HCP HippUnfold and Post HippUnfold Implementations #320
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| #!/bin/bash | ||
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| get_batch_options() { | ||
| local arguments=("$@") | ||
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| command_line_specified_study_folder="" | ||
| command_line_specified_subject="" | ||
| command_line_specified_run_local="FALSE" | ||
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| local index=0 | ||
| local numArgs=${#arguments[@]} | ||
| local argument | ||
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| while [ ${index} -lt ${numArgs} ]; do | ||
| argument=${arguments[index]} | ||
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| case ${argument} in | ||
| --StudyFolder=*) | ||
| command_line_specified_study_folder=${argument#*=} | ||
| index=$(( index + 1 )) | ||
| ;; | ||
| --Subject=*) | ||
| command_line_specified_subject=${argument#*=} | ||
| index=$(( index + 1 )) | ||
| ;; | ||
| --runlocal) | ||
| command_line_specified_run_local="TRUE" | ||
| index=$(( index + 1 )) | ||
| ;; | ||
| *) | ||
| echo "" | ||
| echo "ERROR: Unrecognized Option: ${argument}" | ||
| echo "" | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| done | ||
| } | ||
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| get_batch_options "$@" | ||
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| StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by SubjectID) | ||
| Subjlist="100307 100610" #Space delimited list of subject IDs | ||
| EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script | ||
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| if [ -n "${command_line_specified_study_folder}" ]; then | ||
| StudyFolder="${command_line_specified_study_folder}" | ||
| fi | ||
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| if [ -n "${command_line_specified_subject}" ]; then | ||
| Subjlist="${command_line_specified_subject}" | ||
| fi | ||
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| #Set up pipeline environment variables and software | ||
| source "$EnvironmentScript" | ||
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| # Log the originating call | ||
| echo "$@" | ||
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| #NOTE: syntax for QUEUE has changed compared to earlier pipeline releases, | ||
| #DO NOT include "-q " at the beginning | ||
| #default to no queue, implying run local | ||
| QUEUE="" | ||
| #QUEUE="hcp_priority.q" | ||
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| ########################################## INPUTS ########################################## | ||
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| #Scripts called by this script do assume they run on the outputs of the PostFreeSurfer Pipeline | ||
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| ######################################### DO WORK ########################################## | ||
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| for Subject in $Subjlist ; do | ||
| echo $Subject | ||
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| if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then | ||
| echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh" | ||
| queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh) | ||
| else | ||
| echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/HippUnfoldHCP.sh" | ||
| queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE") | ||
| fi | ||
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| "${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/HippUnfoldHCP.sh \ | ||
| --study-folder="$StudyFolder" \ | ||
| --subject="$Subject" \ | ||
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| # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ... | ||
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| echo "set -- --study-folder=$StudyFolder \ | ||
| --subject=$Subject" \ | ||
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| echo ". ${EnvironmentScript}" | ||
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| done |
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| @@ -0,0 +1,94 @@ | ||
| #!/bin/bash | ||
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| get_batch_options() { | ||
| local arguments=("$@") | ||
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| command_line_specified_study_folder="" | ||
| command_line_specified_subject="" | ||
| command_line_specified_run_local="FALSE" | ||
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| local index=0 | ||
| local numArgs=${#arguments[@]} | ||
| local argument | ||
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| while [ ${index} -lt ${numArgs} ]; do | ||
