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I've attached a new version of dcmunpack. Try running this with -keep-scouts and without -keep-scouts Let me know if this runs successfully in both situations (I'm using you as my tester:)
On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote:
Sorry for the late follow-up.
Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert everything, then use the log/series-info.dat to do further renaming to BIDS—at least that is what I am trying to, but this is another topic.
Thanks for the help and
Have a very good day!
Sébastien
External Email - Use Caution
Great! I happen to be doing a phantom scan session this pm and will get some test data to test that and report back soon. Cheers! Sébastien
From: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Date: Wednesday, April 26, 2023 at 6:52 PM To: Proulx, Jean Sebastien JSPROULX@mgh.harvard.edu, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dcmunpack behavior with scouts I've attached a new version of dcmunpack. Try running this with -keep-scouts and without -keep-scouts Let me know if this runs successfully in both situations (I'm using you as my tester:) On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote: Sorry for the late follow-up.
Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert everything, then use the log/series-info.dat to do further renaming to BIDS—at least that is what I am trying to, but this is another topic.
Thanks for the help and Have a very good day! Sébastien
External Email - Use Caution
It seems to be working fine: -keep-scouts does keep the scouts and removing it discards the scouts.
There was some errors for some runs but they were the same for dcmunpack as distributed in dev so I did not bother investigating further.
I had to remove the -createBIDS flag as it created the following error: mri_convert /autofs/cluster/archive/344/siemens/Terra-79121-20230501-161549-003365/SR.1.3.12.2.1107.5.2.0.79121.30000023042718302602300000392 /space/takoyaki/1/users/proulxs/methods/scoutDicomsForDoug/redPhantom_debug/2023-05-01--bay2--scoutDicomsForDoug/nii/.//0099.PhoenixZIPReport.nii.gz --nskip 0 --ndrop 0 -dcm2niix -createBIDS -no-siemensBVecsCross ERROR: use --dcm2niix-outdir <> to specify output directory for BIDS
For reference, here's how I typically run dcmunpack (and how I run for this test, except with -createBIDS removed): dcmunpack \ -keep-scouts \ -extra-info \ -no-exit-on-error \ -dcm2niix \ -createBIDS \ -auto-runseq nii.gz \ -src $dcmDir \ -targ $targDir/nii
Cheers! Sebastien
On Wed, 2023-04-26 at 18:51 -0400, Douglas N. Greve wrote: I've attached a new version of dcmunpack. Try running this with -keep-scouts and without -keep-scouts Let me know if this runs successfully in both situations (I'm using you as my tester:)
On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote: Sorry for the late follow-up.
Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert everything, then use the log/series-info.dat to do further renaming to BIDS—at least that is what I am trying to, but this is another topic.
Thanks for the help and Have a very good day! Sébastien
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Hi Sebastien.
The BIDS you are getting is because I did some code restructuring yesterday.
If you point me to the script Doug gave you, I can do a merge.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Proulx, Jean Sebastien Sent: Tuesday, May 2, 2023 12:17 PM To: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dcmunpack behavior with scouts
External Email - Use Caution It seems to be working fine: -keep-scouts does keep the scouts and removing it discards the scouts.
There was some errors for some runs but they were the same for dcmunpack as distributed in dev so I did not bother investigating further.
I had to remove the -createBIDS flag as it created the following error: mri_convert /autofs/cluster/archive/344/siemens/Terra-79121-20230501-161549-003365/SR.1.3.12.2.1107.5.2.0.79121.30000023042718302602300000392 /space/takoyaki/1/users/proulxs/methods/scoutDicomsForDoug/redPhantom_debug/2023-05-01--bay2--scoutDicomsForDoug/nii/.//0099.PhoenixZIPReport.nii.gz --nskip 0 --ndrop 0 -dcm2niix -createBIDS -no-siemensBVecsCross ERROR: use --dcm2niix-outdir <> to specify output directory for BIDS
For reference, here's how I typically run dcmunpack (and how I run for this test, except with -createBIDS removed): dcmunpack \ -keep-scouts \ -extra-info \ -no-exit-on-error \ -dcm2niix \ -createBIDS \ -auto-runseq nii.gz \ -src $dcmDir \ -targ $targDir/nii
Cheers! Sebastien
On Wed, 2023-04-26 at 18:51 -0400, Douglas N. Greve wrote: I've attached a new version of dcmunpack. Try running this with -keep-scouts and without -keep-scouts Let me know if this runs successfully in both situations (I'm using you as my tester:) On 4/18/2023 10:51 AM, Proulx, Jean Sebastien wrote: Sorry for the late follow-up.
Yes, that is what I’m doing. With dcmunpack -auto-runseq I convert everything, then use the log/series-info.dat to do further renaming to BIDS—at least that is what I am trying to, but this is another topic.
Thanks for the help and Have a very good day! Sébastien
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Huang, Yujing -
Proulx, Jean Sebastien