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prioux remibernard natacha-beck ttaa9 crocodoyle mcin-armintaheri-archive mprati erinb90 shots47s glatard valhayot cmadjar ribal-aladeeb paulchang04 montrealsergiy safasanamiii akhanf dariusvalevicius rcrucescbrain-plugins-neuro's Issues
Nifti viewer doesn't work for compressed Nifti files
Error message: no viewer code available at this moment for files of type 'NIfTI file (compressed)'
Regex audit
Perform a regex audit as in aces/cbrain#482
FSL tool output naming
Increase flexibility in naming FSL outputs, similarly to CIVET.
Was issue #28 in cbrain-plugins-fsl
Wrongly formatted CSV files create an exception
Exception: ScriptError: Coding error: method before_form() for CbrainTask::FslMelodic raised an exception: CSV::MalformedCSVError: Unquoted fields do not allow \r or \n (line 5).
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1871:in `block (2 levels) in shift'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1836:in `each'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1836:in `block in shift'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1796:in `loop'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1796:in `shift'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1738:in `each'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1752:in `to_a'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1752:in `read'
/home/cbrainsys/.rvm/rubies/ruby-2.2.0/lib/ruby/2.2.0/csv.rb:1298:in `parse'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/cbrain_plugins/installed-plugins/userfiles/csv_file/csv_file.rb:170:in `parse_file_content_as_csv'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/cbrain_plugins/installed-plugins/userfiles/csv_file/csv_file.rb:156:in `create_csv_array'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task/fsl_melodic/portal/fsl_melodic.rb:129:in `parse_csv_file'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/cbrain_plugins/installed-plugins/cbrain_task/fsl_melodic/portal/fsl_melodic.rb:55:in `before_form'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/app/models/portal_task.rb:359:in `wrapper_before_form'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/app/controllers/tasks_controller.rb:225:in `new'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/action_controller/metal/implicit_render.rb:4:in `send_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/abstract_controller/base.rb:167:in `process_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/action_controller/metal/rendering.rb:10:in `process_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/abstract_controller/callbacks.rb:18:in `block in process_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:525:in `block in _run__3217895913174204533__process_action__1227200730664726714__callbacks'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:215:in `block in _conditional_callback_around_1038'
/home/cbrainsys/DEV_CBRAIN/BrainPortal/app/controllers/application_controller.rb:101:in `activate_user_time_zone'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:214:in `_conditional_callback_around_1038'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:513:in `_run__3217895913174204533__process_action__1227200730664726714__callbacks'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:405:in `__run_callback'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:385:in `_run_process_action_callbacks'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/callbacks.rb:81:in `run_callbacks'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/abstract_controller/callbacks.rb:17:in `process_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/action_controller/metal/rescue.rb:29:in `process_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/actionpack/lib/action_controller/metal/instrumentation.rb:30:in `block in process_action'
/home/cbrainsys/.rvm/gems/ruby-2.2.0/bundler/gems/rails-3b4398bb605c/activesupport/lib/active_support/notifications.rb:123:in `block in instrument'
Downloading a file as a 1-step process
It would be nice to be able to download a file from a collection directly, as a one-step process, rather than having to click on "Extract Files from Collection", wait to be taken back to the list of files, then have to scan the entire list of files for the one you just extracted, and then "Download."
FSL melodic: review the launch form, and add documentation (explanations) wherever appropriate.
Was issue #32 in cbrain-plugins-neuro.
MGZ file type should be MGH
MGZ is the compressed version of MGH file... So the model should be MghFile and not MgzFile.
Bug in CIVET when run with multispectral or spectral_mask.
In some case, CIVET raise the following error:
[2016-08-22 12:31:02 EDT] setup_and_submit_job() Exception raised while setting up: NoMethodError: undefined method match' for #<MincFile:0x000000112345z3> [2016-08-22 12:31:02 EDT] .../cbrain_plugins/installed-plugins/cbrain_task/civet/bourreau/civet.rb:134:in
setup'
[2016-08-22 12:31:02 EDT] ..Bourreau/app/models/cluster_task.rb:676:in `block (2 levels) in setup_and_submit_job'
It's due to missing conversion between object and name.
FSL Melodic: specify tool config for fsl_sub
Currently, fsl_sub doesn't specify a tool config when it submits tasks to CBRAIN. The Bourreau picks the first tool_config it finds, which has several issues:
- the new task may be submitted to a different cluster;
- the new task may be submitted with a different version of FSL.
So, at the moment, FSL melodic (group analyses) only work when there is only a single tool config for fsl_sub, with the same version as FSL melodic, and on the same cluster.
