Hi,

Which version of freesurfer tools are you using?

I get the following for bert subject:

$ mincinfo orig.mnc file: orig.mnc image: unsigned byte 0 to 254 image dimensions: xspace yspace zspace dimension name length step start -------------- ------ ---- ----- xspace 256 1 -133.4 yspace 256 1 -128 zspace 256 1 -110

Tosa

Mithun Mukherjee wrote:

Hi Bruce,

mri_convert seems to work fine and writes out the orig.mnc file alright. mritotal spits out the error while using mincinfo to read orig.mnc.

I tried executing mincinfo independently on "orig.mnc" and got an "Invalid dimension id or name" error from ncopen which seems to suggest that the cor to minc conversion did not work right. Below are the outputs of all three.

Thanks.

[pyramidal:subjects/aparna/mri] root# mri_convert orig orig/orig.mnc 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... [pyramidal:subjects/aparna/mri] root#

[pyramidal:subjects/aparna/mri] root# mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm > orig/orig.log mincinfo: Error opening file "orig/orig.mnc" Error executing mincinfo on orig/orig.mnc [pyramidal:subjects/aparna/mri] root#

[pyramidal:aparna/mri/orig] root# mincinfo orig.mnc ncopen: filename "orig.mnc": Invalid dimension id or name miopen: MINC package entry point [pyramidal:aparna/mri/orig] root#

orig.log:

root@pyramidal.rcbi.rochester.edu:/usr/local/freesurfer/subjects/ aparna/mri] [2004-09-17 10:49:17] running: /usr/local/mni/bin/mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm

Loading configuration file /usr/local/mni/etc/mni_autoreg/mritotal.cfg Loading protocol default (protocol file = /usr/local/mni/etc/mni_autoreg/mritotal.default.cfg) Loading protocol icbm (protocol file = /usr/local/mni/etc/mni_autoreg/mritotal.icbm.cfg) source = orig/orig.mnc model = /usr/local/mni/share/mni_autoreg/average_305 transform = transforms/talairach.xfm protocol = icbm: linear fit only subsample heuristically crop according to 0,0 0,0 -25%,0 blur with 16 and 8 mm FHWM kernels pad/unpad correctly (encroach on original volume) default objective function = cross-correlation

On Sep 16, 2004, at 10:04 PM, Bruce Fischl wrote:

...

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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Rochester Center for Brain Imaging University of Rochester Medical Center 575 Elmwood Avenue, Annex Room 1B-101 Rochester, NY 14642 Ph: 585-275-4585

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