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Update hcp_fix to support the MotionRegression=FALSE condition #157

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merged 4 commits into from
Nov 11, 2019
Merged

Update hcp_fix to support the MotionRegression=FALSE condition #157

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7d717b8
Adapt single-run FIX to allow MotionRegression=FALSE if the FIX versi…
mharms Nov 7, 2019
f441da1
Add report of specific FIX version to other ICAFIX scripts
mharms Nov 8, 2019
503dc8a
Update some of the fix-related comments to reflect changes as of fix …
mharms Nov 8, 2019
6ca4875
Log all FIX parameters
mharms Nov 9, 2019
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15 changes: 12 additions & 3 deletions ICAFIX/ReApplyFixMultiRunPipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -366,6 +366,12 @@ show_tool_versions()
fsl_version_get fsl_ver
log_Msg "FSL version: ${fsl_ver}"

# Show specific FIX version, if available
if [ -f ${FSL_FIXDIR}/fixversion ]; then
fixversion=$(cat ${FSL_FIXDIR}/fixversion )
log_Msg "FIX version: $fixversion"
fi

old_or_new_version=$(determine_old_or_new_fsl ${fsl_ver})
if [ "${old_or_new_version}" == "OLD" ] ; then
log_Err_Abort "FSL version 6.0.1 or greater is required."
Expand Down Expand Up @@ -415,9 +421,6 @@ main()
local this_script_dir=$(dirname "$0")
fi

# Show tool versions
show_tool_versions

log_Msg "Starting main functionality"

# Retrieve positional parameters
Expand Down Expand Up @@ -530,6 +533,9 @@ main()
# It is for that reason that the code below needs to use separate calls to fix_3_clean, with and without DoVol
# as an argument, rather than simply passing in the value of DoVol as set within this script.
# Not sure if/when this non-intuitive behavior of fix_3_clean will change, but this is accurate as of fix1.067
# UPDATE (11/8/2019): As of FIX 1.06.12, fix_3_clean interprets its 5th argument ("DoVol") in the usual boolean
# manner. However, since we already had a work-around to this problem, we will leave the code unchanged so that
# we don't need to add a FIX version dependency to the script.

log_Msg "Use fixlist=$fixlist"

Expand Down Expand Up @@ -1105,6 +1111,9 @@ log_Check_Env_Var CARET7DIR
log_Check_Env_Var FSLDIR
log_Check_Env_Var FSL_FIXDIR

# Show tool versions
show_tool_versions

# Determine whether named or positional parameters are used and invoke 'main' function
if [[ ${1} == --* ]]; then
# Named parameters (e.g. --parameter-name=parameter-value) are used
Expand Down
10 changes: 10 additions & 0 deletions ICAFIX/ReApplyFixPipeline.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -268,6 +268,13 @@ show_tool_versions()
log_Msg "Showing FSL version"
fsl_version_get fsl_ver
log_Msg "FSL version: ${fsl_ver}"

# Show specific FIX version, if available
if [ -f ${FSL_FIXDIR}/fixversion ]; then
fixversion=$(cat ${FSL_FIXDIR}/fixversion )
log_Msg "FIX version: $fixversion"
fi

}

# ------------------------------------------------------------------------------
Expand Down Expand Up @@ -423,6 +430,9 @@ main()
# It is for that reason that the code below needs to use separate calls to fix_3_clean, with and without DoVol
# as an argument, rather than simply passing in the value of DoVol as set within this script.
# Not sure if/when this non-intuitive behavior of fix_3_clean will change, but this is accurate as of fix1.067
# UPDATE (11/8/2019): As of FIX 1.06.12, fix_3_clean interprets its 5th argument ("DoVol") in the usual boolean
# manner. However, since we already had a work-around to this problem, we will leave the code unchanged so that
# we don't need to add a FIX version dependency to the script.

log_Msg "Use fixlist=$fixlist"

Expand Down
136 changes: 114 additions & 22 deletions ICAFIX/hcp_fix
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Expand Up @@ -69,6 +69,76 @@ fi

#############################################################

### Support Functions

# Function to return whether FIX version is "NEW" (i.e., 1.06.12 or later).
# Need at least that fix version for proper handling of the
# do_motion_regression=FALSE condition (when highpass>=0)