| argument=${arguments[index]} | ||
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| case ${argument} in | ||
| --StudyFolder=*) | ||
| command_line_specified_study_folder=${argument#*=} | ||
| index=$(( index + 1 )) | ||
| ;; | ||
| --Subject=*) | ||
| command_line_specified_subject=${argument#*=} | ||
| index=$(( index + 1 )) | ||
| ;; | ||
| --runlocal) | ||
| command_line_specified_run_local="TRUE" | ||
| index=$(( index + 1 )) | ||
| ;; | ||
| *) | ||
| echo "" | ||
| echo "ERROR: Unrecognized Option: ${argument}" | ||
| echo "" | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| done | ||
| } | ||
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| get_batch_options "$@" | ||
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| StudyFolder="${HOME}/projects/Pipelines_ExampleData" #Location of Subject folders (named by SubjectID) | ||
| Subjlist="100307 100610" #Space delimited list of subject IDs | ||
| EnvironmentScript="${HOME}/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script | ||
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| if [ -n "${command_line_specified_study_folder}" ]; then | ||
| StudyFolder="${command_line_specified_study_folder}" | ||
| fi | ||
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| if [ -n "${command_line_specified_subject}" ]; then | ||
| Subjlist="${command_line_specified_subject}" | ||
| fi | ||
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| #Set up pipeline environment variables and software | ||
| source "$EnvironmentScript" | ||
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| # Log the originating call | ||
| echo "$@" | ||
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| #NOTE: syntax for QUEUE has changed compared to earlier pipeline releases, | ||
| #DO NOT include "-q " at the beginning | ||
| #default to no queue, implying run local | ||
| QUEUE="" | ||
| #QUEUE="hcp_priority.q" | ||
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| ########################################## INPUTS ########################################## | ||
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| #Scripts called by this script do assume they run on the outputs of the PostFreeSurfer Pipeline | ||
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| ######################################### DO WORK ########################################## | ||
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| for Subject in $Subjlist ; do | ||
| echo $Subject | ||
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| if [[ "${command_line_specified_run_local}" == "TRUE" || "$QUEUE" == "" ]] ; then | ||
| echo "About to locally run ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh" | ||
| queuing_command=("$HCPPIPEDIR"/global/scripts/captureoutput.sh) | ||
| else | ||
| echo "About to use fsl_sub to queue ${HCPPIPEDIR}/HippUnfoldHCP/PostHippUnfoldHCP.sh" | ||
| queuing_command=("$FSLDIR/bin/fsl_sub" -q "$QUEUE") | ||
| fi | ||
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| "${queuing_command[@]}" "$HCPPIPEDIR"/HippUnfoldHCP/PostHippUnfoldHCP.sh \ | ||
| --study-folder="$StudyFolder" \ | ||
| --subject="$Subject" \ | ||
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| # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ... | ||
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| echo "set -- --study-folder=$StudyFolder \ | ||
| --subject=$Subject" \ | ||
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| echo ". ${EnvironmentScript}" | ||
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| done |
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| #!/bin/bash | ||
| set -eu | ||
| pipedirguessed=0 | ||
| if [[ "${HCPPIPEDIR:-}" == "" ]] | ||
| then | ||
| # pipedirguessed=1 | ||
| #fix this if the script is more than one level below HCPPIPEDIR | ||
| export HCPPIPEDIR="$(dirname -- "$0")/.." | ||
| fi | ||
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| source "$HCPPIPEDIR/global/scripts/newopts.shlib" "$@" | ||
| source "$HCPPIPEDIR/global/scripts/debug.shlib" "$@" | ||
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| opts_SetScriptDescription "Make some BIDS structures and run HippUnfold" | ||
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| opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects" | ||
| opts_AddMandatory '--subject' 'Subject' 'subject ID' "" | ||
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There was a problem hiding this comment. This was changed to Session during the refactoring? There was a problem hiding this comment. Same as the other comment. |
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| opts_AddOptional '--hippunfold-dir' 'HippUnfoldDIR' 'path' "location of HippUnfold outputs" | ||
