Hi Stefano, I think I found and fixed the problem. Can you try these?
On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
External Email - Use Caution
Hi Doug,
The raw functional file is firstly passed with motion correction
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.
Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:
preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305
-fsd rest -per-run -sliceorder even -force
There are issues with labels since excluding motion correction doesn't
produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, which
cannot be found because it is not created using the -nomc option.
When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and
rerun preproc, the operation is done and the
fmcpr.odd.sm0.fsaverage.lh is created.
However, when I run the next steps (fcseed-sess -s ID -cfg wm.config
-overwrite), a second error occurs (reported below) because the script
searches for fmcpr, which cannot be produced since I used -mc.
ERROR: could not determine file for
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr
This error seems to be related to the script searching for the fmcpr
file, which isn't available due to the use of -mc.
Thank you.
Best regards,
Stefano
Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi
<sdellipi...@gmail.com> ha scritto:
Hi Doug have you any news
Thank you very much!
Stefano
Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi
<sdellipi...@gmail.com> ha scritto:
Thank you.
I’m attaching the file.
Stefano
<preproc-sess>
Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve
<dgr...@mgh.harvard.edu> ha scritto:
can you send me this file
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:
External Email - Use Caution
It seems to me that I've done what you suggest. Attached is a new
outputs.
Thanks
Stefano
Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve
<dgr...@mgh.harvard.edu> ha scritto:
Are you sure that you are using the new version that I gave you?
It looks like the previous version. Also, it does not look like
the entire terminal output.
On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:
External Email - Use Caution
The entire terminal output is attached.
Thanks!
Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve
<dgr...@mgh.harvard.edu> ha scritto:
entire terminal output
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
whom it is addressed. If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
The information in this e-mail is intended only for the person to
whom it is addressed. If you believe this e-mail was sent to you
in error and the e-mail contains patient information, please
contact the Mass General Brigham Compliance HelpLine at
https://www.massgeneralbrigham.org/complianceline
<https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_Bcgi7ubGv5tYLWaiMMMvai3kMGIy815rdOHCuxa26TgzCG7N39_7gO7R1qweyEpbyWhg2jPzT7Jn6y5R9IDYEnulWkwidyb-Qib5lu4h6a_s5YcAdb0N9IiBeDpqWrbBe0hv15Vk8W8n6xL2cuFQJvTXex04uH4CPIgZEpJ6hpPWv7aOcOY-RxxGp_lf2-1SdLn_S3KEKrLQ68nS_U4WOd-L3Q1TxZnV8azAM2dMdrMpcc6aFGCMa7ROC27axgF_fs3uFwdABdIGbgPRYiaC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
.
