Yes, seems dcmunpack does not work with our new dataset. So can I still use the images obtained from running mri_convert directly? Actually, I got the filenames for run13 by running dcmunpack and then used these filenames with mri_convert directly. ________________________________________ 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 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
how do you know that it is mri_convert that is causing the problem? It could be that unpacksdcmdir does not work. I've noticed that many data sets are coming off the scanner with each run in a separate folder, which breaks unpacksdcmdir. However, dcmunpack should work. On 11/10/2015 04:26 PM, Li, Baojuan wrote: > 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 > > -- 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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