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| opts_ParseArguments "$@" | ||
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| if ((pipedirguessed)) | ||
| then | ||
| log_Err_Abort "HCPPIPEDIR is not set, you must first source your edited copy of Examples/Scripts/SetUpHCPPipeline.sh" | ||
| fi | ||
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| opts_ShowValues | ||
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| T1wFolder="$StudyFolder/$Subject/T1w" # input data | ||
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| if [ -z ${HippUnfoldDIR} ] ; then | ||
| HippUnfoldDIR="${T1wFolder}/HippUnfold" | ||
| fi | ||
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| #Couldn't get non-BIDS to work (wouldn't do anything) | ||
| #HippUnfoldT1wFolder="$HippUnfoldDIR/T1w" | ||
| #HippUnfoldT2wFolder="$HippUnfoldDIR/T2w" | ||
| #HippUnfoldT2wFolder="$HippUnfoldDIR/T1wT2w" | ||
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| HippUnfoldT1wFolder="$HippUnfoldDIR/T1w/sub-${Subject}/anat" | ||
| HippUnfoldT2wFolder="$HippUnfoldDIR/T2w/sub-${Subject}/anat" | ||
| HippUnfoldT1wT2wFolder="$HippUnfoldDIR/T1wT2w/sub-${Subject}/anat" | ||
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| HippUnfoldT1wFolderOut="$HippUnfoldDIR/T1w_hippunfold" | ||
| HippUnfoldT2wFolderOut="$HippUnfoldDIR/T2w_hippunfold" | ||
| HippUnfoldT1wT2wFolderOut="$HippUnfoldDIR/T1wT2w_hippunfold" | ||
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| T1wImage="$T1wFolder/T1w_acpc_dc_restore.nii.gz" | ||
| T2wImage="$T1wFolder/T2w_acpc_dc_restore.nii.gz" | ||
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| if [ ! -f "$T1wImage" ]; then | ||
| echo "Error: T1w image not found at $T1wImage" >&2 | ||
| exit 1 | ||
| fi | ||
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| if [ ! -f "$T2wImage" ]; then | ||
| echo "Error: T2w image not found at $T2wImage" >&2 | ||
| exit 1 | ||
| fi | ||
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| mkdir -p "$HippUnfoldT1wFolder" "$HippUnfoldT2wFolder" "$HippUnfoldT1wT2wFolder" | ||
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| #Couldn't get non-BIDS to work (wouldn't do anything) | ||
| #cp "$T1wImage" "$HippUnfoldT1wFolder/${Subject}_T1w_acpc_dc_restore.nii.gz" | ||
| #cp "$T2wImage" "$HippUnfoldT1wFolder/${Subject}_T2w_acpc_dc_restore.nii.gz" | ||
| #cp "$T1wImage" "$HippUnfoldT2wFolder/${Subject}_T1w_acpc_dc_restore.nii.gz" | ||
| #cp "$T2wImage" "$HippUnfoldT2wFolder/${Subject}_T2w_acpc_dc_restore.nii.gz" | ||
| #cp "$T1wImage" "$HippUnfoldT1wT2wFolder/${Subject}_T1w_acpc_dc_restore.nii.gz" | ||
| #cp "$T2wImage" "$HippUnfoldT1wT2wFolder/${Subject}_T2w_acpc_dc_restore.nii.gz" | ||
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| cp "$T1wImage" "$HippUnfoldT1wFolder/sub-${Subject}_T1w.nii.gz" | ||
| cp "$T2wImage" "$HippUnfoldT1wFolder/sub-${Subject}_T2w.nii.gz" | ||
| cp "$T1wImage" "$HippUnfoldT2wFolder/sub-${Subject}_T1w.nii.gz" | ||
| cp "$T2wImage" "$HippUnfoldT2wFolder/sub-${Subject}_T2w.nii.gz" | ||
| cp "$T1wImage" "$HippUnfoldT1wT2wFolder/sub-${Subject}_T1w.nii.gz" | ||
| cp "$T2wImage" "$HippUnfoldT1wT2wFolder/sub-${Subject}_T2w.nii.gz" | ||
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There was a problem hiding this comment. Does it really need to create There was a problem hiding this comment. This is all necessary for the BIDS wrapping, if we can get working direct input paths, I would not do any of this. There are 3 HippUnfold calls because there are 3 ways to call HippUnfold currently. I am hopeful we could standardize on using both the T1w and T2w in HippUnfold 2.0, but we need to hear from the HippUnfold folks that it is better or at least not worse than using individual inputs. |
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| log_Msg "Created folder structure under $HippUnfoldDIR and copied T1w and T2w images" | ||
| log_Msg "Starting HippUnfold pipeline for subject: $Subject" | ||
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| #Couldn't get non-BIDS to work (wouldn't do anything) #Seriously: don't put a $ here... | ||
| #apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT1wFolder $HippUnfoldT1wFolder participant --modality T1w --path-T1w $HippUnfoldT1wFolder/{Subject}_T1w_acpc_dc_restore.nii.gz --cores all --force-output --generate_myelin_map | ||
| #apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT2wFolder $HippUnfoldT2wFolder participant --modality T2w --path-T2w $HippUnfoldT2wFolder/{Subject}_T2w_acpc_dc_restore.nii.gz --cores all --force-output --generate_myelin_map | ||
| #apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT2wFolder $HippUnfoldT2wFolder participant --modality T2w --path-T2w $HippUnfoldT2wFolder/{Subject}_T2w_acpc_dc_restore.nii.gz --cores all --force-output --generate_myelin_map --force-nnunet-model T1T2w | ||