#! /bin/tcsh -f
#
# preproc-sess - runs preprocessing (mc, spatsmooth, mkbrainmask, inorm)
#
# Original Author: Doug Greve
#
# Copyright © 2021
# The General Hospital Corporation (Boston, MA).
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#
# To get per-run reg with smoothing, make sure -fwhm is after -per-run:
# preproc-sess -s risk001 -per-run -fwhm 5 -fsd bold
# This creates fmcpr.sm5, then
# mkanalysis-sess -native -funcstem fmcpr.sm5 ...
set VERSION = 'preproc-sess @FS_VERSION@';
set inputargs = ($argv);
set DateStr = "`date '+%y%m%d%H%M'`"
set instem = ();
set mcinstem = ();
set mcoutstem = ();
set stcinstem = ();
set stcoutstem = ();
set sminstem = ();
set smoutstem = ();
set inormstem = ();
set maskdir = masks
set maskstem = brain;
set UseSmoothMask = 0;
set fwhm = ();
set surffwhm = ();
set volsurffwhm = (); # for testing
set SliceOrder = ();
set SliceDelayFile = ()
set nSliceGroups = 1;
set fsd = ();
set mcrun = ();
set mctargstem = ();
set mctargframe = ();
set PerRun = 0;
set PerSess = 0;
set RunListFile = ();
set UpdateOnly = 1;
set DoTemplate = 1;
set DoMC = 1;
set DoSTC = 0;
set DoMask = 1;
set DoVolSmooth = 1;
set DoSurfSmooth = 0;
set DoSmooth = 1; # any smoothing
set DoInorm = 0;
set ProjFrac = (); # default will be 0.5
set ProjFracExpKey = ()
set DoProjAvg = 0;
set DoReg = 1;
set ToSurf = 0;
set subject = ();
set hemi = ();
set ToMNI305 = 0;
set ToCVS = 0;
set RawRes = 2;
set RegDOF = 6;
set regfile = ();
set UseB0DC = 0;
set ApplySubCortMask = 1;
set InitCoReg = 1;
set InitFSL = 0;
set InitSPM = 0;
set InitHeader = 0;
set BBRXopts = ()
set IntermediateFSD = ()
set IntermediateStem = ()
set contrast = bold
set UseCortexLabel = 1;
set nskip = 0; # for inorm
set nolog = 0;
set targgrp = ();
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
set PWD = `getpwdcmd`;
if($status) exit 1;
set SessList = `getsesspath $argv`;
if($status || $#SessList == 0) then
getsesspath $argv
exit 1;
endif
source $FREESURFER_HOME/sources.csh
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:
##### Create a log file ######
if($nolog) then
set LF = /dev/null
else
set logdir = log;
mkdir -p $logdir
if(! -e $logdir) then
echo "WARNING: could not create $logdir"
set LF = /dev/null
else
if($#SessList > 1) then
set LF = $logdir/preproc-sess.$$.log
else
set sb = `basename $SessList`
set LF = $logdir/preproc-sess.$sb.log
endif
if(-e $LF) mv $LF $LF.old
endif
endif
echo "--------------------------------------------------------------"
echo "preproc-sess logfile is $LF"
echo "--------------------------------------------------------------"
echo "preproc-sess log file" >> $LF
echo $VERSION | tee -a $LF
echo "$user" | tee -a $LF
echo "setenv FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
uname -a | tee -a $LF
pwd | tee -a $LF
echo $0 | tee -a $LF
echo $inputargs | tee -a $LF
date | tee -a $LF
echo "instem $instem " | tee -a $LF
echo "mc $DoMC $mcinstem $mcoutstem " | tee -a $LF
echo "stc $DoSTC $stcinstem $stcoutstem" | tee -a $LF
echo "sm $DoVolSmooth $sminstem $smoutstem "| tee -a $LF
echo "mask $DoMask $maskstem"| tee -a $LF
set ProjectDir = `pwd`;
set StartTime = `date`;
#------------------------------------------------#
foreach sess ($SessList)
set sessid = `basename $sess`;
set sessparent = `dirname $sess`;
# Create a log file #
if(-w . && $nolog != 1) then
mkdir -p log
