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mri_glmfit-sim outputs several files that may be helpful. If you run it with --help, you will get more info, but is this the final file you want?
csdbase.y.ocn.dat - this is a summary of the input (y) over each
cluster. It has a column for each cluster. Each row is a subject. The
value is the average of the input (y) in each cluster. This is a
simple text file.



On 8/11/2023 9:34 AM, MANSSOUR Wassima wrote:

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Dear FreeSurfer Experts,

I am new to FreeSurfer and I need to extract the mean cortical thickness from a specific region for each subject in my dataset (then for my 2 groups). I have already identified a significant cluster from a group analysis, and I would greatly appreciate your guidance on how to proceed with this analysis.

From what I understand, the general steps involve creating a label for the region of interest and then extracting the necessary statistics. Here's what I've tried so far:

1.Created a label for the significant cluster using the mri_cor2label command:
mri_cor2label --i lh.moca_all.thickness.glmdir/MOCApos/cache.th20.pos.sig.cluster.mgh --id 1 --l ./cluster_label.label

2.Attempted to extract the statistics using the mris_anatomical_stats command for the HCA6002236_V1_MR  subject:
mris_anatomical_stats -l cluster_label.label -f parietal_stats1 HCA6002236_V1_MR lh

However, the output parietal_stats1 from the mris_anatomical_stats command is empty, and I'm not sure where I might be going wrong.

While if I try:
mris_anatomical_stats  -t lh..moca_all.thickness.glmdir/MOCApos/cache.th13.pos.sig.cluster.mgh -f parietal_stats2 HCA6002236_V1_MR lh
I got 0mm in the averge thickness.

You find attached the 2 outputs files.

Thank you for your help.

--

Wassima MANSSOUR

Master Student at INSEA Rabat

M2SI - Information Systems & Intelligent Systems

IMRB Intern -France

wmanssour@insea.ac.ma

wassima.manssour@u-pec.fr


 


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