The solution to allow for more fsl_sub tool_configs is to:
- choose the proper tool_config_id in fsl_melodic (bourreau-side). The tool config should be on the same bourreau, with the same FSL version (fsl_sub currently use different versions than FSL, but this should be fixed in fsl_sub's Boutiques descriptor).
- pass this tool config id to fsl_sub, e.g. through an environment variable.
- make fsl_sub write the tool_config_id in its job submission to CBRAIN.
FSL melodic: make task relocatable.
As noticed by @prioux:
I had a quick look at the work directory of that task, and in the .qsub file
all the data files are always substitued with complete full path to the task's work
directory. Is that really necessary? The entire point of writing a task is to encapsulate
the processing locally in the work directory, to make things relocatable even accross
clusters. Full paths defeat this completely. Couldn't all operations be performed
with relative paths instead? e.g. instead of
# Extracts dimensions of file /gs/project/eim-670-aa/cbrain/data/gridshare/31/01/02/nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz
${FSLINFO} /gs/project/eim-670-aa/cbrain/data/gridshare/31/01/02/nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz | awk '$1=="dim1" || $1=="dim2" || $1=="dim3" || $1=="dim4" {print}'> /gs/project/eim-670-aa/cbrain/data/gridshare/31/01/02/nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz.fslinfo
# Extracts TR of file /gs/project/eim-670-aa/cbrain/data/gridshare/31/01/02/nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz
${FSLHD} /gs/project/eim-670-aa/cbrain/data/gridshare/31/01/02/nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz | awk '$1=="pixdim4" {print $2}' > /gs/project/eim-670-aa/cbrain/data/gridshare/31/01/02/nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz.trvalue
why not :
# Extracts dimensions of file nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz
${FSLINFO} nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz | awk '$1=="dim1" || $1=="dim2" || $1=="dim3" || $1=="dim4" {print}' > nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz.fslinfo
# Extracts TR of file nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz
${FSLHD} nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz | awk '$1=="pixdim4" {print $2}' > nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz.trvalue
Also, the bash commands could be split on multiple lines to make things prettier. And no need to repeat the file name in the comment
# Extracts dimensions
${FSLINFO} \
nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz | \
awk '$1=="dim1" || $1=="dim2" || $1=="dim3" || $1=="dim4" {print}' \
> nmahani-FslMelodic-T310102/Spin002^^^^_resting_post1_SENSE_FSL_14_1.nii.gz.fslinfo
CBRAIN's fsl_sub to submit all subtasks at once
The current 'patch' to fsl_sub to make it work with CBRAIN works like this, when an arrray of tasks need to be submitted:
- loop through each task:
- create a .json file
- wait up to 5 minutes for a .cbid file
Instead of that, loop through all the tasks, create all the .json files, then wait for all the .cbid files to appear.
Move /images/brainbrowser-loader.gif inside the plugins
We have a GIF file installed in the platform that should be moved to this plugin; it is used by the MINC and the CivetOutput userfiles. I suggest duplicating it in the static assets for each.
Once done, notify me so I can remove it from CBRAIN itself.
Civet pattern matching for prefix and subject ID: don't stop at first failure
The pattern matching code used to auto-fill the prefix and subject ID in the CIVET form
should not stop at the first failure to match a pattern. It should try to fill all the fields,
and those that cannot, it should mark them in the errors list so that the input box show
up in red.
Make FSL melodic a recoverable and restartable task
It seems difficult to ensure that the Melodic code is restartable. While it creates unique directories (.ica, .ica+, etc), there is absolutely no guarantee that restarting it in the same directory won't crash or produce side effects. The best solution to date seems to be a mere deletion of the content of the working directory. Name collisions of output files created in CBRAIN should also be tested. Has to be tested for all kinds of tasks (see tests in https://github.com/glatard/cbrain-tests-fsl-melodic)
FSL tools to validate filenames before starting a task.
Looking at the FSL scripts I discovered many of them are written in the TCL programming language, and proper escaping of arguments passed down the stack of utilities is really poor. This explains some of the failures Najma got because she had "^^^^" in her filenames, which are normal characters in filename in a non-interactive use, but mess up all the TCL scripts when they are substituted. It's poor programming on the FSL side, and there's nothing we can do.
I suggest that FSL tools in CBRAIN right from the start apply a simple, stricter filename validation step before they're even launched. In a task's before_form(), a qucik check of all the filenames selected by the user could be made to ensure they only contain alphanums. It's exactly the purpose of the callback before_form(), in fact.