set LF = $ProjectDir/log/preproc-$sessid-$fsd.log
rm -f $LF
else
set LF = /dev/null
endif
echo "preproc-sess" >> $LF
echo $sessid >> $LF
echo $VERSION >> $LF
uname -a >> $LF
date >> $LF
pwd >> $LF
echo $inputargs >> $LF
echo "ProjectDir $ProjectDir" >> $LF
if($DoTemplate) then
set cmd = (mktemplate-sess -s $sessid -d $sessparent -fsd $fsd -funcstem
$instem)
if($#RunListFile) set cmd = ($cmd -rlf $RunListFile);
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
echo "$sessid Template -----------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoReg) then
set cmd = (register-sess -s $sessid -d $sessparent -fsd $fsd -delete-dat)
set cmd = ($cmd -dof $RegDOF -$contrast)
if($#RunListFile) set cmd = ($cmd -rlf $RunListFile);
if($PerRun) set cmd = ($cmd -per-run)
if($PerSess) set cmd = ($cmd -per-session)
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
if($UseB0DC) set cmd = ($cmd -b0dc)
if($InitCoReg) set cmd = ($cmd -init-coreg)
if($InitFSL) set cmd = ($cmd -init-fsl)
if($InitSPM) set cmd = ($cmd -init-spm)
if($InitHeader) set cmd = ($cmd -init-header)
if($#IntermediateFSD) set cmd = ($cmd -bbr-int $IntermediateFSD
$IntermediateStem)
if($#BBRXopts) set cmd = ($cmd -bbr-xopts $BBRXopts)
echo "$sessid Registration -----------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoMask) then # Must be after reg now
set cmd = (mkbrainmask-sess -maskstem $maskstem)
set cmd = ($cmd -fsd $fsd)
set cmd = ($cmd -s $sessid -d $sessparent)
if($PerRun) set cmd = ($cmd -per-run)
if($PerSess) set cmd = ($cmd -per-session)
if($#RunListFile) set cmd = ($cmd -rlf $RunListFile);
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
if($UseB0DC) set cmd = ($cmd -b0dc) # only used to get the right reg file
if($RegDOF != 6) set cmd = ($cmd -dof $RegDOF)
echo "$sessid Mask ------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoMC) then
set cmd = (mc-sess -fstem $mcinstem -fmcstem $mcoutstem)
set cmd = ($cmd -s $sessid -d $sessparent -fsd $fsd)
if($#RunListFile) set cmd = ($cmd -rlf $RunListFile);
if($PerRun) set cmd = ($cmd -per-run)
if($PerSess) set cmd = ($cmd -per-session)
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
echo "$sessid MC -----------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoSTC) then
set cmd = (stc-sess -i $stcinstem -o $stcoutstem -ngroups $nSliceGroups)
if($#SliceOrder) set cmd = ($cmd -so $SliceOrder)
if($#SliceDelayFile) set cmd = ($cmd -sdf $SliceDelayFile)
set cmd = ($cmd -s $sessid -d $sessparent -fsd $fsd)
if($#RunListFile != 0) set cmd = ($cmd -rlf $RunListFile);
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
echo "$sessid STC -----------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($ToSurf) then
set cmd = (rawfunc2surf-sess -fwhm $fwhm)
set cmd = ($cmd -s $sessid -d $sessparent -fsd $fsd)
# By default it will do both, so set -hemi to anything
if("$hemi" == lh || "$hemi" == rh) set cmd = ($cmd -hemi $hemi)
if($subject == self) set cmd = ($cmd -self)
if($subject != self) set cmd = ($cmd -trgsubject $subject)
if($#RunListFile != 0) set cmd = ($cmd -rlf $RunListFile);
if($#SliceOrder) set cmd = ($cmd -stc $SliceOrder)
if($#SliceDelayFile) set cmd = ($cmd -sdf $SliceDelayFile)
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
if($UseB0DC) set cmd = ($cmd -b0dc)
if($RegDOF != 6) set cmd = ($cmd -dof $RegDOF)