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| log_Msg "Running T1w HippUnfold for subject: $Subject" | ||
| apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT1wFolder $HippUnfoldT1wFolderOut participant --modality T1w --cores all --force-output --generate_myelin_map --output-density 0p5mm 1mm 2mm | ||
| log_Msg "T1w HippUnfold completed." | ||
| log_Msg "Running T2w HippUnfold for subject: $Subject" | ||
| apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT2wFolder $HippUnfoldT2wFolderOut participant --modality T2w --cores all --force-output --generate_myelin_map --output-density 0p5mm 1mm 2mm | ||
| log_Msg "T2w HippUnfold completed." | ||
| log_Msg "Running T1wT2w HippUnfold for subject: $Subject" | ||
| apptainer run --bind $StudyFolder -e $HIPPUNFOLDPATH $HippUnfoldT1wT2wFolder $HippUnfoldT1wT2wFolderOut participant --modality T1w --cores all --force-output --generate_myelin_map --output-density 0p5mm 1mm 2mm --force-nnunet-model T1T2w | ||
| log_Msg "T1wT2w HippUnfold completed." | ||
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There was a problem hiding this comment. I knew this day would come sooner or later. This will force us to run containers inside containers (HippUnfold inside QuNex), on paper it should work. I guess we will see in practice if there are any issues with this. What we need to figure out is whether we should put the HippUnfold container inside the QuNex container (this adds a couple GBs to the QuNex size) or if we require users to download it manually. I am leaning towards the first option as it is more user friendly and nowadays size is not that important as we all have good connectivity and enough disk space. A case for having the container outside could be made by saying this is a pipeline that will not be executed by most of our users? Need to think this through a bit. There was a problem hiding this comment. Do they provide their code such that it can be run without their container wrapping it? I think of containers as a convenience of not having to manually configure a bunch of software, not as a replacement for being able to install someone's software. There was a problem hiding this comment. HippUnfold v2.0.0 will be available on conda (ETA ~1 month) There was a problem hiding this comment. Thanks for the info. I felt like adding your whole container into our container would be suboptimal space wise as there should be some overlap between the tools we depend on. We indeed both use wb_command, so that one would be redundant for sure, there could be others. I will first try to do this optimally and install all the dependencies manually. If this does not work and is too much of a hassle, we can go the container route. @glasserm What is your preferred timeline here? Would you like to wait for HippUnfold v2.0.0 and then start processing with this one. Sounds like a major upgrade, that is only a month or so away. Or is this urgent and waiting an extra month is not an option? There was a problem hiding this comment. RE: #Couldn't get non-BIDS to work (wouldn't do anything) #Seriously: don't put a $ here... The There was a problem hiding this comment.
This isn't intended to be merged until HippUnfold v2.0.0 is available and the PR reflects and changes needed for that. I agree that ideally you would install HippUnfold + dependencies in QuNex rather than the container. There was a problem hiding this comment.
I currently wrap in some BIDS because I couldn't get the non-BIDS options to work reliably. If you guys provide an ability to simply specify paths to relevant inputs, I will remove the wrapped BIDS. |
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| log_Msg "HippUnfold pipeline completed successfully for subject: $Subject" | ||
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This seems like a highly specific local path. Do you have any conventions about where users should put external tools that are required to run certain HCP pipelines? For example,
$HCPPIPEDIR/external.There was a problem hiding this comment.
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Users should not add anything inside of the repo folder. That way madness lies.
More to the point, the pipelines setup instructions don't tell users where to install FSL, or freesurfer, or MSM, etc, and I don't think we should start doing so. The standard "set this variable to where you have downloaded hippunfold" formula should apply.
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This is the standard convention we have used for all of the HCP Pipelines so it is odd to be complaining about it here. It is intended to be changed but is not supposed to be blank (unlike the CARET7DIR).