Dear Douglas, This works great with our old dataset. But for our new dataset collected using a new protocol, I ran into another error:
The command was: unpacksdcmdir -src /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 \ -targ /autofs/space/quadra_001/users/baojuan/MRI -fsfast \ -run 13 FSL nii DTI.nii The error was: Scanning directory Tue Nov 10 15:24:52 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 100 ERROR: parsing /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 See logfile /autofs/space/quadra_001/users/baojuan/MRI/unpack.log for more details However, when I used the old version of mri_convert, there was not such error but I could not get the bvecs and bvals files: Scanning directory Tue Nov 10 15:41:57 EST 2015 mri_parse_sdcmdir --sortbyrun --d /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 --o /autofs/space/quadra_001/users/baojuan/MRI/dicomdir.sumfile --status /autofs/space/quadra_001/users/baojuan/MRI/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 Done scanning Tue Nov 10 15:49:52 EST 2015 Finally, I tried to run mri_convert directly: ./mri_convert /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii It worked: reading from /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173... Getting Series No Scanning Directory INFO: Found 1633 files in /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984 INFO: Scanning for Series Number 13 INFO: found 65 files in series INFO: loading series header info. INFO: sorting. RunNo = 12 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName /cluster/archive/312/siemens/Prisma_fit-67026-20151103-135539-000984/MR.1.3.12.2.1107.5.2.43.67026.2015110314191078898762173 ... writing to /autofs/space/quadra_001/users/baojuan/MRI/con_dir/DTI.nii... Saving bvals and bvecs I checked the DTI.nii, bvecs, bvals files, seems they were correct. So what may be the reason for this error? Can I still use the images obtained by running mri_convert directly? Best wishes, Baojuan ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, November 10, 2015 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir Use the development environment (but only for unpacking) source /usr/local/freesurfer/nmr-dev-env On 11/10/2015 02:31 PM, Li, Baojuan wrote: > Dear Douglas, > > Thank you! > > I am using a desktop of the Martinos Center. Seems I am not allowed to > replace the mri_convert file under the $FREESURFER_HOME/bin directory. Is > there another way to use it? > > Best wishes, > Baojuan > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, November 10, 2015 2:05 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] unpacksdcmdir > > It will be distributed with version 6. For now, you can just replace the > current version in $FREESURFER_HOME/bin (just make backup of it before > you do). After that, all programs will use the new version > > On 11/10/2015 01:51 PM, Li, Baojuan wrote: >> 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 >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list 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 . 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