Replace CivetStudy with CivetVirtualStudy
The CivetStudy model stores all the CivetOutputs inside it, which leads to a lot of duplicated data.
Let's create a drop-in replacement, CivetVirtualStudy, that behaves the same way as far as users are concerned but the data is kept as just a list of IDs of the associated CivetOutputs.
Architecture elements:
- store the list of IDs in a CSV file at the top of the CivetVirtualStudy, to be reloaded using the methods provided by the CbrainFileList model. The CbrainFileList object is never to be saved into the DB (ensure it too to prevent programmers making mistakes)
- [REJECTED] maybe access the CSV files using the data provider streaming methods when the CivetVirtualStudy is not synchronized
- adjust the view code to provide view links to the CivetOutputs as needed
- override sync_to_cache() so that syncing a CivetVirtualStudy will sync the CivetOutputs, and create the symlinks to the caches
- [REJECTED] override sync_to_provider() so that the symlinks are NOT sent, and the final status is ProvNewer (because the cached version will be missing the symlinks I assume)
Once the model works well, we'll replace the places int he scientific code where CivetStudies are created so that CivetVirtualStudies are used instead.
Note: was discussed in Redmine issue 3216.
Remove code from the oblique viewer MincNavigator; make it installable using a task (rake or bash?)
We have an entire copy of the MincNavigator codebase in the plugin, as a viewer for files of type MincFile; we should simply remove the directory and provide a tiny script that pulls it from GitHub instead. That woudl simplify maintenance and code fixes on that side.
Restrict BET options for fMRI data
BET can run on 4D fMRI data by selecting option -F. If this option is selected, other ones, such as -B, -S, -R must become unwritable. Otherwise, the output will be seriously erroneous, and only one volume.
Was issue #27 in cbrain-plugins-fsl
FSL first: task successfully completes even when command fails.
For instance, "command not found" error is not handled because:
It doesn't write ERROR in stdout/stderr.
The output directory exists (it's empty) and can be transferred.
Was issue #21 in cbrain-plugins-fsl.
FSL Melodic: Exclude all files that do not comply to the dimension specified in inputs.
Add 4 input params (x,y,z,t) and a checkbox to enable/disable the dimension check. If checkbox is enabled, then any file that doesn't have the required dimension will be excluded from the analysis, with a warning.
CivetCombiner logs are too verbose
When creating a large study, we get one long line for each subject CivetOutput added; I think it's a result of the addlog_to_userfiles_these_created_these() method ; maybe when there are lots of files we can reduce the amount of text.
FSL melodic: add the possibility to use [csv_file_name] key in the output file name.
In documentation, encourage the user to be careful about naming.
Was issue #24 in cbrain-plugins-fsl.
FSL Melodic: add a disclaimer about "post stats and time series" in the documentation
FSL Melodic: Option to change the standard space not functional
In CBRAIN-MELODIC interface, user may chose to "Use custom template file", however there is no way for user to choose this template file.
It can be provided as an option to select a template file together with the CSV and FSF file before launching melodic.
Preferably, this could be added as the 4th column in the CSV file.
In FSL Melodic, separate DEBUG logs from INFO logs.
FSL melodic: show params page sometimes crashes
Exception: ActionView::Template::Error: undefined method `each' for nil:NilClass
BrainPortal/app/views/tasks/cbrain_plugins/installed-plugins/cbrain_task/fsl_melodic/views/_show_params.html.erb:34:in `_app_views_tasks_cbrain_plugins_installed_plugins_cbrain_task_fsl_melodic_views__show_params_html_erb___95173991929139712_328298200'
Properly capture the stdout and stderr of fsl_sub
When fsl_sub handles a single task, it internally redirects the outputs with this code:
/bin/sh <<EOF1 > ${LogDir}${JobName}.o$$ 2> ${LogDir}${JobName}.e$$
$@
EOF1
In the case where this is executing under CBRAIN, this will pollute the work directory with a lot of files named bash.oNNN
and bash.eNNN
instead of storing these in the CBRAIN capture files. The way to fix this is to remove the redirections altogether, if we're running in CBRAIN. (But: how to test that? Env variable?)
Add FSL Aroma (see Redmine #7779)
CIVET params (registration option)
According with Claude:
The defaut is 9 for all versions of CIVET. The CBRAIN defaults should
match the command-line defaults
Update NIAK code to use new revision tracking system
We no longer SVN IDs, there is a single place in the code of
cbrain_task/niak_pipeline_fmri_preprocess/bourreau/niak_pipeline_fmri_preprocess.xml.erb
(line 32) where we invoke svn_id_pretty_file_rev_author_date() .
