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


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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
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   Dept. of Electrical Engineering and Computer Science,
   Massachusetts Institute of Technology

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