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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,112 +1,63 @@ | ||
| #!/bin/bash | ||
| # | ||
| #script for generating a project xml file | ||
| #script for generating a project json file | ||
| # | ||
| # usage project_doc.sh {project} {subject} {session} {process called (heudiconv, mriqc, fmriprep, xcpengine, mridti, scfsl)} {is this a new file? (yes/no)} | ||
| # usage project_doc.sh {project} {subject} {session} {process called (heudiconv, mriqc, fmriprep, xcpengine, mridti, scfsl)} {is this a new file? (yes/no)} {app version} | ||
| # | ||
| # to be called as part of a pipeline for documentation of processing tool calls | ||
| # | ||
| # maybe set up to run on batches with reading in the txt files from batchprocd.sh to the project xml | ||
|
|
||
| project=$1 | ||
| subject=$2 | ||
| session=$3 | ||
| proc=$4 | ||
| newFile=$5 | ||
| version=$6 | ||
|
|
||
| #pull in versions from sif names var in script? | ||
|
|
||
| #Get date and time | ||
| NOW=$(date +"%m-%d-%Y-%T") | ||
|
|
||
| xmlfile="${project}_${subject}_${session}.xml" | ||
| jsonfile="${project}_${subject}_${session}.json" | ||
|
|
||
| if [ "${newFile}" == "yes" ]; | ||
| then | ||
| echo '<?xml version="1.0" encoding="utf-8"?>' > "$xmlfile" | ||
| echo '<proc_log id="${project}">' >> "$xmlfile" | ||
|
|
||
| jo log="pipeline processing" project="${project}" > $jsonfile | ||
| fi | ||
|
|
||
| #if statements for each process (heudiconv, mriqc, fmriprep, xcpengine, mridti, scfsl) | ||
| if [ "${proc}" == "heudiconv" ]; | ||
| then | ||
| echo '<proc id="HeuDiConv">' >> "$xmlfile" | ||
| echo '<source>nipy/heudiconv</source>' >> "$xmlfile" | ||
| echo '<title>HeuDiConv</title>' >> "$xmlfile" | ||
| echo '<version>0.9.0</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description> Heuristic conversion from DICOMs to BIDS-compatible nii.gz images with JSON sidecars.</description>' >> "$xmlfile" | ||
| echo '<conversion_tool>Chris Rordens dcm2niix</conversion_tool>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| cat $jsonfile | jq '.step1["process"] |= "HeuDiConv"' | jq '.step1["Docker"] |= "nipy/heudiconv:'${version}'"' | jq '.step1["date"] |= '"${NOW}"'' | jq '.step1["description"] |= "Heuristic-based conversion from DICOMs to BIDS-compatible nii.gz images with JSON sidecars with dcm2niix"' > tmp | ||
| mv tmp $jsonfile | ||
| elif [ "${proc}" == "mriqc" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="MRIQC">' >> "$xmlfile" | ||
| echo '<source>poldracklab/mriqc</source>' >> "$xmlfile" | ||
| echo '<title>MRIQC</title>' >> "$xmlfile" | ||
| echo '<version>0.16.1</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description> MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data </description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| cat $jsonfile | jq '.step2["process"] |= "MRIQC"' | jq '.step2["Docker"] |= "poldracklab/mriqc:'${version}'"' | jq '.step2["date"] |= '"${NOW}"'' | jq '.step2["description"] |= "MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data"' > tmp | ||
| mv tmp "$jsonfile" | ||
| elif [ "${proc}" == "fmriprep" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="fMRIPrep">' >> "$xmlfile" | ||
| echo '<source>niprep/fmriprep</source>' >> "$xmlfile" | ||
| echo '<title>fMRIPrep</title>' >> "$xmlfile" | ||
| echo '<version>21.0.1</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description>fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc.</description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| cat $jsonfile | jq '.step3["process"] |= "fMRIPrep"' | jq '.step3["Docker"] |= "nipreps/fmriprep:'${version}'"' | jq '.step3["date"] |= '"${NOW}"'' | jq '.step3["description"] |= "fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. It performs basic processing steps (coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc.) providing outputs that can be easily submitted to a variety of group level analyses, including task-based or resting-state fMRI, graph theory measures, surface or volume-based statistics, etc."' > tmp | ||
| mv tmp "$jsonfile" | ||
| elif [ "${proc}" == "xcpengine" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="xcpEngine">' >> "$xmlfile" | ||
| echo '<source>PennBBL/xcpEngine</source>' >> "$xmlfile" | ||
| echo '<title>xcpEngine fc-36p, fc-36p_scrub, fc-aroma</title>' >> "$xmlfile" | ||
| echo '<version>1.2.4</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description> The XCP imaging pipeline (XCP system) is a free, open-source software package for processing of multimodal neuroimages. The XCP system uses a modular design to deploy analytic routines from leading MRI analysis platforms, including FSL, AFNI, and ANTs.</description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| cat $jsonfile | jq '.step4["process"] |= "xcpEngine"' | jq '.step4["Docker"] |= "pennbbl/xcpengine:'${version}'"' | jq '.step4["date"] |= '"${NOW}"'' | jq '.step4["description"] |= "The XCP imaging pipeline (XCP system) is a free, open-source software package for processing of multimodal neuroimages. The XCP system uses a modular design to deploy analytic routines from leading MRI analysis platforms, including FSL, AFNI, and ANTs"' > tmp | ||