if($PerRun) set cmd = ($cmd -per-run)
if($PerSess) set cmd = ($cmd -per-session)
if($DoMC == 0) set cmd = ($cmd -no-mc)
if($#ProjFrac) set cmd = ($cmd -projfrac $ProjFrac -expkey
$ProjFracExpKey)
if($#volsurffwhm) set cmd = ($cmd -volsurffwhm $volsurffwhm) # for testing
if(! $UseCortexLabel) set cmd = ($cmd -no-cortex-label)
echo "$sessid To Surface -----------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($ToMNI305 || $ToCVS) then
set cmd = (rawfunc2tal-sess -fwhm $fwhm )
set cmd = ($cmd -s $sessid -d $sessparent -fsd $fsd)
if($RawRes == 1) set cmd = ($cmd -1mm)
if($#RunListFile != 0) set cmd = ($cmd -rlf $RunListFile);
if($#SliceOrder) set cmd = ($cmd -stc $SliceOrder)
if($#SliceDelayFile) set cmd = ($cmd -sdf $SliceDelayFile)
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
if($UseB0DC) set cmd = ($cmd -b0dc)
if($RegDOF != 6) set cmd = ($cmd -dof $RegDOF)
if($ApplySubCortMask) set cmd = ($cmd -subcort-mask)
if(! $ApplySubCortMask) set cmd = ($cmd -no-subcort-mask)
if($PerRun) set cmd = ($cmd -per-run)
if($PerSess) set cmd = ($cmd -per-session)
if($DoMC == 0) set cmd = ($cmd -no-mc)
if($ToCVS) set cmd = ($cmd -cvs)
echo "$sessid To MNI305 -----------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoVolSmooth) then
set cmd = (spatialsmooth-sess -i $sminstem -o $smoutstem -fwhm $fwhm)
set cmd = ($cmd -fsd $fsd -s $sessid -d $sessparent)
if($UseSmoothMask) set cmd = ($cmd -mask);
if($#RunListFile != 0) set cmd = ($cmd -rlf $RunListFile);
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
echo "$sessid Volume Smoothing ---------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoSurfSmooth) then
set cmd = (surfsmooth-sess -i $sminstem -o $smoutstem -fwhm $fwhm)
set cmd = ($cmd -fsd $fsd -s $sessid -d $sessparent -reg $regfile)
if($#ProjFrac) set cmd = ($cmd -projfrac $ProjFrac)
if($DoProjAvg) set cmd = ($cmd -projfrac-avg)
if($#RunListFile != 0) set cmd = ($cmd -rlf $RunListFile);
if($nolog) set cmd = ($cmd -nolog);
if($UpdateOnly) set cmd = ($cmd -update);
if($PerRun) set cmd = ($cmd -perrun)
echo "$sessid Surface Smoothing ---------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
if($DoInorm) then
# Should probably remove this
set cmd = (inorm-sess -funcstem $inormstem )
set cmd = ($cmd -fsd $fsd -nskip $nskip)
set cmd = ($cmd -s $sessid -d $sessparent)
if($#RunListFile != 0) set cmd = ($cmd -rlf $RunListFile);
if($nolog) set cmd = ($cmd -nolog);
echo "$sessid Inorm ------------------------" |& tee -a $LF
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
end
echo "----------------------------------------" |& tee -a $LF
echo "Started at $StartTime" |& tee -a $LF
echo "Ended at `date`" |& tee -a $LF
echo "preproc-sess done"
exit 0
###############################################
############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "-i":
case "-in":
if ( $#argv == 0) goto arg1err;
set instem = $argv[1]; shift;
breaksw
case "-reg":
set DoReg = 1;
breaksw
case "-noreg":
case "-no-reg":
set DoReg = 0;
breaksw
case "-reg-dof":
if ( $#argv == 0) goto arg1err;
set RegDOF = $argv[1]; shift;
breaksw
case "-bbr-xopts":
if ( $#argv == 0) goto arg1err;
set BBRXopts = $argv[1]; shift
if(! -e $BBRXopts) then
echo "ERROR: cannot find $BBRXopts"
exit 1;
endif
breaksw
case "-mc-in":
case "-mcin":
if ( $#argv == 0) goto arg1err;
set mcinstem = $argv[1]; shift;
