I'm not sure that will work. You should use mri_sclimbic_seg https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic

On 6/27/2022 3:31 AM, Mostafa Fakhri wrote:

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Hello to all of you

I ran recon-all: $ recon-all -sd /share/users/mfakhri/FS/subjects -subject 102109 -i T1w.nii.gz -all

Then I tried segmentation fornix and I used -f on the mri_cc command: $ mri_cc -f -force -sdir /share/users/mfakhri/FS/subjects 102109 including fornix in segmentation processing regardless of existence of cc in input volume using /share/users/mfakhri/freeSurfer-analys/subjects as SUBJECTS_DIR... reading aseg from /share/users/mfakhri/freeSurfer-analys/subjects/102109/mri/aseg.mgz reading norm from /share/users/mfakhri/freeSurfer-analys/subjects/102109/mri/norm.mgz 128569 voxels in left wm, 173189 in right wm, xrange [111, 140] MRIprincipleComponents: unsupported input type 1 searching rotation angles z=[-7  7], y=[-7  7] searching scale 1 Z rot 5.8  global minimum found at slice 128.0, rotations (-0.50, -1.00) final transformation (x=128.0, yr=-0.500, zr=-1.000):  0.99981   0.01745  -0.00873   0.02437; -0.01745   0.99985   0.00015   130.23384;  0.00873  -0.00000   0.99996   126.88302;  0.00000   0.00000   0.00000   1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping

There was no fornix.mgz in mri directory and this error file has been created: $ cat error.log MRIprincipleComponents: unsupported input type 1 I used an HCP 3T preprocess image.

Thanks for the help!

Mostafa

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