External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Proulx, Jean Sebastien
Sent: Tuesday, May 2, 2023 12:17 PM
To: Greve, Douglas N.,Ph.D. <dgr...@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 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 Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