breaksw
case "-mc-out":
case "-mcout":
if ( $#argv == 0) goto arg1err;
set mcoutstem = $argv[1]; shift;
breaksw
case "-stcin":
if ( $#argv == 0) goto arg1err;
set stcinstem = $argv[1]; shift;
breaksw
case "-stcout":
if ( $#argv == 0) goto arg1err;
set stcoutstem = $argv[1]; shift;
breaksw
case "-smin":
if ( $#argv == 0) goto arg1err;
set sminstem = $argv[1]; shift;
breaksw
case "-smout":
if ( $#argv == 0) goto arg1err;
set smoutstem = $argv[1]; shift;
breaksw
case "-mask":
if ( $#argv == 0) goto arg1err;
set maskstem = $argv[1]; shift;
breaksw
case "-maskdir":
if ( $#argv == 0) goto arg1err;
set maskdir= $argv[1]; shift;
breaksw
case "-vol-fwhm":
case "-fwhm":
if ( $#argv == 0) goto arg1err;
set fwhm = $argv[1]; shift;
if($fwhm != 0) then
set DoVolSmooth = 1;
set DoSurfSmooth = 0;
set DoSmooth = 1;
else
set DoVolSmooth = 0;
set DoSurfSmooth = 0;
set DoSmooth = 0;
endif
breaksw
case "-smooth-mask":
set UseSmoothMask = 1;
breaksw
case "-no-smooth-mask":
set UseSmoothMask = 0;
breaksw
case "-surf-fwhm":
if ( $#argv == 0) goto arg1err;
set fwhm = $argv[1]; shift;
if($fwhm != 0) then
set DoVolSmooth = 0;
set DoSurfSmooth = 1;
set DoSmooth = 1;
endif
breaksw
case "-volsurffwhm":
if($#argv < 1) goto arg1err;
set volsurffwhm = $argv[1]; shift;
breaksw
case "-regfile":
if ( $#argv == 0) goto arg1err;
set regfile = $argv[1]; shift;
breaksw
case "-bbr-int":
if($#argv < 2) goto arg2err;
set IntermediateFSD = $argv[1]; shift;
set IntermediateStem = $argv[1]; shift;
breaksw
case "-bold":
case "-t2":
set contrast = bold
breaksw
case "-t1":
set contrast = t1
breaksw
case "-projfrac":
if ( $#argv < 2) goto arg2err;
set ProjFrac = $argv[1]; shift;
set ProjFracExpKey = $argv[1]; shift;
breaksw
case "-projfrac-avg":
set DoProjAvg = 1;
breaksw
case "-nskip":
if ( $#argv == 0) goto arg1err;
set nskip = $argv[1]; shift;
breaksw
case "-fsd":
if ( $#argv == 0) goto arg1err;
set fsd = $argv[1]; shift;
breaksw
case "-runlistfile":
case "-rlf":
if ( $#argv == 0) goto arg1err;
set RunListFile = $argv[1]; shift;
breaksw
case "-nomc":
case "-no-mc":
set DoMC = 0;
breaksw
case "-per-run":
case "-perrun":
set PerRun = 1;
set PerSess = 0;
set DoSmooth = 0;
set DoVolSmooth = 0;
set DoSurfSmooth = 0;
breaksw
case "-per-session":
case "-persession":
set PerSess = 1;
set PerRun = 0;
breaksw
case "-no-stc":
case "-nostc":
set DoSTC = 0;
breaksw
case "-stc":
case "-sliceorder":
case "-so":
if ( $#argv == 0) goto arg1err;
set SliceOrder = $argv[1]; shift;
set DoSTC = 1;
breaksw
case "-sdf":
if ( $#argv == 0) goto arg1err;
set SliceDelayFile = $argv[1]; shift;
if(! -e $SliceDelayFile) then
echo "ERROR: cannot find $SliceDelayFile"
exit 1;
endif
set DoSTC = 1;
breaksw
case "-ngroups":
if ( $#argv == 0) goto arg1err;
set nSliceGroups = $argv[1]; shift;
breaksw
case "-no-smooth":
case "-nosmooth":
set DoVolSmooth = 0;
set DoSurfSmooth = 0;
set DoSmooth = 0;
breaksw
case "-surf":
case "-surface":
if($#argv< 2) goto arg2err;
set subject = $argv[1]; shift;
set hemi = $argv[1]; shift;
set ToSurf = 1;
#set PerRun = 1;
#set PerSess = 0;
if($subject != self && ! -e $SUBJECTS_DIR/$subject) then
echo "ERROR: cannot find $subject in $SUBJECTS_DIR"
exit 1;
endif
breaksw
case "-mni305-2mm":
case "-mni305":
set RawRes = 2;
set ToMNI305 = 1;
set ToCVS = 0;
#set PerRun = 1;
#set PerSess = 0;
breaksw
case "-cvs":
set RawRes = 2;
