Hello Douglas,

I am afraid I am getting error while running "mris_preproc --fsgd steplengthSD_vol.fsgd"

ERROR: no subjects specified

I believe I am missing very basic and doing wrong while exporting specific paths and subject names. Could you please help to resolve the issue?

I am working on bash shell. So, I first ran <source_freesurfer>. like the following

export FREESURFER_HOME=/usr/local/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/subjects
MNI_DIR /usr/local/freesurfer/mni
FSL_DIR /usr/local/fsl

All my 'recon-all -all -qcache' data are kept in /usr/local/freesurfer/subjects. I have created a folder 'glm' here and transferred all the data. I have also created.fsgd and .mtx file and saved them inside the 'glm' folder.

So, next two steps I did-

export SUBJECTS_DIR=/usr/local/freesurfer/subjects

cd $SUBJECTS_DIR/glm

Thank you for your time and help.

Regards,

On Mon, Feb 14, 2022 at 10:48 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Yes, single group just means a single class in the FSGD file. Then just include your clinical measure as a variable in the FSGD

On 2/14/2022 11:39 AM, Koustav Chatterjee wrote:
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Thanks.

I am afraid since I am working on a single group ( only patient group), can I run the same?
On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve, <dgreve@mgh.harvard.edu> wrote:
You can run a group analysis
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One of the outputs will be the correlation (along with the sig of the correlation)

On 2/13/2022 6:35 PM, Koustav Chatterjee wrote:
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Dear FreeSurfer experts,

I am trying to find the correlation between the regional cortical thickness and volume with different clinical measures of a neurodegenerative condition. I am using DK atlas to get the cortical measures and establish the correlation using SPSS, a statistical software.

But, I would like to get FreeSurfer developed images. I would like to learn how to get the areas through images (the FreeSurfer pipeline generated images showing brain regions associated with clinical measures I am interested in).

Looking for your kind help.

Regards,

KC
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