# NOTE:
# Don't echo anything in this function other than the last echo
# that outputs the return value
#
determine_old_or_new_fix()
{
# Default to "OLD", and change to "NEW" only if version is 1.06.12 or later
local old_or_new="OLD"

fix_version_file="${FSL_FIXDIR}/fixversion"

if [ -f "${fix_version_file}" ]; then

fix_version=$(cat "${fix_version_file}")

# parse the FIX version information into primary, secondary, and tertiary parts
fix_version_array=(${fix_version//./ })

fix_primary_version="${fix_version_array[0]}"
fix_primary_version=${fix_primary_version//[!0-9]/}

fix_secondary_version="${fix_version_array[1]}"
fix_secondary_version=${fix_secondary_version//[!0-9]/}

fix_tertiary_version="${fix_version_array[2]}"
fix_tertiary_version=${fix_tertiary_version//[!0-9]/}

# Important: Use single bracket for following tests, since double bracket results in interpretation
# of a leading zero as an octal number.
# [Alternatively, could force a base-10 interpretation using a "$(( 10#$ver ))" construction].
if [ ${fix_primary_version} -ge 2 ] ; then
old_or_new="NEW"
elif [ ${fix_primary_version} -eq 1 ] ; then
if [ ${fix_secondary_version} -ge 7 ] ; then
old_or_new="NEW"
elif [ ${fix_secondary_version} -eq 6 ] ; then
if [ ${fix_tertiary_version} -ge 12 ] ; then
old_or_new="NEW"
fi
fi
fi

fi

echo ${old_or_new}
}

function interpret_as_bool()
{
case $(echo "$1" | tr '[:upper:]' '[:lower:]') in
(true | yes | 1)
echo TRUE
;;
(false | no | none | 0)
echo FALSE
;;
(*)
log_Err_Abort "error: '$1' is not valid for this argument, please use TRUE or FALSE"
;;
esac
}

#############################################################

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

Expand Down Expand Up @@ -106,11 +176,21 @@ log_Msg "Showing FSL version"
fsl_version_get fsl_ver
log_Msg "FSL version: ${fsl_ver}"

# Show specific FIX version, if available
if [ -f ${FSL_FIXDIR}/fixversion ]; then
fixversion=$(cat ${FSL_FIXDIR}/fixversion )
log_Msg "FIX version: $fixversion"
fi

# Log FSL_FIX_MATLAB_MODE (from the settings.sh file)
log_Msg "FSL_FIX_MATLAB_MODE: ${FSL_FIX_MATLAB_MODE}"

#############################################################

## ---------------------------------------------------------------------------
## Parse and check parameters
## ---------------------------------------------------------------------------

fmri=$1
cd `dirname $fmri`
fmri=`basename $fmri` # After this, $fmri no longer includes the leading directory components
Expand All @@ -121,28 +201,18 @@ fi

hp=$2

function interpret_as_bool()
{
case $(echo "$1" | tr '[:upper:]' '[:lower:]') in
(true | yes | 1)
echo TRUE
;;
(false | no | none | 0)
echo FALSE
;;
(*)
log_Err_Abort "error: '$1' is not valid for this argument, please use TRUE or FALSE"
;;
esac
}

doMotionRegression=$(interpret_as_bool "$3")
# 5/20/2019: For the time being, do_motion_regression=FALSE doesn't work properly with single-run FIX,
# so don't allow that mode of operation
# do_motion_regression=FALSE combined with hp filtering doesn't work properly with single-run FIX,
# for fix versions earlier than 1.06.12, so don't allow that mode of operation if the fix version
# isn't recent enough.
# https://github.com/Washington-University/HCPpipelines/issues/108
# Check and abort early if we can't implement the requested options with the fix version in use.
if [[ "$doMotionRegression" == "FALSE" ]]
then
log_Err_Abort "Due to a restriction in the FIX argument parsing, do_motion_regression=$3 is not currently supported"
old_or_new_fix=$(determine_old_or_new_fix)
if [ "${old_or_new_fix}" == "OLD" ] && (( hp >= 0 )) ; then
log_Err_Abort "Due to a restriction in the FIX argument parsing, do_motion_regression=$3 is not supported for FIX versions prior to 1.06.12"
fi
fi

unset TrainingData
Expand All @@ -160,13 +230,23 @@ if [ -z "${FixThresh}" ]; then
FixThresh=10
fi

## ---------------------------------------------------------------------------
## Report parameters
## ---------------------------------------------------------------------------

log_Msg "fMRI Name: ${fmri}"
log_Msg "highpass: ${hp}"
log_Msg "doMotionRegression: ${doMotionRegression}"
log_Msg "TrainingData: ${TrainingData}"
log_Msg "FixThresh: ${FixThresh}"
log_Msg "DeleteIntermediates: ${DeleteIntermediates}"

## ---------------------------------------------------------------------------
## Preparation (highpass)
## ---------------------------------------------------------------------------

tr=`$FSLDIR/bin/fslval $fmri pixdim4`
log_Msg "tr: ${tr}"
log_Msg "processing FMRI file ${fmri} with highpass ${hp}"

fmrihp=${fmri}_hp${hp}
if (( hp > 0 )); then
Expand Down Expand Up @@ -337,12 +417,24 @@ fi
log_Msg "using training data file: ${TrainingData}"

# set up fix command
# use array for whitespace safety, even if the rest of the script isn't
if [[ ${doMotionRegression} == "TRUE" ]]; then
#use array for whitespace safety, even if the rest of the script isn't
fix_cmd=("${FSL_FIXDIR}/fix" "${fmrihp}.ica" "${TrainingData}" "${FixThresh}" -m -h "${hp}")
else
#-h is actually a subargument to -m, and will cause problems if specified without (or even not directly following) -m
fix_cmd=("${FSL_FIXDIR}/fix" "${fmrihp}.ica" "${TrainingData}" "${FixThresh}")
old_or_new_fix=$(determine_old_or_new_fix)
if [[ "${old_or_new_fix}" == "NEW" ]]; then
# In the "NEW" (1.06.12 or later) version of FIX, -h is no longer a subargument to -m, and can occur by itself
fix_cmd=("${FSL_FIXDIR}/fix" "${fmrihp}.ica" "${TrainingData}" "${FixThresh}" -h "${hp}")

elif (( hp < 0 )); then
# Ok to proceed regardless of FIX version, since not filtering, so we don't need the filtering of the CIFTI
# that occurs in fix_3_clean. Simply don't supply either the -m or -h flags.
fix_cmd=("${FSL_FIXDIR}/fix" "${fmrihp}.ica" "${TrainingData}" "${FixThresh}")

else # "OLD" and (hp >= 0)
# Already aborted in this case earlier, but include again here for completeness
log_Err_Abort "Due to a restriction in the FIX argument parsing, do_motion_regression=$3 is not supported for FIX versions prior to 1.06.12"
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fi
fi
log_Msg "fix_cmd: ${fix_cmd[*]}"
## MPH: The 'fix' script itself will continue to log to its own custom files
Expand Down
83 changes: 54 additions & 29 deletions ICAFIX/hcp_fix_multi_run
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Expand Up @@ -140,6 +140,12 @@ log_Msg "Showing FSL version"
fsl_version_get fsl_ver
log_Msg "FSL version: ${fsl_ver}"

# Show specific FIX version, if available
if [ -f ${FSL_FIXDIR}/fixversion ]; then
fixversion=$(cat ${FSL_FIXDIR}/fixversion )
log_Msg "FIX version: $fixversion"
fi

# Log FSL_FIX_MATLAB_MODE (from the settings.sh file)
log_Msg "FSL_FIX_MATLAB_MODE: ${FSL_FIX_MATLAB_MODE}"

Expand All @@ -150,7 +156,8 @@ FSL_FIX_WBC=${Caret7_Command} # Used by fix_3_clean in interpreted matlab/octav

