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Documentation of the Courtois NeuroMod project

Home Page: http://docs.cneuromod.ca/

License: Other

Makefile 0.33% HTML 73.27% CSS 10.19% JavaScript 14.61% Batchfile 0.42% Python 1.17%

readthedocs sphinx

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cneuromod_docs's Issues

Update categories under MRI

I find it strange to have acquisition parameters listed under the parent category "BIDS formatting". I suggest instead:

MRI
- Image acquisition
  - MR scanner
  - Personalized head cases
  - Sequence parameters
  - BIDS formatting
    etc.

number of restingstate runs missing in the description of hcptrt

add publication section

We are starting to have a few cneuromod publications, if we include modelling, software and opinion pieces. It's time to add a section!

add instructions to checkout a specific version

Currently the instructions are to check out only the latest version.

document flip angles of anatomical sequences

On that page, flip angles of anatomical sequences are not specified.
https://docs.cneuromod.ca/en/latest/MRI.html

document the version of datalad and git-annex

describe the subjects

The current version of the docs give no description of the subjects demographics

description of missing processed runs

this section needs to be updated
https://docs.cneuromod.ca/en/latest/DERIVATIVES.html#missing-outputs

specify anatomical location for spinal cord imaging

I think it would be valuable to specify the spinal level covered for each acquisition of the spinal cord protocol.

turn "acknowledgements" into a stand-alone section

The Courtois project on neural modelling was made possible by a generous donation from the Courtois foundation, administered by the Fondation Institut Gériatrie Montréal at CIUSSS du Centre-Sud-de-l’île-de-Montréal and University of Montreal. The Courtois NeuroMod team is based at “Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal”, with several other institutions involved. See the cneuromod documentation for an up-to-date list of contributors (https://docs.cneuromod.ca).

B1 map does not exist

The documentation for the Brain Anatomical Sequences has:
B1+ field map (duration 0:21 min, voxel size = 6 mm isotropic)

This image does not appear to exist for any of the subjects and could be removed from the documentation.

add HBM poster on the 2020 release

there should both be the text of the reference, to be cited in the suggested acknowledgment paragraph, and a pdf of the poster itself.

move access info to cneuromod.ca/access/access

The two first paragraphs on this page
https://docs.cneuromod.ca/en/latest/ACCESS.html

should move here:
https://www.cneuromod.ca/access/access/

The technical docs should simply say they need to apply for access (link) and this will give them an S3 key.

add CRIUGM logo

Link to DataLad Handbook

In the section on Downloading the dataset it might be helpful to link to the DataLad Handbook.

Since DataLad can be quite confusing to first-time users, I think it'd be a valuable resource to link out -- and we could link in specific sections on e.g. updating datasets so you don't need to explain them in text !

error: file not available

I am missing some files when running datalad get, see example for sub01-ses001:

julien-macbook:~/temp/neuromod $ datalad install -r [email protected]:courtois-neuromod/anat.git
[INFO   ] scanning for annexed files (this may take some time)                                                       
[INFO   ] Unable to parse git config from origin                                                                     
[INFO   ] [ERROR] [Errno 32] Broken pipe (BrokenPipeError) 
[INFO   ] Remote origin does not have git-annex installed; setting annex-ignore
|   This could be a problem with the git-annex installation on the remote. Please make sure that git-annex-shell is available in PATH when you ssh into the remote. Once you have fixed the git-annex installation, run: git annex enableremote origin 
[INFO   ] RIA store unavailable. -caused by- file:///data/neuromod/ria-sequoia/data/neuromod/ria-sequoia/ria-layout-version not found. -caused by- [Errno 2] No such file or directory: '/data/neuromod/ria-sequoia/ria-layout-version' 
[INFO   ] access to 2 dataset siblings ria-beluga-storage, cneuromod.anat.mri.sensitive not auto-enabled, enable with:
| 		datalad siblings -d "/Users/julien/temp/neuromod/anat" enable -s SIBLING 
install(ok): /Users/julien/temp/neuromod/anat (dataset)
[INFO   ] Installing Dataset(/Users/julien/temp/neuromod/anat) to get /Users/julien/temp/neuromod/anat recursively 
julien-macbook:~/temp/neuromod $ cd anat/      
julien-macbook:~/temp/neuromod/anat $ datalad get sub-01/ses-001/
get(ok): sub-01/ses-001/anat/sub-01_ses-001_T1w.nii.gz (file) [from cneuromod.anat.mri...]                                                                                                 
get(ok): sub-01/ses-001/anat/sub-01_ses-001_T2w.nii.gz (file) [from cneuromod.anat.mri...]                                                                                                 
get(ok): sub-01/ses-001/anat/sub-01_ses-001_UNIT1.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_bp-cspine_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_T2starw.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_T2w.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-2_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_flip-2_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_inv-1_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_inv-2_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_UNIT1.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-on_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-2_mt-off_MTS.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_inv-1_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_inv-2_MP2RAGE.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_T1w.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_T2w.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/anat/sub-01_ses-001_rec-norm_mod-T1w_defacemask.nii.gz (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-AP_bp-cspine_dwi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-AP_dwi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-AP_sbref.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-PA_dwi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/dwi/sub-01_ses-001_dir-PA_sbref.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-anat_TB1TFL.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-famp_TB1TFL.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-AP_run-01_epi.nii.gz (file) [from cneuromod.anat.mri...]
get(ok): sub-01/ses-001/fmap/sub-01_ses-001_acq-sbref_dir-PA_run-01_epi.nii.gz (file) [from cneuromod.anat.mri...]
get(error): sub-01/ses-001/sub-01_ses-001_scans.tsv (file) [not available; (Note that these git remotes have annex-ignore set: origin)]
get(impossible): sub-01/ses-001 (directory) [could not get some content in /Users/julien/temp/neuromod/anat/sub-01/ses-001 ['/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-axial_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-coronal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_bp-cspine_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_acq-sagittal_localizer.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-1_mt-on_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_bp-cspine_flip-2_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_flip-1_mt-on_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_flip-2_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-1_mt-on_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-dis2d_flip-2_mt-off_MTS.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/anat/sub-01_ses-001_rec-norm_mod-T1w_defacemask.nii.gz', '/Users/julien/temp/neuromod/anat/sub-01/ses-001/sub-01_ses-001_scans.tsv']]
action summary:
  get (error: 16, impossible: 1, ok: 21)

update ethics documents

current docs do not include the last renewal

Issue when git cloning with SSH

Hello!

I wanted to install cneuromod data as per the doc. What I did / What I got:

p101317@joplin:~/data_nvme_p101317$ datalad install -r [email protected]:courtois-neuromod/cneuromod.git
Clone attempt:   0%|                                                                     | 0.00/1.00 [00:00<?, ? Candidate locations/s][email protected]: Permission denied (publickey).
install(error): /home/GRAMES.POLYMTL.CA/p101317/data_nvme_p101317/cneuromod (dataset) [Failed to clone from all attempted sources: ['[email protected]:courtois-neuromod/cneuromod.git']]
[ERROR  ] ValueError(No installed dataset found at /home/GRAMES.POLYMTL.CA/p101317/data_nvme_p101317/cneuromod.) (ValueError)

Note: I think I have the proper git creds:

p101317@joplin:~/data_nvme_p101317$ git config --global user.name 
jcohenadad
p101317@joplin:~/data_nvme_p101317$ git config --global user.email
[email protected]

And I also have the AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY set.

Note: using HTTPS git clone works fine:

p101317@joplin:~/data_nvme_p101317$ datalad install -r https://github.com/courtois-neuromod/anat.git
[INFO   ] scanning for unlocked files (this may take some time)                                                                        
[INFO   ] Remote origin not usable by git-annex; setting annex-ignore                                                                  
[INFO   ] Configured RIA store not found at ria+file:///data/neuromod/ria-sequoia 
[INFO   ] access to 2 dataset siblings ria-beluga-storage, cneuromod.anat.mri.sensitive not auto-enabled, enable with:
| 		datalad siblings -d "/home/GRAMES.POLYMTL.CA/p101317/data_nvme_p101317/anat" enable -s SIBLING 
install(ok): /home/GRAMES.POLYMTL.CA/p101317/data_nvme_p101317/anat (dataset)
[INFO   ] Installing Dataset(/home/GRAMES.POLYMTL.CA/p101317/data_nvme_p101317/anat) to get /home/GRAMES.POLYMTL.CA/p101317/data_nvme_p101317/anat recursively

Possibly related to #22

add doc on varying fMRI run length

The runs length in movie10 and hcptrt varies across participants and repetitions (change in console program, or manually stopped during scanning). A clear explaination should be given in the doc to help.
This problem should be overcome by the data fetcher.

Sessions not found

Hello !

In cneuromod data, movie10, some sessions are skipped in the case of subject 3, session 8 is missing for a total of 12 sessions for this subject. Similarly, subject 5 does not have session 6.

Any idea why this failed @bpinsard ?

add shima to the team

renaming in movie10

following PR4 in movie10, the task, session, runs and stimuli have all been renamed.
This needs to be incorporated in the "DATASETS" section.