set ToMNI305 = 0;
set ToCVS = 1;
#set PerRun = 1;
#set PerSess = 0;
breaksw
case "-usual":
set subject = fsaverage;
set hemi = lhrh
set ToSurf = 1;
set RawRes = 2;
set ToMNI305 = 1;
set PerRun = 1;
set PerSess = 0;
set fwhm = 5;
breaksw
case "-mni305-1mm":
set RawRes = 1;
set ToMNI305 = 1;
#set PerRun = 1;
#set PerSess = 0;
breaksw
case "-subcort-mask":
case "-subcort":
set ApplySubCortMask = 1;
breaksw
case "-no-subcort-mask":
case "-no-subcort":
set ApplySubCortMask = 0;
breaksw
case "-init-coreg":
set InitCoReg = 1;
set InitFSL = 0;
set InitSPM = 0;
set InitHeader = 0;
breaksw
case "-init-fsl":
set InitCoReg = 0;
set InitFSL = 1;
set InitSPM = 0;
set InitHeader = 0;
breaksw
case "-init-spm":
set InitCoReg = 0;
set InitFSL = 0;
set InitSPM = 1;
set InitHeader = 0;
breaksw
case "-init-header":
set InitCoReg = 0;
set InitFSL = 0;
set InitSPM = 0;
set InitHeader = 1;
breaksw
case "-b0dc":
set UseB0DC = 1;
breaksw
case "-a":
case "-analysis":
if($#argv< 1) goto arg1err;
set analysis = $argv[1]; shift;
if(! -e $analysis) then
echo "ERROR: cannot find $analysis"
exit 1;
endif
set fsd = `getana -a $analysis -t fsd`;
set RunListFile = `getana -a $analysis -t runlistfile`;
set RegDOF = `getana -a $analysis -t RegDOF`;
set PerRun = `getana -a $analysis -t IsPerRun`;
set PerSess = `getana -a $analysis -t IsPerSession`;
set UseB0DC = `getana -a $analysis -t UseB0DC`;
if($#UseB0DC == 0) set UseB0DC = 0;
set ApplySubCortMask = `getana -a $analysis -t ApplySubCortMask`;
set fwhm = `getana -a $analysis -t RawFWHM`;
if($fwhm == 0 || $PerRun) set DoVolSmooth = 0;
set SliceOrder = `getana -a $analysis -t stc`;
if($SliceOrder != none) set DoSTC = 1;
if($SliceOrder == none) set SliceOrder = ();
set SliceDelayFile = `getana -a $analysis -t sdf`;
if($SliceDelayFile != none) then
set DoSTC = 1;
set SliceDelayFile = $analysis/$SliceDelayFile
else
set SliceDelayFile = ()
endif
set nSliceGroups = `getana -a $analysis -t nslicegroups`;
set ToSurf = `getana -a $analysis -t IsSurface`;
if($ToSurf) then
set subject = `getana -a $analysis -t subject`;
set hemi = `getana -a $analysis -t hemi`;
endif
set ToMNI305 = `getana -a $analysis -t IsMNI305`;
set ToCVS = `getana -a $analysis -t IsCVS`;
if($ToMNI305 || $ToCVS) then
set RawRes = `getana -a $analysis -t RawRes`;
endif
set volsurffwhm = `getana -a $analysis -t VolSurfFWHM`;
if($#volsurffwhm && $volsurffwhm != 0) set DoVolSmooth = 1;
breaksw
case "-no-inorm":
case "-noinorm":
set DoInorm = 0;
breaksw
case "-inorm":
set DoInorm = 1;
breaksw
case "-no-template":
set DoTemplate = 0;
breaksw
case "-no-mask":
case "-nomask":
set DoMask = 0;
breaksw
case "-no-cortex-label":
set UseCortexLabel = 0;
breaksw
case "-cortex-label":
set UseCortexLabel = 1;
breaksw
case "-update":
set UpdateOnly = 1;
breaksw
case "-force":
case "-noupdate":
case "-no-update":
set UpdateOnly = 0;
breaksw
case "-nolog":
set nolog = 1;
breaksw
case "-verbose":
set verbose = 1;
breaksw
case "-echo":
set echo = 1;
breaksw
case "-debug":
set verbose = 1;
set echo = 1;
breaksw
case "-g":
case "-s":
case "-sf":
case "-d":
case "-df":
shift;
# ignore getsesspath arguments
breaksw
case "-cwd":
# ignore getsesspath arguments
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#instem == 0) set instem = "f";
if($#fsd == 0) then
echo "ERROR: you must specify a functional subdirectory with -fsd"
