Description:
I am getting an error running during hcp_dedrift_and_resample (actually I run hcp_msmall which automatically executes hcp_dedrift_and_resample). The error seems to be in the incorrect naming of the highpass parameter in the dedrift_and_resample script (the specified parameter is called ‘–high-pass’ and should be called ‘–highpass’ (see log below).
Call:
Logs:
# Generated by QuNex 0.97.1 on 2023-05-17_18.49.25.367708
#
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Running external command via QuNex:
/opt/HCP/HCPpipelines/DeDriftAndResample/DeDriftAndResamplePipeline.sh --path="/dfs4/som/XXXXX/qunex_study/sessions/subjects/XXXXX
/hcp" --subject="XXXXX" --high-res-mesh="164" --low-res-meshes="32" --registration-name="MSMAll_InitialReg_
2_d40_WRN" --dedrift-reg-files="/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@/opt/HCP/HC
Ppipelines/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii" --concat-reg-name="MSMAll" --maps="sulc@c
urvature@corrThickness@thickness" --myelin-maps="MyelinMap@SmoothedMyelinMap" --multirun-fix-names="rfMRI_REST1_AP@rfMRI_REST1_PA@rfMRI_
REST2_AP@rfMRI_REST2_PA" --multirun-fix-concat-names="fMRI_CONCAT_ALL" --fix-names="NONE" --dont-fix-names="NONE"
--smoothing-fwhm="2" --high-pass="0" --matlab-run-mode="0" --motion-regression="None" --myelin-target-file="NO
NE" --input-reg-name="NONE"
------------------------------------------------------------
Wed May 17 18:49:25 PDT 2023:DeDriftAndResamplePipeline.sh: While running '/opt/HCP/HCPpipelines/DeDriftAndResample/DeDriftAndResamplePipeline.sh --path=/dfs4/s
om/XXXXX/qunex_study/sessions/subjects/XXXXX/hcp --subject=XXXXX --high-res-mesh=164 --low-res-meshes=32 --registration-name=MSMAll_Initi
alReg_2_d40_WRN --dedrift-reg-files=/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@/opt/HCP/HCPpipelin
es/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii --concat-reg-name=MSMAll --maps=sulc@curvature@corrThickness@thickness --m
yelin-maps=MyelinMap@SmoothedMyelinMap --multirun-fix-names=rfMRI_REST1_AP@rfMRI_REST1_PA@rfMRI_REST2_AP@rfMRI_REST2_PA --multirun-fix-concat-names=fMRI_CONCAT_
ALL --fix-names=NONE --dont-fix-names=NONE --smoothing-fwhm=2 --high-pass=0 --matlab-run-mode=0 --motion-regression=None --myelin-target-file=NONE --input-reg-n
ame=NONE':
Wed May 17 18:49:25 PDT 2023:DeDriftAndResamplePipeline.sh: While running '/opt/HCP/HCPpipelines/DeDriftAndResample/DeDriftAndResamplePipeline.sh --path=/dfs4/s
om/XXXXX/qunex_study/sessions/subjects/XXXXX/hcp --subject=XXXXX --high-res-mesh=164 --low-res-meshes=32 --registration-name=MSMAll_Initi
alReg_2_d40_WRN --dedrift-reg-files=/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@/opt/HCP/HCPpipelin
es/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii --concat-reg-name=MSMAll --maps=sulc@curvature@corrThickness@thickness --m
yelin-maps=MyelinMap@SmoothedMyelinMap --multirun-fix-names=rfMRI_REST1_AP@rfMRI_REST1_PA@rfMRI_REST2_AP@rfMRI_REST2_PA --multirun-fix-concat-names=fMRI_CONCAT_
ALL --fix-names=NONE --dont-fix-names=NONE --smoothing-fwhm=2 --high-pass=0 --matlab-run-mode=0 --motion-regression=None --myelin-target-file=NONE --input-reg-n
ame=NONE':
Wed May 17 18:49:25 PDT 2023:DeDriftAndResamplePipeline.sh: ERROR: unrecognized option: '--high-pass'
Wed May 17 18:49:25 PDT 2023:DeDriftAndResamplePipeline.sh: ERROR: unrecognized option: '--high-pass'
DeDriftAndResamplePipeline.sh: resamples many types of data after a surface registration
Usage: DeDriftAndResamplePipeline.sh PARAMETER ...
A parameter enclosed in [ ] is optional.
All other parameters must be specified.
Anything enclosed in < > is a placeholder for a user supplied value.
[--help or -h] - show this usage information and exit
--study-folder=<path> - folder that contains all subjects
--subject=<100206> - one subject ID
--high-res-mesh=<meshnum> - high resolution mesh node count (in thousands),
like '164' for 164k_fs_LR
--low-res-meshes=<meshnum@meshnum@...> - low resolution mesh node counts (in
thousands) delimited by @, like '32@59' for 32k_fs_LR and 59_k_fs_LR
--registration-name=<MSMAll> - the registration string corresponding to the
input files, e.g. 'MSMAll_InitalReg'
--maps=<non@myelin@maps> - @-delimited map name strings corresponding to
maps that are not myelin maps, e.g. 'sulc@curvature@corrThickness@thic-
kness'
--smoothing-fwhm=<number> - Smoothing FWHM that matches what was used in the
fMRISurface pipeline
--highpass=<integer> - the high pass value that was used when running FIX
--motion-regression=<TRUE or FALSE> - whether FIX should do motion
regression
--msm-all-templates=<path> - path to directory containing MSM All template
files, e.g. 'YourFolder/global/templates/MSMAll'
[--dedrift-reg-files=<string>] - </Path/to/File/Left.sphere.surf.gii@/Path/t-
o/File/Right.sphere.surf.gii>] Usually the spheres in
global/templates/MSMAll/, defaults to ''.
---cut---
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