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Fix/pre free surfer pipeline #314

Draft

TakJim wants to merge 19 commits into Washington-University:NHP_merge from RIKEN-BCIL:fix/PreFreeSurferPipeline

TakJim commented Oct 30, 2024

Pull Request Summary

This PR refactors the processing pipeline for enhanced modularity, flexibility, and improved parameter control in T1w and T2w image processing.

Key Changes

1.	Modular Functions: Created ACPCAlignment, BrainExtraction, T2wToT1wRegAndBiasCorrection, and AtlasRegistration functions, and a main function to control execution flow via RunMode.
2.	Expanded Parameters: Added support for additional phase encodes, patient positioning, and brain extraction settings, improving custom workflow compatibility.
3.	Custom Mask and Existing Data Handling: Improved custom mask application and logic to skip unnecessary steps for existing data.
4.	Enhanced Logging and Structure: Standardized output directory structure and logging, facilitating traceability and maintainability.

TakJim added 12 commits

October 31, 2024 04:51


          feat: Add support for additional Spin Echo phase encoding directions


          fix: Remove leading whitespace in T1w and T2w input image paths

ecda36d


          fix: Set T2wFolder to "NONE" if no T2w images are available and add l…

9047f5b

…ogging


          feat: Add support for custom brain masks and configure default parame…

…ters for brain extraction


          feat: Add reference volume resampling for T1w and T2w images with dif…

f7a05b2

…fering resolutions


          feat: Enhance gradient nonlinearity correction with orientation adjus…

3ff59f4

…tments and brain extraction checks


          refactor: Modularize ACPC alignment and brain extraction with paramet…

02d2909

…erized function


          refactor: Modularize FNIRT-based brain extraction with new parameters

4743d51


          refactor: Modularize T2w to T1w registration with enhanced readout di…

b2ece58

…stortion correction


          feat: Enhance T2w to T1w distortion correction script with additional…

03517ea

… phase encodes and patient positioning


          fix: Correct BiasFieldSmoothingSigma parameter for T1w-only bias fiel…

…d correction


          refactor: Modularize atlas registration and resampling with main exec…

5fdfd8c

…ution flow

TakJim marked this pull request as draft

October 30, 2024 21:35

TakJim marked this pull request as ready for review

October 30, 2024 21:35

TakJim marked this pull request as draft

October 30, 2024 21:36

coalsont reviewed

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coalsont reviewed

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Contributor

glasserm commented Nov 4, 2024

Is TakJim affiliated with Takuya Hayashi's lab at RIKEN? These changes appear to potentially be related to trying to merge the NHP HCP Pipelines back into the HCP Pipelines. We should encourage this.

TakJim added 2 commits

November 22, 2024 15:58


          Refactor parameter initialization to use opts_AddOptional

a02af6e


          Refactor main function to streamline RunMode handling

dd39eae

coalsont reviewed

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coalsont reviewed

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PreFreeSurfer/PreFreeSurferPipeline.sh

Comment on lines +790 to +792

+                      --SEPhaseNeg2=${SpinEchoPhaseEncodeNegative2} \
+                      --SEPhasePos2=${SpinEchoPhaseEncodePositive2} \
+                      --SEPhaseZero=${SpinEchoPhaseEncodeZero} \

Member

coalsont Nov 22, 2024 •

edited

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You need to include the edits to T2wToT1wDistortionCorrectAndReg.sh that add this functionality.

coalsont reviewed

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PreFreeSurfer/PreFreeSurferPipeline.sh

+                      --SEPhaseNeg2=${SpinEchoPhaseEncodeNegative2} \
+                      --SEPhasePos2=${SpinEchoPhaseEncodePositive2} \
+                      --SEPhaseZero=${SpinEchoPhaseEncodeZero} \
+                      --echospacing=${DwellTime} \

Member

coalsont Nov 22, 2024 •

edited

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DwellTime isn't defined, and also --echospacing isn't supported by the human version of T2wToT1wDistortionCorrectAndReg.sh. Is this intended to be different from --seechospacing?

coalsont reviewed

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PreFreeSurfer/PreFreeSurferPipeline.sh

@@ @@ -628,6 +870,8 @@ if [ "$CustomBrain" = "NONE" ] ; then @@
                 else  # -- No T2w image
                   log_Msg "Performing Bias Field Correction using T1w image only"
+                  BiasFieldFastSmoothingSigma="20"
+                  BiasFieldFastSmoothingSigma="--bfsigma=${BiasFieldFastSmoothingSigma}"

Member

coalsont Nov 22, 2024

This doesn't get used, and hardcodes a smoothing kernel size.

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PreFreeSurfer/PreFreeSurferPipeline.sh

+              	RefRes=$(${FSLDIR}/bin/fslval ${T1wTemplate} pixdim1 | awk '{printf "%0.2f", $1}')
+              	log_Msg "Resolution of structure: $StrucRes"
+              	log_Msg "Resolution of T1wTemplate: $RefRes"
+              	if [ ! "$StrucRes" == "$RefRes" ] ; then

Member

coalsont Nov 23, 2024

This would trigger on, say, a 0.71mm human scan (or even a 0.7mm if someone specified the 0.8mm template), and use a voxel grid different than the specified template file for all the MNINonLinear/ volume files. I'm not sure what we want to happen.

takuya-hayashi and others added 5 commits

November 24, 2024 15:13


          Update PreFreeSurferPipeline.sh

3e85592

minor edits


          add CorrectVolumeOrientation

d9576e9


          Merge branch 'fix/PreFreeSurferPipeline' of https://github.com/RIKEN-…

e2cd537

…BCIL/HCPpipelinesNHPmerge into fix/PreFreeSurferPipeline


          feat: Add modularity to PreFreeSurferPipeline with runmode-based cond…

f245f81

…itional processing


          Fix: Correct syntax in imtest command for conditional check

fbf4a27

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