replace the old _BC block with MyelinMap_BC #259
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cyang31
changed the title
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Should we also edit the _1res version while we are at it? |
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I didn't find lines in |
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I said that before I looked at it, yes it seems _1res it just resamples the existing native mesh maps, which makes sense. |
| @@ -63,12 +63,15 @@ opts_AddMandatory '--lowresmesh' 'LowResMeshes' 'number' "usually '32', the stan | |||
| opts_AddMandatory '--subcortgraylabels' 'SubcorticalGrayLabels' 'file' "location of FreeSurferSubcorticalLabelTableLut.txt" | |||
| opts_AddMandatory '--freesurferlabels' 'FreeSurferLabels' 'file' "location of FreeSurferAllLut.txt" | |||
| opts_AddMandatory '--refmyelinmaps' 'ReferenceMyelinMaps' 'file' "high-resolution group myelin map to use for bias correction" | |||
| opts_AddMandatory '--msm-all-templates' 'MSMAllTemplates' 'path' "path to directory containing MSM All template files, e.g. 'YourFolder/global/templates/MSMAll'" | |||
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This is an odd variable name for PostFreeSurfer that precedes MSMAll by quite a few lines. I am not a huge fan of tying the myelin target file to a specific folder either. I would have preferred a full path and a single argument.
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I changed the myelin target as a single argument with an absolute path wherever the MyelinMap_BC is involved.
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I didn't write the 1res code. That is a patch for if someone does not want to rerun PostFreeSurfer but wants to add a new lowres mesh resolution. |
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tested without error: |
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Looks reasonable to me, and I think @glasserm's comment was addressed. |
Background
There remain several legacy _BC code block that is not replaced by the module
MyelinMap_BC.sh.Main changes
MSMAll.shwithMyelinMap_BC.shCreateMyelinMaps.shused gifti based _BC which is now replaced by the cifti-basedMyelinMap_BC.sh, while the gifti files are keptPostFreeSurferPipeline.shto adapt the moduleMyelinMap_BC.shPostFreeSurferPipelineBatch.sh--myelin-target-fileas a single argument with absolute file path that doesn't depend on--msm-all-templatesEvaluation
MSMAllPipeline logs with no error:
/media/myelin/alex/MSMAll_optimization/MSMAllPipeline.sh.e49165/media/myelin/alex/MSMAll_optimization/MSMAllPipeline.sh.o49165PostFreeSurferPipeline logs with no error:
/media/myelin/alex/MSMAll_optimization/PostFreeSurferPipeline.sh.e162416/media/myelin/alex/MSMAll_optimization/PostFreeSurferPipeline.sh.o162416