#############################################################

#
### Support Functions

# NOTE:
# Don't echo anything in this function other than the last echo
# that outputs the return value
Expand Down Expand Up @@ -241,18 +248,40 @@ demeanMovementRegressors() {
echo "${AllOut}" > ${Out}
}

fsl_version_get fsl_ver
log_Msg "FSL version: ${fsl_ver}"
function interpret_as_bool()
{
case $(echo "$1" | tr '[:upper:]' '[:lower:]') in
(true | yes | 1)
echo TRUE
;;
(false | no | none | 0)
echo FALSE
;;
(*)
log_Err_Abort "error: '$1' is not valid for this argument, please use TRUE or FALSE"
;;
esac
}

old_or_new_version=$(determine_old_or_new_fsl ${fsl_ver})
#############################################################

## ---------------------------------------------------------------------------
## Check whether FSL version is recent enough
## ---------------------------------------------------------------------------

old_or_new_version=$(determine_old_or_new_fsl ${fsl_ver})
if [ "${old_or_new_version}" == "OLD" ] ; then
log_Err_Abort "FSL version 6.0.1 or greater is required."
fi

## ---------------------------------------------------------------------------
## Parse and check parameters
## ---------------------------------------------------------------------------

fmris=`echo ${1} | sed 's/@/ /g'` # replaces the @ that combines the filenames with ' '

hp=$2
if [[ "${hp}" == "0" ]]; then
log_Msg "hp=0 corresponds to a linear detrend"
pdFlag=TRUE
fi
if [[ "${hp}" == pd* ]]; then
Expand All @@ -271,27 +300,7 @@ if [[ $(echo "${hpNum} < 0" | bc) == "1" ]]; then #Logic of this script does no
log_Err_Abort "highpass value must not be negative"
fi

log_Msg "hp: ${hp}"

fmris=`echo ${1} | sed 's/@/ /g'` # replaces the @ that combines the filenames with ' '
log_Msg "fmris: ${fmris}"
ConcatName="${3}"
log_Msg "ConcatName: ${ConcatName}"

function interpret_as_bool()
{
case $(echo "$1" | tr '[:upper:]' '[:lower:]') in
(true | yes | 1)
echo TRUE
;;
(false | no | none | 0)
echo FALSE
;;
(*)
log_Err_Abort "error: '$1' is not valid for this argument, please use TRUE or FALSE"
;;
esac
}

doMotionRegression=$(interpret_as_bool "$4")

Expand All @@ -310,10 +319,23 @@ if [ -z "${FixThresh}" ]; then
FixThresh=10
fi

DIR=`pwd`
log_Msg "PWD : $DIR"
## ---------------------------------------------------------------------------
## Report parameters
## ---------------------------------------------------------------------------

#echo $fmris | tr ' ' '\n' #separates paths separated by ' '
log_Msg "fMRI Names: ${fmris}"
log_Msg "highpass: ${hp}"
if [[ "${hp}" == "0" ]]; then
log_Msg "hp=0 corresponds to a linear detrend"
fi
log_Msg "ConcatName: ${ConcatName}"
log_Msg "doMotionRegression: ${doMotionRegression}"
log_Msg "TrainingData: ${TrainingData}"
log_Msg "FixThresh: ${FixThresh}"
log_Msg "DeleteIntermediates: ${DeleteIntermediates}"

DIR=`pwd`
log_Msg "PWD: $DIR"

## ---------------------------------------------------------------------------
## Preparation (highpass) on the individual runs
Expand Down Expand Up @@ -738,11 +760,14 @@ fi
log_Msg "using training data file: ${TrainingData}"

# set up fix command
# use array for whitespace safety, even if the rest of the script isn't
if [[ ${doMotionRegression} == "TRUE" ]]; then
#use array for whitespace safety, even if the rest of the script isn't
fix_cmd=("${FSL_FIXDIR}/fix" "${concatfmrihp}.ica" "${TrainingData}" "${FixThresh}" -m -h "${AlreadyHP}")
else
#-h is actually a subargument to -m, and will cause problems if specified without (or even not directly following) -m
# Update (11/8/2019): No longer true as of FIX 1.06.12, but since filtering of the CIFTI in MR-FIX occurs in
# functionhighpassandvariancenormalize it doesn't matter, so we leave the code unchanged so that we don't
# need to add a FIX version dependency to the script
fix_cmd=("${FSL_FIXDIR}/fix" "${concatfmrihp}.ica" "${TrainingData}" "${FixThresh}")
fi
log_Msg "fix_cmd: ${fix_cmd[*]}"
Expand Down