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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.mamailto:wmanssour@insea.ac.ma wassima.manssour@u-pec.frmailto:wassima.manssour@u-pec.fr
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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:
External Email - Use Caution
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.mamailto:wmanssour@insea.ac.ma
wassima.manssour@u-pec.frmailto:wassima.manssour@u-pec.fr__
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Douglas N. Greve -
MANSSOUR Wassima