NHP fMRIVolume

[TakJim]

This PR applies fMRIVolume to NHP data.

Some additional modifications are still required. The parts that I have not been able to address yet are listed below.

TODO

• In GenericfMRIVolumeProcessingPipelineBatchNHP.sh, accept arguments via opts_AddMandatory / opts_AddOptional
• In BatchNHP.sh, reorganize the parameters defined in hcppipe_conf.txt and allow users to specify them directly within BatchNHP.sh
• Apply the IsLongitudinal=TRUE processing logic to PipelineBatchNHP.sh

[glasserm]

My overall comment is that I think we should properly merge the NHP changes in to the fMRIVolume pipeline rather than bifurcate the pipelines. There is a lot of reused code between fMRIVolume and the BBR code and these are not really a completely separate process like they were for FreeSurferNHP. On initial review the changes to one step resampling and motion correction looked okay.

[TakJim]

@glasserm
#372 (review)

Thank you for the comment — that makes sense.

To confirm, should
fMRIVolume/scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbasedNHP.sh
also be combined into the main DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh, rather than being kept as an NHP-specific variant?

After discussing with @takuya-hayashi, we felt that this script includes quite a lot of NHP-specific logic.
I’d appreciate your thoughts on whether it should still be merged or kept separate.

[glasserm]

@glasserm #372 (review)

Thank you for the comment — that makes sense.

To confirm, should fMRIVolume/scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbasedNHP.sh also be combined into the main DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh, rather than being kept as an NHP-specific variant?

After discussing with @takuya-hayashi, we felt that this script includes quite a lot of NHP-specific logic. I’d appreciate your thoughts on whether it should still be merged or kept separate.

Yes please.

[mmilch01]

betspecieslabel is not currently defined for human stream (including in SetUpSpecies.sh on main branch) and breaks processing.

[glasserm]

betspecieslabel is not currently defined for human stream (including in SetUpSpecies.sh on main branch) and breaks processing.

This will be followed up with a specific location where there is an issue.

[glasserm]

@coalsont We need to rebase this PR with the PreFreeSurfer merged PR so that all of this PR's dependencies are present. @mmilch01 has more details on this issue.

[coalsont]

@TakJim did rebase it against our master after the PreFS merge.

[mmilch01]

This command would currently fail because tcsEchoesGdc, etc. are being defined in the next block. I'll wait for this to be fixed before continuing testing the human stream.

[mmilch01]

Suggested change

	#structural image resolution
	StructRes=0.4

[mmilch01]

Suggested change

	if [ -z "$StructRes" ]; then
	StructResOption=""
	else
	StructResOption="--structres=$StructRes"
	fi
	echo "StructResOption: $StructResOption"

[coalsont]

--structres is mandatory, so it doesn't need the flag in a variable.

[mmilch01]

Suggested change

	source "$HCPPIPEDIR"/Examples/Scripts/SetUpSPECIES.sh --species="$SPECIES"
	source "$HCPPIPEDIR"/FreeSurfer/custom/SetUpFSNHP.sh
	source "$HCPPIPEDIR"/Examples/Scripts/SetUpSPECIES.sh --species="$SPECIES $StructResOption"
	source "$HCPPIPEDIR"/FreeSurfer/custom/SetUpFSNHP.sh "$SPECIES" "$isFLAIR" "$isT1wDivFLAIR"

[coalsont]

Suggested change

	source "$HCPPIPEDIR"/Examples/Scripts/SetUpSPECIES.sh --species="$SPECIES"
	source "$HCPPIPEDIR"/FreeSurfer/custom/SetUpFSNHP.sh
	source "$HCPPIPEDIR"/Examples/Scripts/SetUpSPECIES.sh --species="$SPECIES" --structres="$StructRes"
	source "$HCPPIPEDIR"/FreeSurfer/custom/SetUpFSNHP.sh "$SPECIES" "$isFLAIR" "$isT1wDivFLAIR"

[mmilch01]

Suggested change

	#Whether T2w image is FLAIR, 0 or 1
	isFLAIR=0
	#Whether T2 image is T1w divided by FLAIR, 0 or 1
	isT1wDivFLAIR=1

[coalsont]

Suggested change

	# If not a human, just custom fMRI resolution, else, if 1mm or 2mm use standard fMRI resolutions, else, use a custom fMRI resolution.
	# If not a human, just use -applyisoxfm