External Email - Use Caution
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