Closed dkp closed 5 years ago
Lestropie
commented
5 years ago That looks to me like the same issue as #47. The path should be:
freesurfer/mri/aparc.HCPMMP1+aseg.mgz
, not:
freesurfer/mri/aparc.HCPMMP1+aseg.mgz/aparc.HCPMMP1+aseg.mgz
, and the rectification in #43 should address that directly. Running "cat /version" within the container should print "0.4.2"; can you confirm whether or not that is the case?
dkp
commented
5 years ago It seems I had version 0.41. I just pulled again from dockerhub and this looks like 0.42. Thanks, I will try again.
-Dianne
On Thu, May 16, 2019 at 7:06 PM Robert Smith notifications@github.com wrote:
That looks to me like the same issue as #47 https://github.com/BIDS-Apps/MRtrix3_connectome/issues/47. The path should be: freesurfer/mri/aparc.HCPMMP1+aseg.mgz , not: freesurfer/mri/aparc.HCPMMP1+aseg.mgz/aparc.HCPMMP1+aseg.mgz , and the rectification in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43 should address that directly. Running "cat /version" within the container should print " 0.4.2"; can you confirm whether or not that is the case?
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dkp
commented
5 years ago All worked well: hcpmmp1 and verbosity level 3...it just took a lot longer to run than my previous configuration. Thanks! -Dianne
On Thu, May 16, 2019 at 9:06 PM Dianne Patterson dkp@email.arizona.edu wrote:
It seems I had version 0.41. I just pulled again from dockerhub and this looks like 0.42. Thanks, I will try again.
-Dianne
On Thu, May 16, 2019 at 7:06 PM Robert Smith notifications@github.com wrote:
That looks to me like the same issue as #47 https://github.com/BIDS-Apps/MRtrix3_connectome/issues/47. The path should be: freesurfer/mri/aparc.HCPMMP1+aseg.mgz , not: freesurfer/mri/aparc.HCPMMP1+aseg.mgz/aparc.HCPMMP1+aseg.mgz , and the rectification in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43 should address that directly. Running "cat /version" within the container should print " 0.4.2"; can you confirm whether or not that is the case?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/MRtrix3_connectome/issues/48?email_source=notifications&email_token=AAHLUQGB5753DTY3K7GOAZDPVYHIRA5CNFSM4HNOQJIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVTQT5A#issuecomment-493292020, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHLUQACA6KJ7CQLXZ5USLLPVYHIRANCNFSM4HNOQJIA .
-- Dianne Patterson, Ph.D. Research Scientist dkp@email.arizona.edu dkp@u.arizona.edu or diannepat@gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill)
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Lestropie
commented
5 years ago hcpmmp1 and verbosity level 3...it just took a lot longer to run than my previous configuration.
This will be due to the number of streamlines generated. If not specified explicitly, the number of streamlines to produce is calculated as a multiple of the number of edges in the connectome; this scales quadratically with the number of nodes, so quickly grows with more dense parcellations.
dkp
commented
5 years ago Thanks so much! A wonderful tool. We'll be using it.
-Dianne
On Mon, May 20, 2019 at 1:30 AM Robert Smith notifications@github.com wrote:
hcpmmp1 and verbosity level 3...it just took a lot longer to run than my previous configuration.
This will be due to the number of streamlines generated. If not specified explicitly, the number of streamlines to produce is calculated as a multiple of the number of edges in the connectome; this scales quadratically with the number of nodes, so quickly grows with more dense parcellations.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/MRtrix3_connectome/issues/48?email_source=notifications&email_token=AAHLUQHLVOUPIZYZGFVZKKTPWJOS3A5CNFSM4HNOQJIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVYCOMA#issuecomment-493889328, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHLUQDCVRECL32IMT5UMETPWJOS3ANCNFSM4HNOQJIA .
I think the test run got further this time, but is still failing to complete. We must be very close. The error log is attached: error.txt
The docker command I ran was this: docker run -i --rm -v ${PWD}:/bids_dataset -v ${PWD}/derivatives:/outputs bids/mrtrix3_connectome /bids_dataset /outputs participant --participant_label 102 --parcellation hcpmmp1 --output_verbosity 3 --debug --skip-bids-validator
The directory does not contain the anat, dwi, connectome or tractogram subdirectories.
As always, thanks for continuing to work on this, and I stand ready to provide any additional information you might need.
-Dianne