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 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 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

[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

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 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 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

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

[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

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

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

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 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

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 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

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 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

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. 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

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

[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

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

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 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

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

[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

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

[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

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: > >    

[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 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

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

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

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

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

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

[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 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 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 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

[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 file for mri_glmfit in longitudinal 2-stage model {Disarmed}

, 2015 1:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed} Hi Koushik, you could create a stack for tp2 and a stack for tp3, then subtract and do a osgm. I am not sure what you mean with the "results from tp

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

you are providing. > Thank you > Koushik > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Govindarajan, > Koushik Athreya > Sent: Wednesday, July 22, 2015 8:12 PM > To: Freesurfer s

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

...@nmr.mgh.harvard.edu] On Behalf Of Govindarajan, Koushik Athreya Sent: Wednesday, July 22, 2015 8:12 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed} Thanks Martin. I will try that. Regards Koushik

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

list Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed} Hi Koushik, If that is what you want to do, the first option works: (tp2-tp1) - (tp3-tp1) = tp2 - tp3 Best, Martin On 07/22/2015 06:25 PM, Govindarajan, Koushik Athreya wrote: > Thanks again Mar

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

.@nmr.mgh.harvard.edu] on behalf of Martin Reuter > [mreu...@nmr.mgh.harvard.edu] > Sent: Wednesday, July 22, 2015 4:11 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage > model {Disarmed} > > Yes, I mean the base name, but

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

arvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: Wednesday, July 22, 2015 4:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed} Yes, I mean the base

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

:* Wednesday, July 22, 2015 3:44 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model Hi Koushik, the output of the long_mris_slopes will be (by default) in each subjects base/template directory, so you would have to map things to, e.g

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model {Disarmed}

Behalf Of Martin Reuter Sent: Wednesday, July 22, 2015 3:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model Hi Koushik, the output of the long_mris_slopes will be (by default) in each subjects base/template directory, so you would h

Re: [Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model

Hi Koushik, the output of the long_mris_slopes will be (by default) in each subjects base/template directory, so you would have to map things to, e.g. fsaverage and stack +smooth everythibng before running mri_glmfit. You can also make use of the long_mris_slope flags --stack-spc and --qcac

[Freesurfer] FSGD file for mri_glmfit in longitudinal 2-stage model

Dear Freesurfers, I am trying to use the longitudinal 2-stage model to run a mri_glmfit analysis. How do I specify my FSGD file so that I compared spc or pc1 maps instead of the regular thickness maps? Also, it is my understanding that I do not have to run mris_preproc and mri_surf2su

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 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

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'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

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

[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 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

Re: [Freesurfer] FSGD file with two set of regressors adding up to 1

Hi Orjan, it looks like there are some errors in your design. The "Variables" function is only for continuous variables (covariates) such as Age. Sex and diagnosis are discrete variables and they should be coded as part of the class (eg, if you only wanted to add sex, then you'd have 4 classes

Re: [Freesurfer] fsgd file for 3 groups and 4 covariates

That is correct. doug Jose Luis Cantero Lorente wrote: > Dear all, > > I have a data set with a diagnosis factor (three groups) and four > covariates, the fsgd.txt file is pasted below: > > > > GroupDescriptorFile 1 > > Title Thickness-subj > > Class control > > Class EHM > > Class NEHM > > va

[Freesurfer] fsgd file for 3 groups and 4 covariates

Dear all, I have a data set with a diagnosis factor (three groups) and four covariates, the fsgd.txt file is pasted below:

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 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

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 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

[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

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

[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

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

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

[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.