echo " eg, -fsd bold or -fsd rest"
exit 1
endif
if($DoMC || $DoReg) then
if($PerRun == 0 && $PerSess == 0) then
echo "ERROR: You must specify -per-run or -per-session"
exit 1;
endif
endif
if($DoMC) then
if($#mcinstem == 0) set mcinstem = $instem
if($#mcoutstem == 0) then
if($PerRun) then
set mcoutstem = $mcinstem"mcpr"
else # PerSess
set mcoutstem = $mcinstem"mc"
endif
endif
else
# Don't append "pr" even if per-run
set mcoutstem = $instem;
endif
if($DoSTC) then
if($#stcinstem == 0) set stcinstem = $mcoutstem
if($#stcoutstem == 0) then
if($#SliceOrder) set stcoutstem = $stcinstem.$SliceOrder
if($#SliceDelayFile) set stcoutstem = $stcinstem.sdf
endif
else
set stcoutstem = $mcoutstem
endif
if($ToSurf || $ToMNI305 || $ToCVS) then
if($#fwhm == 0) then
echo "ERROR: must specify -fwhm with -surface or -mni305 or -cvs."
echo " Set it to 0 for no smoothing"
exit 1;
endif
set DoVolSmooth = 0;
set DoSurfSmooth = 0;
set DoSmooth = 0;
endif
if($DoSmooth) then
if($#fwhm == 0) then
echo "ERROR: must specify FWHM when doing smoothing"
echo "If not smoothing, use -nosmooth"
exit 1;
endif
if($#sminstem == 0) set sminstem = $stcoutstem
if($#smoutstem == 0) then
if($DoVolSmooth) set smoutstem = $sminstem."sm"$fwhm
if($DoSurfSmooth) set smoutstem = $sminstem."sm"$fwhm
endif
endif
if($DoInorm && $#inormstem == 0) then
if($DoVolSmooth) then
set inormstem = $smoutstem;
else if($DoMC) then
set inormstem = $mcoutstem;
else
set inormstem = $mcinstem;
endif
endif
if(! $DoMC && ! $DoSTC && ! $DoSmooth && ! $DoMask && ! $DoTemplate) then
echo "ERROR: nothing to do"
exit 1;
endif
if($#ProjFrac && $DoProjAvg) then
echo "ERROR: cannot -projfrac and -projfrac-avg"
exit 1;
endif
if($UseB0DC && $#ProjFracExpKey) then
# This can actually be done but will create a conflict at the time of
mkanalysis
echo "WARNING: specifying -b0dc and -projfrac at the same time may create a
conflict when mkanalysis-sess is run"
#exit 1;
endif
if($#regfile == 0) then
if(! $UseB0DC) set regfile = register.dof$RegDOF.lta
if($UseB0DC) set regfile = register.dof$RegDOF.b0dc.lta
endif
if($#SliceDelayFile != 0 && $#SliceOrder != 0) then
echo "ERROR: cannot specify both -so and -sdf"
exit 1;
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
arg2err:
echo "ERROR: flag $flag requires two arguments"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo ""
echo "USAGE: preproc-sess"
echo ""
echo " -per-run : motion cor and reg to middle TP of each run"
echo " -per-session : motion cor and reg to 1st TP of 1st run"
echo " -fwhm FWHM : smoothing level (mm)"
echo ""
echo " -update : only run a stage if input is newer than output
(default)"
echo " -force : force reprocessing of all stages (turns off -update)"
echo " -no-update : same as -force"
echo " -sliceorder so : turn on slice timing correction (STC) with the given
slice order"
echo " -ngroups nSliceGroups : number of SMS slice groups for STC"
echo " -surface subject hemi : set hemi to lhrh to do both"
echo " -mni305-2mm : sample raw data to mni305 at 2mm (same as -mni305)"
echo " -mni305-1mm : sample raw data to mni305 at 1mm"
echo " -cvs : sample raw data to cvs_avg35_inMNI152 at 2mm (not with
-mni305)"
echo " -b0dc : apply B0 distortion correction (looks for
fsd/b0dcmap.nii.gz); see epidewarp.fsl"
echo ""
echo "Session Arguments (some combination required)"
echo " -sf sessidfile ..."
