carriage returns (look like ^M in the file). Try using a simple text editor under linux. On 11/27/15 2:32 PM, Shady El Damaty wrote: Hi Freesurfers, I'm having some issues running mri_glmfit using a simple custom GLM

Re: [Freesurfer] FSGD file FS-FAST

Have you looked at https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? On 4/17/17 5:32 PM, std...@virgilio.it wrote: Hi list, please could you suggest me the group.effect.mtx and the file.mtx relative to Null Hypothesis for 4 Groups (1 Factor, 4 Levels), Zero Covariates. DODS or DOSS. T

[Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y file was created as previously explained in another discussion ( https://www.mail-archive.com/freesurfer@nmr.mgh.ha

Re: [Freesurfer] fsgd file - glmfit error

Please send the fsgd file On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Dear Freesurfer experts, Hope this email finds you well. I am having some trouble with the fsgd file for gl

Re: [Freesurfer] fsgd file - glmfit error

External Email - Use Caution Here is my fsgd file. Thank you! On Mon, Jul 27, 2020 at 8:44 PM Douglas N. Greve wrote: > Please send the fsgd file > > On 7/27/2020 11:34 PM, Lab of Autism and Developmental Neuroscience, Lab > of Autism and Developmental Neuroscience wrote: > >

Re: [Freesurfer] fsgd file - glmfit error

Try putting 1 after GroupDescriptorFile, ie, GroupDescriptorFile 1 On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: External Email - Use Caution Here is my fsgd file. Thank you! On Mon, Jul 27, 2020 at 8:44 PM

Re: [Freesurfer] fsgd file - glmfit error

External Email - Use Caution Thank you Douglas! On Tue, Jul 28, 2020 at 9:34 AM Douglas N. Greve wrote: > Try putting 1 after GroupDescriptorFile, ie, > > GroupDescriptorFile 1 > > On 7/28/2020 12:21 PM, Lab of Autism and Developmental Neuroscience, Lab > of Autism and Developm

Re: [Freesurfer] FSGD Contrast Setup Question

Hi Adam, you have a "repeated measures" design. In your case, this is best handled using a paired analysis. You can search for "paired" on the wiki to get instructions. The easiest way to do this is to run mris_preproc with the --paired-diff option, then follow the instructions for the "standar

Re: [Freesurfer] FSGD Contrast Setup Question

To: Adam Nitenson > Cc: freesurfer@nmr.mgh.harvard.edu; Roffman, Joshua L.,M.D. > Subject: Re: [Freesurfer] FSGD Contrast Setup Question > > Hi Adam, you have a "repeated measures" design. In your case, this is > best handled using a paired analysis. You can search for &quo

Re: [Freesurfer] FSGD Contrast Setup Question

paired analysis if we are missing pre or > > post > > data for some subjects? > > Best, > > Josh > > > > > > -Original Message- > > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > > Sent: Thu 9/15/2011 4:54 PM > > To: A

[Freesurfer] FSGD for dtrecon group analysis

Dear Lilla, 1) I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the structural data i

Re: [Freesurfer] fsgd and contrast matrix

Just set the CDR-related slope components in the contrast matrix to 0. If you truly believe that the CDR has no effect, then you can create a new fsgd without CDR as a variable. This will improve both DOF and efficiency. doug Martin Kavec wrote: > Hi, > > I would like to study cortical thickne

Re: [Freesurfer] fsgd and contrast matrix

Thanks, Dough. On Thursday 24 September 2009 21:31:34 Douglas N Greve wrote: > Just set the CDR-related slope components in the contrast matrix to 0. > If you truly believe that the CDR has no effect, then you can create a > new fsgd without CDR as a variable. No no, I believe that the CDR has an

Re: [Freesurfer] fsgd file from qdec

It will be in the glmfit output dir (as y.fsgd). doug Rajagopalan, Venkateswaran wrote: > > Dear All, > > I am new to freesurfer. I am wondering is it possible to save the fsgd > created automatically by qdec. > > Thanks > venkat > > === > > P Please consider the

Re: [Freesurfer] FSGD and design matrix

There are two ways to do a paired-t. The easiest, I think, is to use the --paired-t option to mris_preproc. The other option is to set it up in the fsgd file, but that's more complicated and less flexible. What do you mean by "group"? A class in the fsgd gets it's on mean regressor and possib

[Freesurfer] FSGD 3-way interaction contrast

External Email - Use Caution Dear FS experts, If I wanted to do an interaction of Handedness x ROIsInteractionTerm x Age, controlling for eTIV and Sex, would I use the following contrast? [0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5] FSGD attached. Thank you so much for y

Re: [Freesurfer] FSGD file and constrast

That is correct for DOSS (note that you don't need to do the pos and neg separately as you can handle that at the next stage; in the sig maps, the pos will show up as red/yellow and neg will show up as blue). For DODS you would need 0 0 0 0 0.5 0.5 On 10/4/2023 10:34 AM, Steve Petersen wrote:

[Freesurfer] FSGD error: class Input not defined

Dear Freesurfer experts, I am trying to perform the resting state fMRI analysis as in: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough I got stuck with the STEP8, when I tried to use my own fsgd file. I tried to test for two group difference, no covariance as in:

Re: [Freesurfer] FSGD file formatting for Xhemi

What are you trying to test? Usually you don't have lh and rh in the same glm On 10/17/19 7:09 AM, Jose Graterol wrote: External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y

Re: [Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution Thanks for your answer. I want to correlate TMS values in 17 stroke patients. Following the instructions provided to Anders in this link https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+s

Re: [Freesurfer] FSGD file formatting for Xhemi

If you are trying to determine whether the hemispheres are different, then you need to do the subtraction between the hemis (ie, the --paired-diff). If you want to look at the hemispheres separately, then don't combine them in a single file On 10/21/19 4:58 AM, Jose Graterol wrote: > >

