External Email - Use Caution 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.