FSL bedpostx add --model option
From one of our user:
Only a flag is missing (--model). Could you please check whether it's sth that you can fix easily?
Multi-Shell Model : Use this option if the data contain more than one non-zero bvalue. This will use the model described in Jbabdi et al. MRM 2012, where the diffusion coefficient is modelled using a Gamma distribution. This option will output the posterior mean of a diffusivity variance parameter mean_d_stdsamples. Command line argument: --model=2. It can be either 1 or 2 for singel-shell or multi-shell analysis.
the default is 1, but we should be able to run it for multishell data too.
FSL Melodic: allow to upload time series file (see melodic GUI)
NIfTI file viewer has a bug
Generates an exception:
ActionView::MissingTemplate: Missing template BrainPortal/cbrain_plugins/installed-plugins/userfiles/functional_nifti_file/views/_volume_viewer_loader with {:locale=>[:en], :formats=>[:html], :handlers=>[:erb, :builder]}. Searched in: * "BrainPortal/app/views" * "BrainPortal" * "/"
with trace:
BrainPortal/cbrain_plugins/installed-plugins/userfiles/minc_file/views/_volume_viewer.html.erb:540:in `_cbrain_plugins_installed_plugins_userfiles_minc_file_views__volume_viewer_html_erb__3427599092687694237_281994820'
(...)BrainPortal/app/views/userfiles/show.html.erb:246:in `_app_views_userfiles_show_html_erb__383784840519253085_295074060'
See also exception log 1178 in the CBRAIN service
The "FslMelodic Output" viewer code is all broken.
When rendering userfiles of that type, the view code contains full paths on the cluster sides for rendering the images, so it's all borken. See screenshot.
The image's SRC URL in the HTML is all weird:
577603/content?arguments=melodic-output-305651-3.gica//nfs3_ib/evans-ms.nfs/tank/nfs/evans/nobackup/share/prioux/gridshare/30/56/51/asimioni-FslMelodic-T305651/denoised_func_data_nonaggr_run1_s06202.nii_melodic-output-305651-3.ica/reg/example_func2standard1.png&content_loader=collection_file&content_viewer=off&viewer=image_file&viewer_userfile_class=ImageFile
Freesurfer recon-all option to use different surface template, smoothing levels
The following are advanced options not desirable for all users, but would be helpful for expert users - (1) is particularly for members or affiliates of our lab interested in direct comparisons between Freesurfer and CIVET, (2)-(3) are more generally useful. Not urgent but would be nice.
There are 3 parts to this request that could work independently or together:
(1) To use an alternative template than the default fsaverage (namely, our CIVET template which I have already converted to FS format)
(2) To use smoothing levels other than the 5-25mm offered by -qcache
(3) To do either of the above (or default -qcache) after a finished run of recon-all without running the entire thing from scratch.
For example:
(1): run everything from scratch with $template = CIVET2_average
recon-all -s $subj -all -qcache -target CIVET2_average
(2): run everything from scratch with smoothing = 30mm (default fsaverage template)
recon-all -s $subj -all -qcache -measure thickness -fwhm 30
(1,2): run everything from scratch with smoothing = 30mm and $template = CIVET2_average
recon-all -s $subj -all -qcache -measure thickness -fwhm 30 -target CIVET2_average
Or simply remove the -all flag for any (3): (1,2,3): post-process a finished recon-all run with smoothing = 30mm and $template = CIVET21_average
recon-all -s $subj -qcache -measure thickness -fwhm 30 -target CIVET2_average
(3): Postprocess finished recon-all with default -qcache and default template fsaverage
recon-all -s $subj -qcache
I have placed the CIVET2_average template (good for 2.0 or 2.1) for you to play around with here:
http://www.bic.mni.mcgill.ca/users/llewis/CIVET2_average.tar.gz
Place it in the Freesurfer subjects directory / in same directory as fsaverage.
Thank you! Let me know if you have any questions.
nii2minc should not allow launching a task with one selection box left to default
There is a selection box in the nii2minc task view code that says:
Write voxel data in type [selection box]
There are three values in it, but the task code allows launching a task with the blank value still selected, which crashes on the bourreau side with
CbrainError: Unexpected voxel int sign
Adjust after_form().
In FSL Melodic output viewer, for .gica directories, check that results of .ica children analyses are synchronized
In particular in the "Registration summary" page, images corresponding to non-synchronized children analyses do not show.
