On 11/9/15 7:41 PM, Li, Baojuan wrote:
Hi all,
I am using unpacksdcmdir to unpack our data (collected using a Siemens scanner) but running into an error.
I have two questions and hope someone can kindly help me with them:
1. Why can not I successully unpack images for run10?
Looks like the dicom file is missing a tag (28 30). This is the voxel size, which is weird to not be there. Is this a special output from the scanner? Some kind of derived data?
2. I got the DTI.nii image, the bvecs and bvals for run4 now. Can I use them for my analyses? Seems this run has an error. Does this error matter?
The err does not matter. Off hand, I don't know for sure that the bvals and bvecs are correct for 5.3. You can try the new version of mri_convert in which I have a lot more confidence.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
Thank you so much for your help!
Best wishes,
Baojuan
The logfile is as follows:
Done scanning Mon Nov 9 19:10:43 EST 2015
------------------------------------------
1 localizer ok 512 512 3 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515075082139361714
2 AAScout ok 128 128 128 2 MR.1.3.12.2.1107.5.2.32.35162.2012120515084521701761763
3 T1_MPRAGE_sag ok 256 256 128 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371
4 DIFFUSION_HighRes err 128 128 64 70 MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212
5 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954318286428
6 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954396886429
7 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954482386430
8 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954528786431
9 DIFFUSION_HighRes ok 128 128 64 1 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954607786432
10 DIFFUSION_HighRes ok 128 128 1 64 MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433
11 ge_functionals ok 64 64 33 150 MR.1.3.12.2.1107.5.2.32.35162.2012120515373932869186918
unpacking config ------------------
{3 T1 mgz T1.mgz} {4 DTI nii DTI.nii} {10 DTI nii DTI.nii}
-----------------------------------
---------------------------------------------------------
Run 3 -----------------------------------------
Mon Nov 9 19:10:43 EST 2015
3 T1 mgz T1.mgz
mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515211411553363371 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/T1.mgz --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/T1/003/flf
-ot mgz --nspmzeropad 3 --in_type siemens_dicom
---------------------------------------------------------
Run 4 -----------------------------------------
Mon Nov 9 19:10:56 EST 2015
4 DTI nii DTI.nii
INFO: this run has an error, but trying anyway
mri_convert /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515244054044164212 /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/DTI.nii --sdcmlist /autofs/space/quadra_001/users/baojuan/old_lab_datatset/DTI/004/flf
-ot nii --nspmzeropad 3 --in_type siemens_dicom
---------------------------------------------------------
Run 10 -----------------------------------------
Mon Nov 9 19:11:19 EST 2015
10 DTI nii DTI.nii
ERROR: reading /cluster/archive/302/siemens/TrioTim-35162-20121205-150656-604000/MR.1.3.12.2.1107.5.2.32.35162.2012120515335954660486433 tag 28 30
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