[Freesurfer] mincinfo error opening orig.mnc
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 -- x-tad-biggerRochester Center for Brain Imaging/x-tad-biggerx-tad-bigger /x-tad-biggerx-tad-biggerUniversity of Rochester Medical Center/x-tad-biggerx-tad-bigger /x-tad-biggerx-tad-bigger575 Elmwood Avenue, Annex Room 1B-101/x-tad-biggerx-tad-bigger /x-tad-biggerx-tad-biggerRochester, NY 14642/x-tad-biggerx-tad-bigger /x-tad-biggerx-tad-biggerPh: 585-275-4585/x-tad-bigger [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 ... ... x-tad-bigger /x-tad-bigger___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mincinfo error opening orig.mnc
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 . ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
