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bids-apps / MRtrix3_connectome

Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package.
http://www.mrtrix.org/
Apache License 2.0
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single reverse phase encode image still causes crash in 0.4.1 #46

Closed dkp closed 5 years ago

dkp commented 5 years ago

Hi,

I am still running into this problem: I am using the docker container bids/mrtrix_connectome, pulled today May 5, 2018. It appears to be tagged 0.4.1

Despite this same issue being closed as of 0.4.0, If I have a single reverse phase encode B0 image in the fmap directory, MRtrix fails.

error.txt attached. I have removed the reverse phase encode image for testing purposes, but how should I proceed?

Thanks much,

Dianne

error.txt

_Originally posted by @dkp in https://github.com/BIDS-Apps/MRtrix3_connectome/issues/37#issuecomment-489478742_

Lestropie commented 5 years ago

Hi Diane,

I suspect you've come across the same problem as I discovered in #43.

Unfortunately I can't merge that fix right away, as CircleCI has ceased support for its own version 1.0. My previous attempts to migrate my CI script from 1.0 to 2.0 were unsuccessful; but now that 1.0 has been dropped completely I'm going to have to go back and revisit it.

If possible, it would be useful for me to know, if you make the code changes manually, whether it resolves your issue (as I can't tell with 100% certainty whether this is the same issue as that fixed in #43). If you're using a downloaded container rather than building locally from source, this can still be done, by executing docker run with --entrypoint=/bin/bash and omitting the standard command-line inputs to the script, modifying file mrtrix3_connectome.py using e.g. nano within the container environment, and then executing that script and providing the usual command-line arguments.

dkp commented 5 years ago

I'll give it a try and report back. Thanks! -Dianne

On Sun, May 5, 2019 at 6:52 PM Robert Smith notifications@github.com wrote:

Hi Diane,

I suspect you've come across the same problem as I discovered in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43.

Unfortunately I can't merge that fix right away, as CircleCI has ceased support for its own version 1.0 https://circleci.com/sunset1-0/. My previous attempts https://github.com/BIDS-Apps/MRtrix3_connectome/tree/circleci to migrate my CI script from 1.0 to 2.0 were unsuccessful; but now that 1.0 has been dropped completely I'm going to have to go back and revisit it.

If possible, it would be useful for me to know, if you make the code changes manually https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43/files#diff-7bcc5dd45845d84a9690fa9e09c12ff2, whether it resolves your issue (as I can't tell with 100% certainty whether this is the same issue as that fixed in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43). If you're using a downloaded container rather than building locally from source, this can still be done, by executing docker run with --entrypoint=/bin/bash and omitting the standard command-line inputs to the script, modifying file mrtrix3_connectome.py using e.g. nano within the container environment, and then executing that script and providing the usual command-line arguments.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/MRtrix3_connectome/issues/46#issuecomment-489483032, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHLUQGELF6AAADKXXMRTQLPT6FN7ANCNFSM4HK4S6LA .

-- 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)

If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account.

Antipiphany: That moment when you realize how little you actually know

dkp commented 5 years ago

Hi, We pulled the git repo and then switched to your hotfix branch to build. The container is running now and got past the previous choke point....it is now running topup. Seems promising.

-Dianne

On Mon, May 6, 2019 at 9:24 AM Dianne Patterson dkp@email.arizona.edu wrote:

I'll give it a try and report back. Thanks! -Dianne

On Sun, May 5, 2019 at 6:52 PM Robert Smith notifications@github.com wrote:

Hi Diane,

I suspect you've come across the same problem as I discovered in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43.

Unfortunately I can't merge that fix right away, as CircleCI has ceased support for its own version 1.0 https://circleci.com/sunset1-0/. My previous attempts https://github.com/BIDS-Apps/MRtrix3_connectome/tree/circleci to migrate my CI script from 1.0 to 2.0 were unsuccessful; but now that 1.0 has been dropped completely I'm going to have to go back and revisit it.

If possible, it would be useful for me to know, if you make the code changes manually https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43/files#diff-7bcc5dd45845d84a9690fa9e09c12ff2, whether it resolves your issue (as I can't tell with 100% certainty whether this is the same issue as that fixed in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43). If you're using a downloaded container rather than building locally from source, this can still be done, by executing docker run with --entrypoint=/bin/bash and omitting the standard command-line inputs to the script, modifying file mrtrix3_connectome.py using e.g. nano within the container environment, and then executing that script and providing the usual command-line arguments.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/MRtrix3_connectome/issues/46#issuecomment-489483032, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHLUQGELF6AAADKXXMRTQLPT6FN7ANCNFSM4HK4S6LA .

