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Dear FreeSurfer Developers, I am trying to run the “mri_cc” command to obtain a segmentation of the corpus callosum (CC) that is thicker then the usual 5mm (i.e. 5 voxel in my image). I would like indeed to cover the "entire" CC volume and label it with the canonical 5 values (let's say at least for the central CC, mid anterior and mid posterior).
I tried mri_cc -force -T 30 -aseg aseg.mgz -o aseg.auto_CC_30seg.mgz Control001
and it prints at screen processing regardless of existence of cc in input volume setting callosum thickness to 61 mm will read input aseg from aseg.mgz writing aseg with cc labels to aseg.auto_CC_30seg.mgz reading aseg from /Users/Desktop/fsurfer/Control001/mri/aseg.mgz reading norm from /Users/Desktop/fsurfer/Control001/mri/norm.mgz 97532 voxels in left wm, 30641 in right wm, xrange [126, 142] MRIprincipleComponents: unsupported input type 1 No such file or directory searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot 6.3 global minimum found at slice 132.0, rotations (0.75, -0.50) final transformation (x=132.0, yr=0.750, zr=-0.500): 0.99988 0.00873 0.01309 -3.98366; -0.00873 0.99996 -0.00011 129.15181; -0.01309 0.00000 0.99991 129.72784; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 129] in xformed coordinates best xformed slice 127 cc center is found at 127 0 0 MRIprincipleComponents: unsupported input type 1 No such file or directory eigenvectors: 0.00000 0.00000 0.00000; 0.00000 0.00000 0.00000; 0.00000 0.00000 0.00000; writing aseg with callosum to /Users/Desktop/fsurfer/Control001/mri/aseg.auto_CC_30seg.mgz... corpus callosum segmentation took 1.3 minutes
But when I open the file asset.auto_CC_30seg.mgz on the image brain.mgz I still get a thickness of just 5 voxels. Could you please help me out in understanding why?
I am wondering if this could be related to the warning MRIprincipleComponents: unsupported input type 1 No such file or directory
But I do not understand to what it is referring to. The input aseg.mgz looks fine to me and the command “recon_all” did not give me any apparent issue.
I hope you can help me with this and I thank you in advance for your time.
Best regards, Simona