Add option to compute dwi sh #41
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Conflict + I agree you should have specific parameters here. |
ppoulin91
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I moved the SH fitting after pre-processing (following the same logic as DTI/FODF Metrics processes). Let me know if this is okay or if I should move stuff around/rename variables and processes. |
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Currently testing it on my remote machine, I'll let you know if everything runs smoothly |
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Fixed a typo, everything works on my end |
USAGE
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| @@ -57,6 +57,14 @@ OPTIONAL BIDS ARGUMENTS (current value) | |||
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| OPTIONAL ARGUMENTS (current value) | |||
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| --sh_fitting Compute a Spherical Harmonics fitting onto the DWI, and output the SH coefficients in a Nifti file ($compute_sh). | |||
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| --sh_fitting Compute a Spherical Harmonics fitting onto the DWI, and output the SH coefficients in a Nifti file ($compute_sh). | |
| --sh_fitting Compute a Spherical Harmonics fitting onto the DWI, and output the SH coefficients in a Nifti file ($sh_fitting). |
USAGE
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| -sh_order=6 for 28 directions | ||
| --sh_fitting_shell Shell selected to compute the SH fitting ($sh_fitting_shell). | ||
| NOTE: SH fitting works only on single shell. | ||
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These options should not be at the top.
main.nf
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| export OMP_NUM_THREADS=1 | ||
| export OPENBLAS_NUM_THREADS=1 | ||
| scil_extract_dwi_shell.py $dwi \ | ||
| $bval $bvec 0 $params.sh_fitting_shell ${sid}__dwi_sh_fittting.nii.gz \ |
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| $bval $bvec 0 $params.sh_fitting_shell ${sid}__dwi_sh_fittting.nii.gz \ | |
| $bval $bvec 0 $params.sh_fitting_shell ${sid}__dwi_sh_fitting.nii.gz \ |
main.nf
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| export OMP_NUM_THREADS=1 | ||
| export OPENBLAS_NUM_THREADS=1 | ||
| scil_extract_dwi_shell.py $dwi \ | ||
| $bval $bvec 0 $params.sh_fitting_shell ${sid}__dwi_sh_fitting.nii.gz \ |
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I think we must to use the same kind of thing that fodf_shells "0 1000".
Maybe we can raise an error when we select sh_fitting and don't set sh_fitting_shell. You have an example with fodf/dti_shells
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Tested it on my side and it works perfectly, I get all b0 + b1000 extracted. the script arg is set to nargs='+', so it automatically detects all b-vals. I thought the "quote" thing was specifically for nextflow because it couldn't handle multiple args
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Sorry for the delay, I agree with @GuillaumeTh . you should have a warning when we select sh_fitting and don't set sh_fitting_shell and you should use the same kind of input as fodf_shells: "0 1000". Otherwise almost ready to be merged
Optional --compute_sh option, useful to compute metrics from the signal ODF in the future.
Question: