Dear all,
Our group is having trouble unpacking functional scans.
If we ran the command: unpacksdcmdir -src ./all/ -targ ../bold/ -fsfast -run 5 bold nii f.nii
We get the following error message: mri_convert ./all/64806020 ../bold/005/f.nii --sdcmlist ../bold//bold/005/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child process exited abnormally
We have recently upgraded the scanner (from Trio to Prisma), and since we've never seen this error message before with Trio, it might be related to the scanner upgrade. We used both Freesurfer 5.1 and 4.5, but got the same error message.
The flag with ‘-scanonly’ will run, and we could unpack anatomical scan without any issues.
The log output looks like this (we’ve been trying to unpack runs 4-11):
99 PhoenixDocument err -1 -1 1 12 64766421 1 localizer ok 512 512 3 1 64818818 2 t1_mprage ok 256 256 160 1 64818847 3 ep2d3X3X3.5 ok 384 384 1 70 64816899 4 ep2dtask ok 384 384 1 76 64812417 5 ep2dtask ok 384 384 1 76 64806020 6 ep2dtask ok 384 384 1 76 64809896 7 ep2dtask ok 384 384 1 76 64803519 8 ep2dtask ok 384 384 1 76 64797142 9 ep2dtask ok 384 384 1 76 64790747 10 ep2dROI ok 384 384 1 101 64794623 11 ep2dROI ok 384 384 1 101 64789521 12 ep2d_resting ok 384 384 1 203 64784419
Please let us know if you have any ideas how to fix this issue. Thank you!
Can you try this version of mri_convert and let me know if it works?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Copy it to $FREESURFER_HOME/bin (make a backup of the one that is there)
doug
On 11/14/2015 12:12 PM, Tan, Qingleng wrote:
Dear all,
Our group is having trouble unpacking functional scans.
If we ran the command: unpacksdcmdir -src ./all/ -targ ../bold/ -fsfast -run 5 bold nii f.nii
We get the following error message: mri_convert ./all/64806020 ../bold/005/f.nii --sdcmlist ../bold//bold/005/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child process exited abnormally
We have recently upgraded the scanner (from Trio to Prisma), and since we've never seen this error message before with Trio, it might be related to the scanner upgrade. We used both Freesurfer 5.1 and 4.5, but got the same error message.
The flag with ‘-scanonly’ will run, and we could unpack anatomical scan without any issues.
The log output looks like this (we’ve been trying to unpack runs 4-11):
99 PhoenixDocument err -1 -1 1 12 64766421 1 localizer ok 512 512 3 1 64818818 2 t1_mprage ok 256 256 160 1 64818847 3 ep2d3X3X3.5 ok 384 384 1 70 64816899 4 ep2dtask ok 384 384 1 76 64812417 5 ep2dtask ok 384 384 1 76 64806020 6 ep2dtask ok 384 384 1 76 64809896 7 ep2dtask ok 384 384 1 76 64803519 8 ep2dtask ok 384 384 1 76 64797142 9 ep2dtask ok 384 384 1 76 64790747 10 ep2dROI ok 384 384 1 101 64794623 11 ep2dROI ok 384 384 1 101 64789521 12 ep2d_resting ok 384 384 1 203 64784419
Please let us know if you have any ideas how to fix this issue. Thank you!
-- Qingleng Tan, Graduate Student Department of Cognitive, Linguistic and Psychological Science Laboratory for Cognitive and Perceptual Learning Brown University Box 1821, 190 Thayer Street, Providence, RI 02912-1821
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Tan, Qingleng