Re: [Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution Thanks for your answer. A follow up question: How should I then specify the variable's values per hemisphere while making the FSGD file if I want to add covariates when running mri_glmfit? Thanks in advance. On Fri, Oct 25, 2019 at 12:18 AM Greve, Dou

Re: [Freesurfer] FSGD file formatting for Xhemi

I don't understand. What per hemisphere variable? On 10/25/2019 3:15 AM, Jose Graterol wrote: External Email - Use Caution Thanks for your answer. A follow up question: How should I then specify the variable's values per hemisphere while making the FSGD file if I want to add covariates w

Re: [Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution My doubt is, if it is possible to use a FSGD file to add variables to a --paired-diff analysis. If it is, what would be the right way to format the FSGD file. Thanks in advance. On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harv

Re: [Freesurfer] FSGD file formatting for Xhemi

There are not any restrictions, just do the same as you would for a non-paired analysis. In any event, you are creating a linear model y = a +b1*x1 + b2*x2 ... where y is the input (paired diff) and x1, x2, etc, are your factors. You are the one who knows your data and what models would be approp

Re: [Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution I believe I found my problem. I was trying to run the analysis with xhemi. Therefore it asked for 34 inputs (17subjects * 2 hemispheres). I was doing it that way because I flipped the hemispheres of the right affected stroke subjects. That was done with

Re: [Freesurfer] FSGD file formatting for Xhemi

what do you mean "flip" them? On 11/5/2019 6:10 AM, Jose Graterol wrote: External Email - Use Caution I believe I found my problem. I was trying to run the analysis with xhemi. Therefore it asked for 34 inputs (17subjects * 2 hemispheres). I was doing it that way because I flipped the

Re: [Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution I have a group of stroke patients. Most of them have a left-sided stroke, the others right-sided. I would like to swap the affected right hemisphere with the unaffected left hemisphere in the patients with a right-sided stroke. I have done that successf

Re: [Freesurfer] FSGD file formatting for Xhemi

You'll have to use fsaverage_sym since you are swapping sides. To do a "normal" group analysis, you'll have to first run mris_preproc on all the subjects who have the unaffected on the left, then again for those on the right. This will give you two files. run mri_concat lh.fsaverage_sym.mgz rh.f

[Freesurfer] FSGD design for multi-centre study

Dear Freesurfer Developers, I'd like to do a standard CT analysis (patients vs. controls, covaried for age and sex) on data from a multi-centre study and I'm wondering how I should construct my FSGD file to code centre as a dummy variable. Currently, my FSGD looks something like this: GroupDesc

Re: [Freesurfer] FSGD for dtrecon group analysis

Hi Antonella, 1) I will be very grateful if you let me know what data I should use for my fsgd when I run the GLM group analysis: the dti data after running the dtrecon (for example for my first control I called this directory C01_dti or the FS data after running recon-all on the structural

Re: [Freesurfer] FSGD 3-way interaction contrast

External Email - Use Caution I think you would need an interaction term with age as well (ie, multiplying age by the ROI). You are starting to get into complicated territory with complicated interactions between continuous variables. In theory, you would need to have each continu

Re: [Freesurfer] FSGD error: class Input not defined

You have a rogue non-ascii character between HM-HR10-002Rest and Group1 (between others). Make sure you create your fsgd file in a simple ascii text editor. On 06/23/2016 01:48 AM, Jarek Rokicki wrote: > Dear Freesurfer experts, > > I am trying to perform the resting state fMRI analysis as in:

[Freesurfer] FSGD and contrast files for group analysis

Dear Marie,I want to run a group analysis on a set of subjects, correcting for gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass NoFocus_Fem

Re: [Freesurfer] FSGD design for multi-centre study

Create a separate class for each combination of diagnosis, sex, and center, then create contrasts that average over center. On 4/6/18 7:11 AM, C.P.E. Rollins wrote: > Dear Freesurfer Developers, > > I'd like to do a standard CT analysis (patients vs. controls, covaried > for age and sex) on data

Re: [Freesurfer] FSGD design for multi-centre study

Hi Douglas, Thanks for your response. I just wanted to confirm how the FSGD and contrast files might look for the multicentre study. If I'm to create a separate class for each combination of diagnosis, sex, and center, would there then be 24 classes? (as there are 2 diagnoses (patient vs. cont

Re: [Freesurfer] FSGD design for multi-centre study

That looks right to me. If you use a DOSS model and have a lot of subjects, I don't think there should be a problem with so many classes. On 04/09/2018 09:50 AM, C.P.E. Rollins wrote: > Hi Douglas, > > Thanks for your response. I just wanted to confirm how the FSGD and > contrast files might loo

Re: [Freesurfer] FSGD design for multi-centre study

Thanks for your help. I've noticed, however, that 2 of the centres contribute a smaller number of subjects and don't in fact have any female controls. Should I remove these as classes (ie. take out control_Female_centre1 and control_Female_centre2) and then change the subsequent contrast file t

Re: [Freesurfer] FSGD design for multi-centre study

Hi, I just wanted to ask again regarding my question below. I've noticed that 2 of the centres contribute a smaller number of subjects and don't in fact have any female controls. Should I remove these as classes (ie. take out control_Female_centre1 and control_Female_centre2) and then change t

Re: [Freesurfer] FSGD design for multi-centre study

sorry for the delay ... You will definitely need to change the contrast values so that the positives and negatives both add to the same number (with opposite sign). It is a bit of a judgement call in terms of removing them entirely. With an unbalanced design, you cannot remove the fixed effect

Re: [Freesurfer] FSGD design for multi-centre study

External Email - Use Caution Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and ha

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