| mv tmp "$jsonfile" | ||
| elif [ "${proc}" == "mridti" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="mridti">' >> "$xmlfile" | ||
| echo '<source>mrfil/mridti</source>' >> "$xmlfile" | ||
| echo '<title>MRI DTI with FSL</title>' >> "$xmlfile" | ||
| echo '<version>1.0.0</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description>Diffusion tensor processing pipeline with FSL bedpostx, probtrackx2.0</description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| elif [ "${proc}" == "scfsl" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="scfsl">' >> "$xmlfile" | ||
| echo '<source>mrfil/scfsl</source>' >> "$xmlfile" | ||
| echo '<title>Structural Connectivity with FSL </title>' >> "$xmlfile" | ||
| echo '<version>1.0.0</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description> FSL-based structural connectivity analysis with fibre-tracking between 68 cortical regions, 14 subcortical regions, and the left and right cerebellar cortices defined by the Freesurfer recon-all parcellation using the Desikan-Killiany Atlas</description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| cat $jsonfile | jq '.step5["process"] |= "MRIDTI FSL"' | jq '.step5["Docker"] |= "mrfilbi/neurodoc:'${version}'"' | jq '.step5["date"] |= '"${NOW}"'' | jq '.step5["description"] |= "Diffusion tensor processing pipeline with FSL "' > tmp | ||
| mv tmp "$jsonfile" | ||
| elif [ "${proc}" == "qsiprep" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="qsiprep">' >> "$xmlfile" | ||
| echo '<source>pennbbl/qsiprep</source>' >> "$xmlfile" | ||
| echo '<title>Diffusion Preprocessing with QSIprep</title>' >> "$xmlfile" | ||
| echo '<version>0.15.1</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description>The preprocessing pipelines are built based on the available BIDS inputs, ensuring that fieldmaps are handled correctly. The preprocessing workflow performs head motion correction, susceptibility distortion correction, MP-PCA denoising, coregistration to T1w images, spatial normalization using ANTs_ and tissue segmentation.</description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| #QSIPrep is preferred over mridti due to more complete preprocessing | ||
| cat $jsonfile | jq '.step5["process"] |= "QSIPrep preprocessing"' | jq '.step5["Docker"] |= "pennbbl/qsiprep:'${version}'"' | jq '.step5["date"] |= '"${NOW}"'' | jq '.step5["description"] |= "The preprocessing pipelines are built based on the available BIDS inputs, ensuring that fieldmaps are handled correctly. The preprocessing workflow performs head motion correction, susceptibility distortion correction, MP-PCA denoising, coregistration to T1w images, spatial normalization using ANTs_ and tissue segmentation. This requires step 6 to include the reorient_fslstd reconstruction method to use outputs in FSL space!"' > tmp | ||
| mv tmp "$jsonfile" | ||
| elif [ "${proc}" == "qsirecon" ]; | ||
| then | ||
| head -n -1 "$xmlfile" > temp.txt ; mv temp.txt "$xmlfile" | ||
| echo '<proc id="qsirecon">' >> "$xmlfile" | ||
| echo '<source>pennbbl/qsiprep</source>' >> "$xmlfile" | ||
| echo '<title>Tractography with Anatomical Constrains using QSIprep MRtrix implementation </title>' >> "$xmlfile" | ||
| echo '<version>0.15.1</version>' >> "$xmlfile" | ||
| echo "<exec_date>${NOW}</exec_date>" >> "$xmlfile" | ||
| echo '<description> This workflow uses the msmt_csd algorithm [Jeurissen2014] to estimate FODs for white matter, gray matter and cerebrospinal fluid using multi-shell acquisitions. The white matter FODs are used for tractography and the T1w segmentation is used for anatomical constraints [Smith2012]. </description>' >> "$xmlfile" | ||
| echo '</proc>' >> "$xmlfile" | ||
| cat $jsonfile | jq '.step6["process"] |= "QSIPrep reconstruction"' | jq '.step6["Docker"] |= "pennbbl/qsiprep:'${version}'"' | jq '.step6["date"] |= '"${NOW}"'' | jq '.step6["description"] |= "QSIPrep reconstructions performed include: mrtrix_multishell_msmt_ACT-hsvs, dsi_studio_gqi, amico_noddi, and reorient_fslstd. More details at https://qsiprep.readthedocs.io/en/latest/reconstruction.html#"' > tmp | ||
| mv tmp "$jsonfile" | ||
| elif [ "${proc}" == "scfsl" ]; | ||
| then | ||
| cat $jsonfile | jq '.step7["process"] |= "SCFSL GPU"' | jq '.step7["Docker"] |= "mrfilbi/scfsl_gpu:'${version}'"' | jq '.step7["date"] |= '"${NOW}"'' | jq '.step7["description"] |= "CUDA-accelerated FSL-based structural connectivity analysis with fibre-tracking between 68 cortical regions, 14 subcortical regions, and the left and right cerebellar cortices defined by the Freesurfer recon-all parcellation using the Desikan-Killiany Atlas"' > tmp | ||
| mv tmp "$jsonfile" | ||
| fi | ||
| echo "</proc_log>" >> "$xmlfile" | ||
|
|
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