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Merge/icafix dev #8

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56a86b3
add working files for merge
TakJim Jun 1, 2022
8c64bd4
add new params and condition
TakJim Jun 1, 2022
68b4ede
Delete an unnecessary file
TakJim Jun 1, 2022
a3c9601
add newest version file
TakJim Jun 8, 2022
eab493e
modified to match HCPv4.3.0
TakJim Jun 8, 2022
3d10102
modified to match HCPv4.3.0
TakJim Jun 8, 2022
8d682e5
Fixed varargin to accept new params(ndhpvol etc)
TakJim Jun 8, 2022
00014a2
mod make concatenated folder to the same as HCP
TakJim Jun 8, 2022
219254b
Modified merge volumes to the same as HCP
TakJim Jun 8, 2022
cead08a
new args for functionhighpassandvariancenormalize
TakJim Jun 23, 2022
76591cd
Modified def params to the same as HCP
TakJim Jun 23, 2022
5320186
add new params
TakJim Jun 29, 2022
4673989
Modified to the same as HCP
TakJim Jun 29, 2022
a7574e1
fix unnecessary change add template mask
TakJim Jun 30, 2022
36242ed
rm OW option
TakJim Jun 30, 2022
43d8fd3
rm RunMode
TakJim Jun 30, 2022
26e1f24
rm RData
TakJim Jun 30, 2022
72c4a16
fix matlab run
TakJim Jun 30, 2022
5ec56d7
Modified to the same as HCP
TakJim Jun 30, 2022
76ecf44
fix matlab run
TakJim Jun 30, 2022
358f6b3
fix PostFix
TakJim Jun 30, 2022
2c2d516
rename param ndvol to ndconcatvol
TakJim Jul 6, 2022
561382a
fix varargin, add docifti to varargin
TakJim Jul 6, 2022
c0d1ffd
fix positional arg RegString
TakJim Jul 6, 2022
97e4212
Add docifti conditional branch
TakJim Jul 6, 2022
1528a2f
add merge working file
TakJim Jul 6, 2022
f6f3de3
modify same to HCP v4.30
TakJim Jul 6, 2022
0280ceb
modify same to HCP v4.30
TakJim Jul 6, 2022
5737dfa
Set G_DEFAULT_LOW_RES_MESH for each species
TakJim Jul 7, 2022
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6 changes: 3 additions & 3 deletions ICAFIX/ReApplyFixMultiRunPipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -564,11 +564,11 @@ main()
if [ -e ${ConcatNameNoExt}_hp${hp}_wf.txt ] ; then
ndhpvol="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $1}'`"
ndhpcifti="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $2}'`"
ndcifti="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $3}'`"
ndconcatvol="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $3}'`"
elif [ -z "$p_WF" ] ; then
ndhpvol="`echo $p_WF | cut -d ',' -f1`"
ndhpcifti="`echo $p_WF | cut -d ',' -f2`"
ndcifti="`echo $p_WF | cut -d ',' -f3`"
ndconcatvol="`echo $p_WF | cut -d ',' -f3`"
else
log_Err_Abort "ERROR: cannot find Ndist used in MR-FIX. Please use option --wf to set Ndist"
fi
Expand Down Expand Up @@ -715,7 +715,7 @@ main()
fi

# ${hp} needs to be passed in as a string, to handle the hp=pd* case
local matlab_cmd="${ML_PATHS} functionhighpassandvariancenormalize(${tr}, '${hp}', '${fmri}', '${Caret7_Command}', '${RegString}');"
local matlab_cmd="${ML_PATHS} functionhighpassandvariancenormalize(${tr}, '${hp}', '${fmri}', '${Caret7_Command}','${RegString}', '${ndhpvol}', '${ndhpcifti}', '${ndconcatvol}');"

log_Msg "Run interpreted MATLAB/Octave (${interpreter[@]}) with command..."
log_Msg "${matlab_cmd}"
Expand Down
35 changes: 4 additions & 31 deletions ICAFIX/ReApplyFixMultiRunPipeline_RIKEN_merge.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -564,11 +564,11 @@ main()
if [ -e ${ConcatNameNoExt}_hp${hp}_wf.txt ] ; then
ndhpvol="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $1}'`"
ndhpcifti="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $2}'`"
ndcifti="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $3}'`"
ndconcatvol="`cat ${ConcatNameNoExt}_hp${hp}_wf.txt | awk '{print $3}'`"
elif [ -z "$p_WF" ] ; then
ndhpvol="`echo $p_WF | cut -d ',' -f1`"
ndhpcifti="`echo $p_WF | cut -d ',' -f2`"
ndcifti="`echo $p_WF | cut -d ',' -f3`"
ndconcatvol="`echo $p_WF | cut -d ',' -f3`"
else
log_Err_Abort "ERROR: cannot find Ndist used in MR-FIX. Please use option --wf to set Ndist"
fi
Expand Down Expand Up @@ -715,8 +715,8 @@ fi
fi

# ${hp} needs to be passed in as a string, to handle the hp=pd* case
local matlab_cmd="${ML_PATHS} functionhighpassandvariancenormalize(${tr}, '${hp}', '${fmri}', '${Caret7_Command}', '${RegString}');"
local matlab_cmd="${ML_PATHS} functionhighpassandvariancenormalize(${tr}, '${hp}', '${fmri}', '${Caret7_Command}','${RegString}', '${ndhpvol}', '${ndhpcifti}', '${ndconcatvol}');"

log_Msg "Run interpreted MATLAB/Octave (${interpreter[@]}) with command..."
log_Msg "${matlab_cmd}"

Expand Down Expand Up @@ -1088,22 +1088,6 @@ fi
Start=`echo "${Start} + ${NumTPS}" | bc -l`
done

## ---------------------------------------------------------------------------
## Remove all the large time series files in ${ConcatFolder}
## ---------------------------------------------------------------------------

## Deleting these files would save a lot of space.
## But downstream scripts (e.g., RestingStateStats) assume they exist, and
## if deleted they would therefore need to be re-created "on the fly" later

# cd ${ConcatFolder}
# log_Msg "Removing large (concatenated) time series files from ${ConcatFolder}"
# $FSLDIR/bin/imrm ${concatfmri}
# $FSLDIR/bin/imrm ${concatfmri}_hp${hp}
# $FSLDIR/bin/imrm ${concatfmri}_hp${hp}_clean
# /bin/rm -f ${concatfmri}_Atlas${RegString}.dtseries.nii
# /bin/rm -f ${concatfmri}_Atlas${RegString}_hp${hp}.dtseries.nii
# /bin/rm -f ${concatfmri}_Atlas${RegString}_hp${hp}_clean.dtseries.nii
cd ${DIR}

log_Msg "Completed!"
Expand All @@ -1113,14 +1097,6 @@ fi
# "Global" processing - everything above here should be in a function
# ------------------------------------------------------------------------------

set -e # If any command exits with non-zero value, this script exits

# Establish defaults
G_DEFAULT_REG_NAME="NONE"
G_DEFAULT_LOW_RES_MESH=32
G_DEFAULT_MATLAB_RUN_MODE=1 # Use interpreted MATLAB
G_DEFAULT_MOTION_REGRESSION="FALSE"

# Set global variables
g_script_name=$(basename "${0}")

Expand Down Expand Up @@ -1159,9 +1135,6 @@ log_Check_Env_Var FSL_FIXDIR
# Show tool versions
show_tool_versions

# Establish default MATLAB run mode
G_DEFAULT_MATLAB_RUN_MODE=1 # Use interpreted MATLAB

# Establish default low res mesh for NHP
if [ "$SPECIES" = "Macaque" ] ; then
G_DEFAULT_LOW_RES_MESH=10
Expand Down
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