FSL Melodic: Print a warning if the number of saved .ica files is not consistent with the number of input files.
Enable the grouping of Melodic results in a MelodicStudy
Melodic results should be grouped in a "MelodicStudy" when user selects option in launch form (defaults to yes). Launching melodic should launch a new task that will wait for the others to complete and then group the results. Replicate what is done in CivetCombiner.
Volume viewer loader fails for files of type Minc1 or Minc2
When files are assigned a more specific type of Minc1 or Minc2, the volume viewer special hook loader fails. That hook is at:
FSL MELODIC: Account for intermediate registration to highres fMRI
In CBRAIN-Melodic interface, there has to be an option to register to "expanded functional Image"
The input files will be presented in a .CSV file.
Each column of the file will correspond to
Column 1: RSfMRI_1.nii.gz (compulsory, must be UNIQUE)
Column 2: BET-MRI_1.nii.gz (compulsory, same file may be repeated across rows)
Columns3: BET-Highres-FMRI_1.nii.gz (optional)
Program fail if Column1 and 2 are empty.
FSL melodic: re-implement it in Boutiques using a wrapper script
Was issue #33 in cbrain-plugins-fsl
ProbtrackX2 overwrites input files in the cache
The Boutiques command-line starts with "cp -r inputdir outputdir" which simply copies the symbolic link as is, instead of making a real distinct copy:
[cbrain@lg-1r17-n05 admin_nbeck-FslProbtrackx2-T371048]$ ls -l
total 0
lrwxrwxrwx 1 cbrain cbrain 49 Dec 19 12:13 DTI_merged.bedpostX -> ../../../../DP_Cache/82/13/27/DTI_merged.bedpostX
lrwxrwxrwx 1 cbrain cbrain 49 Dec 19 14:32 probtrackx2_output -> ../../../../DP_Cache/82/13/27/DTI_merged.bedpostX
lrwxrwxrwx 1 cbrain cbrain 54 Dec 19 12:13 ROI_Executive_bin.nii.gz -> ../../../../DP_Cache/82/14/06/ROI_Executive_bin.nii.gz
lrwxrwxrwx 1 cbrain cbrain 53 Dec 19 12:13 ROI_Striatum_bin.nii.gz -> ../../../../DP_Cache/82/14/07/ROI_Striatum_bin.nii.gz
FSL first: move files in save_results method, not in command.
Was issue #22 in cbrain-plugins-fsl.
Adjust CivetCombiner view code
The two view files for CivetCombiner crash abominably when the Combiner was created directly from a Civet's form.
That's because the view files still only expect the task's inputs to be IDs to files (CivetOutputs), but internally the task
supports providing no file ID but providing the IDs of Civet tasks instead; then it fetches the IDs from the tasks
(presumably, the task created these CivetOutputs).
When a user tries to VIEW the CivetCombiner or EDIT a CivetCombiner, it fails.
Recovery and input file sync error handling in CIVET
If CIVET is sent to 'recover' mode when its T1 input file has been cleared from the DP cache, it fails in a different way that CBRAIN can't detect right now, so the task is erroneously marked as Completed
.
Two improvements to fix this:
- re-sync input files in cluster_commands() (which is invoked after error recovery) to make sure the T1 is there
- check for the string
Stopped processing all pipelines.
at the end of the CIVET output.
Migrate FSL bet, first and fast to Boutiques.
- No Docker container should be used for these tools as FSL is largely installed on the clusters.
- For bet, #6 should also be considered.
- Try to be as exhaustive as possible on the supported options.
Add option to CivetCombiner so it can combine CivetOutputs despite different prefixes.
Right now the Combiner will refuse to create a CivetStudy unless all CivetOutputs were built with the same 'prefix'.
Add a checkbox in the interface and allow the program to proceed even if the civet outputs have different prefixes. With a warning to the user.
FSL melodic: support for analysis types 2, 6 and 4.
Need to start from previously pre-processed data.
Was issue #18 in cbrain-plugins-fsl
Update MincBet, fsl_anat and ICA-AROMA using the latest Boutiques features
Non exhaustive list:
- Add parameter groups wherever relevant.
- Add mutual exclusion between input file and input dir in FSL anat.
- Add one of a set requirement between input files in ICA AROMA.
Following @Najmahan comment, it would also be useful to add the type of files that need to be selected to the description of these tools (e.g., for MINCBet "This tool processes a MINC file." or for FSL anat "This tool processes a NIFTI file or a .anat directory").
@ttaa9 I cannot assign this issue to you until you accept the invitation to the repo, but it is for you :)
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