json and invocation for testing new CBRAIN tool for DWI denoise prepr… #326
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…ocessing DesignerV2
| "/home/hayabusa/PROJECT_MPN/MPN_TESTS/sub-MPN0000087/ses-MPN1Scan1/dwi/sub-MPN0000087_ses-MPN1Scan1_acq-multib38_dir-AP_dwi.nii.gz", | ||
| "/home/hayabusa/PROJECT_MPN/MPN_TESTS/sub-MPN0000087/ses-MPN1Scan1/dwi/sub-MPN0000087_ses-MPN1Scan1_acq-multib70_dir-AP_dwi.nii.gz" | ||
| ] | ||
| } |
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we do not store invocations in this folder, please remove. It will likely create problems
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You can attach file separately to the PR, if you like
| "custom": { | ||
| "cbrain:author": "Alexandre Pastor-Bernier <alexandre.pastor@mcgill.ca>", | ||
| "cbrain:readonly-input-files": true, | ||
| "cbrain:integrator_modules": { |
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in cbrain, you should use actually existing id, such as phase, no input has 'input' id. This will cause an error during integration or run
| "url":"https://nyu-diffusionmri.github.io/DESIGNER-v2/", | ||
| "command-line": "B0=[RPE_B0]; SUBJECT=$(basename $B0); SID=${SUBJECT%%_ses}; designer [MAG] [OUT_DIR] -denoise -shrinkage frob -algorithm jespersen [PHASE] -degibbs -pf 0.75 [PENDIR] -eddy [RPE_B0] -normalize -b1correct [PROCESSING] -nocleanup", | ||
| "container-image": { | ||
| "image": "designer2_v2.0.13", |
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use exact image name in dockerhub format
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I think it is
nyudiffusionmri/designer2:v2.0.13
it seems a bit strange as 2 appears both in the name and the version tag, yet a
correct docker name will help us (eventually) update to 2.0.14 or higher when needed
| "optional": false, | ||
| "value-key": "[PHASE]", | ||
| "command-line-flag":"-phase" | ||
| }, |
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you would need to create CBRAIN file lists ahead for this, let's discuss other options.
|
In MPN data provider, you register subject folders rather than individual files. Therefore, for the purposes of the MPN project, it would be better to have boutiques that accept a single folder as input. In fact, we could use BidsSingleSubjectMaker so it appears as a BIDS app tool with dataset input and subject. Then, perhaps paths could be passed as string parameters. What do you think? I understand that for many users, especially those familiar with Designer 2, a more straightforward implementation might work better. If you like, we can integrate it this way and then determine what changes are needed to fit MPN’s requirements. Perhaps we could also create an additional tool, such as MPN-designer or MPN-diffuse, which would more closely match your original script. Additionally, there are a few technical issues within the boutiques code that need attention. |
MontrealSergiy
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MontrealSergiy
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Please see above comments, namely
- correct docker name
- correct "input" key to something properly defined
- discuss applicability to MNP
| "/home/hayabusa/PROJECT_MPN/MPN_TESTS/sub-MPN0000087/ses-MPN1Scan1/dwi/sub-MPN0000087_ses-MPN1Scan1_acq-multib38_dir-AP_dwi.nii.gz", | ||
| "/home/hayabusa/PROJECT_MPN/MPN_TESTS/sub-MPN0000087/ses-MPN1Scan1/dwi/sub-MPN0000087_ses-MPN1Scan1_acq-multib70_dir-AP_dwi.nii.gz" | ||
| ] | ||
| } |
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You can attach file separately to the PR, if you like
| "url":"https://nyu-diffusionmri.github.io/DESIGNER-v2/", | ||
| "command-line": "B0=[RPE_B0]; SUBJECT=$(basename $B0); SID=${SUBJECT%%_ses}; designer [MAG] [OUT_DIR] -denoise -shrinkage frob -algorithm jespersen [PHASE] -degibbs -pf 0.75 [PENDIR] -eddy [RPE_B0] -normalize -b1correct [PROCESSING] -nocleanup", | ||
| "container-image": { | ||
| "image": "designer2_v2.0.13", |
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I think it is
nyudiffusionmri/designer2:v2.0.13
it seems a bit strange as 2 appears both in the name and the version tag, yet a
correct docker name will help us (eventually) update to 2.0.14 or higher when needed
| "input": [ "NiftiFile", "SingleFile" ] | ||
| }, | ||
| "BoutiquesOutputFileTypeSetter": { | ||
| "output_dir": "DesignerOutput" |
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On top of all the changes suggested by Sergiy, this Userfile model 'DesignerOutput' does not exist and is not provided in the PR.
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alex, maybe delete this type setter for now. It is optional, mostly to distinguish given tool output conveniently.
Of course if you can define DesignerOutput type if you have a gist of ruby coding, or just following few other examples.
No need of this file for CBRAIN -> in reply to Segey
Added a new descriptor for the FreeSurfer cortical defacing ad refacing process, including command-line options and input/output specifications.
Removed and restructured output definitions in the freesurfer8_MiDeFace descriptor.
Updating to load with FS8 # But need to bind wrapper-script !
Removed input for NIFTI file and updated session input details.
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