[Freesurfer] local gyrification index - contrast and doss vs. dods

Dear Freesurfer Developers, I'm following the very well-documented steps proposed by Marie Schaer for measuring local gyrification index in the paper "How to Measure Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute Local Gyrification Index" (https://www.ncbi.nlm.nih.gov/pmc/

[Freesurfer] demean age in CT analysis in QDEC?

Dear Freesurfer developers, I'm running a standard cortical thickness analysis between 2 patient groups (patients with schizophrenia with hallucinations (H) vs. patients with schizophrenia without hallucinations (NH)). I'm looking at the main effect of group (H vs. NH), while controlling for s

[Freesurfer] bad aseg but WM and pial surfaces look good

Hi Freesurfer developers, I've processed my sample of T1 scans through recon-all and have corrected the pial and WM surfaces. The surfaces look mostly good, though when I checked the aseg segmentations they are pretty poor and there is huge variability in the volumes I get from asegstats2table

[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 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

Cambridge Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ On 2018-04-09 14:50, C.P.E. Rollins wrote: > 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

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

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

[Freesurfer] orig.mgz versus T1.mgz

External Email - Use Caution Dear Freesurfer developers, A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "

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

and 12 (1) as opposed to 12 and 12. Could you please clarify? Thanks again, Colleen Original Message Subject: Re: [Freesurfer] FSGD design for multi-centre study Date: 2018-04-20 11:19 From: "C.P.E. Rollins" To: Freesurfer Thanks a lot for the explanation. The i

[Freesurfer] orig.mgz versus T1.mgz

External Email - Use Caution Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way? Thanks again, Colleen Original Message Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.E. Rollins" To:

Re: [Freesurfer] orig.mgz versus T1.mgz

: 2018-05-02 10:24 From: "C.P.E. Rollins" To: Freesurfer Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way? Thanks again, Colleen Original Message Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.

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

ld no longer add up to 0. For instance if I remove only class "patient_centre2_female", then my contrast would have 11 (-1) and 12 (1) as opposed to 12 and 12. Could you please clarify? Thanks again, Colleen On 2018-04-30 14:43, C.P.E. Rollins wrote: > I thought that I could not remo

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

External Email - Use Caution Ah, I think I understand now, thanks. I've attached my contrast and FSGD file to confirm. In the FSGD file, the format for the classes are __. Please let me know. Thanks again, Colleen On 2018-05-04 09:49, C.P.E. Rollins wrote: Hi, Sorr

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

deviation. My contrast was 1 -1 -1 -1 -1 -1 -1 -1 -1 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 and FSGD attached (does not include full list of subjects). Thanks again, Colleen On 2018-05-08 16:56, C.P.E. Rollins wrote: Ah, I think I

[Freesurfer] matrix and contrast design for multi-centre study

External Email - Use Caution Dear Freesurfer developpers, I posted a while back asking how to control for scanner site in a multi-centre study. I think I now understand the formatting to do so for a DOSS model, but was wondering how this would look for a DODS model. There are 6

Re: [Freesurfer] matrix and contrast design for multi-centre study

dividing by the standard deviation. Might you have any other suggestions? Thanks again, Colleen On 2018-06-04 14:28, C.P.E. Rollins wrote: Dear Freesurfer developpers, I posted a while back asking how to control for scanner site in a multi-centre study. I think I now understand the formatting

[Freesurfer] make_average_subject error

External Email - Use Caution Hello Freesurfer Developpers, I'm attempting to make a study specific template using all of my subjects as input using the make_average_subject command, but am receiving the following error: Building hash of lh white Building hash of lh pial Build

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hello Freesurfer Developpers, I'm trying to use mri_glmfit-sim to make clusterwise corrections but am running into the following error: - XFM matrix (RAS2RAS) --- /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/mri/

Re: [Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hi Douglas, Yes, the file (/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white) exists, I can view it in Freeview and have read permissions. I had recently tried downloading this patch: https://surfer.nmr.mgh.harvard.edu/pub/dis

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Hi Douglas, Yes - attached here is the make_average_subject.log file. The command used was: make_average_subject --out average_v2 --subjects $(cat subjects.txt) subjects.txt also attached. Thanks again for your help Colleen setenv SUBJECTS_DIR /lustr

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --su

[Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --su

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Thanks Douglas, I've attached here the output from mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug Could you clarify how to use permutation to correct for MC for LGI? (as in what to enter for command line

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Hi Douglas, Thanks for the response. Yes, I confirm that the file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Any other possible errors? Also, would you mind elaborating how to use permutation to correc

[Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In run

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

for an LGI analysis? 2) I've attached here the output from ls -Rl $FREESURFER_HOME/subjects/fsaverage. Thanks again, Colleen On 2018-11-23 16:26, C.P.E. Rollins wrote: Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for mul

[Freesurfer] mean LGI per hemisphere

External Email - Use Caution Dear Freesurfer developers, I have a quick question regarding calculating mean LGI (Marie Schaer's measure) per hemisphere. I believe that I can get the mean LGI per hemisphere with a command like: mri_segstats --slabel subject_ID lh $SUBJECTS_DIR/s

[Freesurfer] Fwd: Re: mri_glmfit-sim error correcting for MC for LGI analysis

irectory Original Message Subject: Re: mri_glmfit-sim error correcting for MC for LGI analysis Date: 2018-11-27 11:46 From: "C.P.E. Rollins" To: Freesurfer Hi Douglas, Thanks a lot for your answers. 1) For the permutations, would you recommend using this for cont

[Freesurfer] reporting fsl PALM results

External Email - Use Caution Dear Freesurfer Developers, I'm using PALM to run permutation analyses to correct for multiple comparisons on Freesurfer cortical thickness and LGI data. fspalm from a command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2 pos --cwp .05 --

Re: [Freesurfer] reporting fsl PALM results

hanks again Colleen On 2019-02-08 11:16, C.P.E. Rollins wrote: > Dear Freesurfer Developers, > I'm using PALM to run permutation analyses to correct for multiple > comparisons on Freesurfer cortical thickness and LGI data. fspalm from > a command like "mri_glmfit-sim --glmdir

[Freesurfer] how to calculate Euler number

External Email - Use Caution Dear Freesurfer Developers, It is not clear to me how to calculate the Euler number. Using mri_segstats reports something like: Computing euler number orig.nofix lheno = -18, rheno = -20 orig.nofix lhholes = 10, rhholes = 11 However, I had understo

Re: [Freesurfer] how to calculate Euler number

External Email - Use Caution Thanks for the clarification Bruce. Would it make sense then to report -18 ? As suggested by the Rosen 2018 paper in Neuroimage. Thanks again, Colleen On 2020-09-03 17:16, C.P.E. Rollins wrote: > Dear Freesurfer Developers, > > It is not