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


--

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[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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