Hi Corinna,
the 001.mgz is the first file created in the cross sectional stream (when you import your dicom) it is the input image to the stream and just the dicom converted into mgz format. If it is corrupted, you should rerun this cross sectional time point (just to be safe), the base and the all the long runs.
Best, Martin
On 04/28/2014 09:31 AM, Corinna Bauer wrote:
Hi Martin, Neither freeview nor tkmedit could open the 001.mgz file. It could not read 262144 bytes at slice 4. At this point is my best option to re-run this time point from the beginning?
Corinna
On Mon, Apr 28, 2014 at 9:18 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Corinna, try to open /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz in freeview to see if maybe the file is corrupted. Best, Martin On 04/25/2014 03:46 PM, Corinna Bauer wrote:Hello, I am on the recon-all -long step of the longitudinal processing stream and the final time point exits with errors at the mri_convert stage. mri_convert -at /home/Documents/longitudinal_morph/meta/test_subject_template/mri/transforms/test_subject_2ndpostop_to_test_subject_template.lta -odt uchar -rt cubic /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz /home/Documents/longitudinal_morph/meta/test_subject_2ndpostop.long.test_subject_template/mri/orig.mgz mghRead(/home/Documents/longitudinal_morph/meta/test_subject_2ndpostop/mri/orig/001.mgz): could not read 262144 bytes at slice 4 I still have plenty of space left on the drive total used free shared buffers cached Mem: 16348132 14856524 1491608 0 534916 6193928 -/+ buffers/cache: 8127680 8220452 Swap: 16690172 573232 16116940 Any suggestions? The two previous timepoints finished without error. Corinna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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