Include information on non-steady state volumes

I can't seem to find the number of non-steady state volumes included at the start of each run. Do these vary by task ?

I ask as an example HCPTRT run (sub-01_ses-002_task-relational_run-01_events.tsv) lists the first stimulus onset at 10.033 seconds, while another (sub-01_ses-002_task-wm_run-01_events.tsv) lists the first stimulus onset at 10.516 seconds. For the listed TR of 1.49s, I would then expect to drop 6 TRs for the first task and 7 TRs for the second.

Having this information available directly in the documentation would help in correctly interpreting this -- at least for me ! Thanks 😸

fmriprep version

the boilerplate description of the fmriprep processing likely needs to be updated, at least re version https://docs.cneuromod.ca/en/latest/DERIVATIVES.html#pipeline-description

list the runs that failed in fMRIprep

add fMRIPprep automatically generated description to the docs

Add reference to RTD site

It would be great to (create ? and) add a link to the RTD site in the repo description on GitHub, as well as in the README.

One fun suggestion in this vein: ReadTheDocs recently released a beta workflow that can run on every PR so you see an updated version of the documentation with your proposed changes. You can see it in action on tedana, for example here.

mention that movies are presented in English

and maybe mention that some of the subjects are not native English speakers

add DTA to the doc

add CoC

Link to BIDS

In the Functional sequences section, the link to "BIDS dataset" goes to the dataset directly.

This fails for users without access (or who are not logged in), so I'm not sure linking it out makes sense. Additionally, I was actually expecting that it would link to the BIDS website.

So, I'm wondering -- would it be worth explaining that the data are formatted in BIDS and linking to this resource at the top of the MRI section ? I might suggest that the link to the dataset goes towards the Access, so it won't return a 404 for some (significant?) subset of users.

add an "How to Acknowledge" section

Update fMRIPrep description, link autogenerated methods

I know that the fMRIPrep section in Derivatives is still being finalized, but I'd love if the final section could include:

The version used (from the current docs, I assume it is this one: https://github.com/poldracklab/fmriprep/releases/tag/1.5.0)
The exact command line arguments used in calling (though it makes sense to scrub the paths, here !)
The autogenerated methods boilerplate. If / when folks use the NeuroMod data in their publications, it would be really helpful to have this section available to copy/paste !

add a section on subjects demographics

description of missing processed runs

this section needs to be updated
https://docs.cneuromod.ca/en/latest/DERIVATIVES.html#missing-outputs

datalad instructions OS

are the datalad instructions only for linux? will they work on mac? please add in the docs. We don't have to give windows instuctions I think.

mention which version of git-annex is used for datalad installation

describe filtering of auditory stimuli

Document transition from custom resp-belt to biopac one

Will need to be documented when releasing the physio data.

BIDS conversion seems to ignore important files

It seems like the BIDS conversion removes some important scans, e.g. sub-06_ses-ana002 includes an MTon, however this file does not appear in the BIDS dataset.

It would be nice if the documentation could include a link to the dcm2bids config file so we could help fix some of the issues

indicate how to get a particular release of the data

add anatomical scans to the list of datasets

include table of datasets

The table from the data release paper should be adapted and included in the docs.

remove friends S02

friends S02 will be included in the 2021 release.

change all reference to git.unf-montreal.ca to github

following switch to GH

B1 map to be re-listed in the documentation

The B1 map dicom images were not converted to nifti during dcm2bids conversion. Since they do in fact exist, they should be re-listed in the documentation. Apologies for the mixup!

Update dataset access information with need for GitHub SSH key

In the Downloading the dataset section, the description currently only references the need for a SSH key on the UNF git (hosted with gitea). However, since the documentation itself is separately hosted on GitHub, users need to have their public SSH keys on both the UNF git and GitHub. Trying to access the dataset with only the an SSH key for the UNF git results in the following error:

[email protected]: Permission denied (publickey).
ConnectionOpenFailedError: command '['ssh', '-fN', '-o', 'ControlMaster=auto', '-o', 'ControlPersist=15m', '-o', 'ControlPath=/home/emdupre/.cache/datalad/sockets/be7bf7bb', '[email protected]']' failed with exitcode 255
Failed to open SSH connection (could not start ControlMaster process)

Adding information on both SSH keys could help avoid this error for some users !

add cneuromod reference in the docs

https://ww4.aievolution.com/hbm2101/index.cfm?do=abs.viewAbs&src=ext&abs=2109

include instructions to load confounds

Currently no mention is done of the fmriprep_load_confounds project, or how to use it. This creates lots of mistakes for the people analyzing the data who don't have a neuroimaging background.