Hi Mithun,
if you can send us the output from mri_convert/talairach that fails, and we'll take a look.
cheers, Bruce
On Thu, 16 Sep 2004, Mithun Mukherjee wrote:
Hi everybody,
I am trying to run segment_subject on one run of data which was originally in BRIK format and then converted to COR using mri_convert.
In the initial registration to talairach process, mincinfo can't seem to read the .mnc file that mri_convert gave it. As a result the talairach.xfm transformation matrix is not created by mritotal.
The remaining procedures continue but I'm not sure if the registration to talairach space worked.
I checked the file permissions on orig.mnc and that doesn't seem to be the problem.
Is the COR to .mnc conversion the source of the error ?
I tried reading the image information from "orig.mnc" independently with mincinfo but that didn't work either. Below are the error logs for both mincinfo and segment_subject.
Thanks for your help. Mithun
-- Rochester Center for Brain Imaging University of Rochester Medical Center 575 Elmwood Avenue, Annex Room 1B-101 Rochester, NY 14642 Ph: 585-275-4585
[pyramidal:aparna/mri/orig] madmin% mincinfo -image_info orig.mnc ncopen: filename "orig.mnc": Invalid dimension id or name miopen: MINC package entry point [pyramidal:aparna/mri/orig] madmin%
[pyramidal:/usr/local/freesurfer] root# segment_subject aparna
cp: /usr/local/freesurfer/subjects/scripts/brain.dat: No such file or directory
/usr/local/freesurfer/subjects/aparna/scripts /usr/local/freesurfer
registering aparna
mri_convert orig orig/orig.mnc
reading from orig...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to orig/orig.mnc...
mincinfo: Error opening file "orig/orig.mnc"
Error executing mincinfo on orig/orig.mnc
Error: could not open file "/usr/local/freesurfer/subjects/aparna/mri/transforms/talairach.xfm".
System message: No such file or directory
mri_add_xform_to_header: could not read xform file '/usr/local/freesurfer/subjects/aparna/mri/transforms/talairach.xfm'
No such file or directory reading from ../mri/orig... normalizing image... MRInormInit: Talairach origin at (128, 147, 114) wsize 10, windows 14 above, 9 below max gradient 1.000 0: 82 --> 82 1: 87 --> 113 2: 92 --> 119 3: 97 --> 121 ........ ........ .........
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