[Freesurfer] bad segmentation [newbie]
Hi to all, In our last analysis, among 12 subjects after -stage 1 and -stage 2 we got only 3 reasonable brain surfaces. Most of the other brains have a very odd shape: -pieces of skull -coharse lack of cortex -holes -bridges -bad cutting planes -cerebellar attachments It seems to be a segmentation problem. How to solve some of these problems is clearly explained in the 'FreesurferGuide' but the whole analysis seems to be too much affected! I have to fix those errors manually? Can repeat the -stage 1 changing some parameters in the intensity normalization and/or segmentation process? I attach some examples (small jpg files) Thank you in advance. Cheers Francesco Musso Laboratory of Molecular Neuroimaging Electrophysiology, Department of Psychiatry, Johannes Gutenberg-University, Mainz, Germanyattachment: bad_fsf_seg6.jpgattachment: bad_fsf_seg1.jpg___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Update for mris_register
There is an updated version of mris_register available for download. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar.gz Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.gz Download the tarfile and expand it in your FREESURFER_HOME/bin/OS/ directory. -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Update for mris_register
The filenames are wrong. The correct ones are: mris_register-040916-Darwin.tar.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mris_register-040916-Darwin.tar.gz 901 KB 09/16/2004 04:58:00 PM mris_register-040916-Linux.tar.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mris_register-040916-Linux.tar.gz 1289 KB 09/16/2004 04:58:00 PM Tosa Kevin Teich wrote: There is an updated version of mris_register available for download. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar.gz Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.gz Download the tarfile and expand it in your FREESURFER_HOME/bin/OS/ directory. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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
[Freesurfer] Re: bad segmentation [newbie]
Hi Francesco, these look pretty bad. Can you describe the acquisitions? How many? Did you motion correct and average them? What is the resolution? What field strength? What receive coil(s)? cheers, Bruce On Thu, 16 Sep 2004, F.Musso wrote: Hi to all, In our last analysis, among 12 subjects after -stage 1 and -stage 2 we got only 3 reasonable brain surfaces. Most of the other brains have a very odd shape: -pieces of skull -coharse lack of cortex -holes -bridges -bad cutting planes -cerebellar attachments It seems to be a segmentation problem. How to solve some of these problems is clearly explained in the 'FreesurferGuide' but the whole analysis seems to be too much affected! I have to fix those errors manually? Can repeat the -stage 1 changing some parameters in the intensity normalization and/or segmentation process? I attach some examples (small jpg files) Thank you in advance. Cheers Francesco Musso Laboratory of Molecular Neuroimaging Electrophysiology, Department of Psychiatry, Johannes Gutenberg-University, Mainz, Germany ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
