Dear Douglas, Thank you so much for your help. I have tried the new version of mri_convert and it works very well, giving me the bvecs and bvals correctly!
Is the new mri_convert available from the latest version of Freesurfer? Because we will need to unpack data from a directory, I think it will be great if we can use the new version of mri_convert through unpacksdcmdir. Best wishes, Baojuan ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, November 09, 2015 11:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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