Good news! Thank you :) ________________________________________ 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 4:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacksdcmdir
yes On 11/10/2015 04:35 PM, Li, Baojuan wrote: > 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 > > -- 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 . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