-- 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)

If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account.

Antipiphany: That moment when you realize how little you actually know

-- 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)

If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account.

Antipiphany: That moment when you realize how little you actually know

dkp commented 5 years ago

The hotfix version of MRtrix completes, and, to the extent I understand, the output looks fine

[Saci:sub-103: 559] $ tree . |-- anat | |-- sub-103_5TT.nii.gz | |-- sub-103_T1w.nii.gz | |-- sub-103_brainmask.nii.gz | |-- sub-103_parc-desikan_indices.nii.gz | -- sub-103_tissues3D.nii.gz |-- connectome | |-- sub-103_parc-desikan_level-participant_connectome.csv |-- sub-103_parc-desikan_meanlength.csv |-- dwi | |-- eddyqc | | |-- eddy_movement_rms | | |-- eddy_outlier_map | | |-- eddy_outlier_n_sqr_stdev_map | | |-- eddy_outlier_n_stdev_map | | |-- eddy_outlier_report | | |-- eddy_parameters | | |-- eddy_post_eddy_shell_PE_translation_parameters | | |-- eddy_post_eddy_shell_alignment_parameters | | -- eddy_restricted_movement_rms | |-- sub-103_brainmask.nii.gz | |-- sub-103_bvalues.txt | |-- sub-103_dwi.bval | |-- sub-103_dwi.bvec | |-- sub-103_dwi.nii.gz | |-- sub-103_meanbzero.nii.gz | |-- sub-103_model-tensor_fa.nii.gz | |-- sub-103_tissue-WM_ODF.nii.gz |-- sub-103_tissue-WM_response.txt -- tractogram -- sub-103_mu.txt

5 directories, 26 files

Thanks so much! I put a copy of the built container on dockerhub: diannepat/mrtrix3-hotfix:latest

-Dianne

On Mon, May 6, 2019 at 6:33 PM Dianne Patterson dkp@email.arizona.edu wrote:

Hi, We pulled the git repo and then switched to your hotfix branch to build. The container is running now and got past the previous choke point....it is now running topup. Seems promising.

-Dianne

On Mon, May 6, 2019 at 9:24 AM Dianne Patterson dkp@email.arizona.edu wrote:

I'll give it a try and report back. Thanks! -Dianne

On Sun, May 5, 2019 at 6:52 PM Robert Smith notifications@github.com wrote:

Hi Diane,

I suspect you've come across the same problem as I discovered in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43.

Unfortunately I can't merge that fix right away, as CircleCI has ceased support for its own version 1.0 https://circleci.com/sunset1-0/. My previous attempts https://github.com/BIDS-Apps/MRtrix3_connectome/tree/circleci to migrate my CI script from 1.0 to 2.0 were unsuccessful; but now that 1.0 has been dropped completely I'm going to have to go back and revisit it.

If possible, it would be useful for me to know, if you make the code changes manually https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43/files#diff-7bcc5dd45845d84a9690fa9e09c12ff2, whether it resolves your issue (as I can't tell with 100% certainty whether this is the same issue as that fixed in #43 https://github.com/BIDS-Apps/MRtrix3_connectome/pull/43). If you're using a downloaded container rather than building locally from source, this can still be done, by executing docker run with --entrypoint=/bin/bash and omitting the standard command-line inputs to the script, modifying file mrtrix3_connectome.py using e.g. nano within the container environment, and then executing that script and providing the usual command-line arguments.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BIDS-Apps/MRtrix3_connectome/issues/46#issuecomment-489483032, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHLUQGELF6AAADKXXMRTQLPT6FN7ANCNFSM4HK4S6LA .

-- 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)

If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account.

Antipiphany: That moment when you realize how little you actually know

-- 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)

If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account.

Antipiphany: That moment when you realize how little you actually know

-- 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)

If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account.

Antipiphany: That moment when you realize how little you actually know

Lestropie commented 5 years ago

Remembered that pull requests on this repo are not blocked by CI... Fix is now on Docker Hub tagged as 0.4.2.