echo " -df srchdirfile ..."
echo " -s sessid ..."
echo " -d srchdir ..."
echo " -fsd fsd <bold>"
echo " -rlf rlf : run list file (default all runs)"
echo ""
echo "Registration options"
echo " -init-fsl : use fsl to initialize bbr registration"
echo " -init-spm : use spm to initialize bbr registration (needs matlab)"
echo " -init-header : use geometry to initialize bbr registration"
echo " -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem"
echo ""
echo "Other options (probably not too useful)"
echo ""
echo " -nomc : don't do motion correction"
echo " -nostc : don't do slice-timing correction"
echo " -nosmooth : don't do smoothing"
echo " -nomask : don't create brain mask"
echo " -noreg : don't do registration"
echo " -noinorm : don't do inorm"
echo " -no-subcort-mask : do not apply subcortical masking"
echo ""
echo " -mcin mcinstem : stem to use as input to MC"
echo " -mcout mcoutstem : stem to use as output of MC"
echo " -stcin stcinstem : stem to use as input to STC "
echo " -stcout stcoutstem : stem to use as output of STC "
echo " -smin sminstem : stem to use as input to smoothing "
echo " -smout sminstem : stem to use as output of smoothing "
echo " -mask maskstem : <brain>"
echo ""
echo " -i instem : stem to use as overal input <f>"
# echo " -vol-fwhm fwhm : 3D fwhm (mm) (not with -surf-fwhm)"
# echo " -surf-fwhm fwhm : 2D fwhm (mm) (not with -vol-fwhm)"
# echo " -smooth-mask : use mask when volume smoothing"
# echo " -no-smooth-mask: do not use mask when volume smoothing"
# echo " -inorm : perform intensity normalization (off by default)"
# echo " -nskip N : do not use first N TRs when inorming"
echo ""
echo ""
echo " -regfile regfile : registration file for use with -surf-fwhm
(register.dat)"
echo " -bbr-xopts bbr.xopts : pass expert options to bbregister"
echo " -projfrac frac expkey : projection fraction for use with -surf-fwhm
(0.5)"
echo " expkey is a code string used to make sure that the output file name
is unique."
echo " This should be passed to mkanalysis-sess with -expkey. "
echo " Example: -projfrac 0.2 pf020"
echo " -projfrac-avg : average over ribbon (not with -projfrac)"
echo " -no-cortex-label : do not use cortex label for masking surfaces"
echo ""
if(! $PrintHelp) exit 1;
echo $VERSION
cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;
#---- Everything below here is printed out as part of help -----#
BEGINHELP
This will run preprocessing steps: motion correction (MC),
slice-timing correction (STC), functional-anatomical registration,
mask creation, intensity normalization, resampling to common space,
and spatial smoothing.
-per-run
Motion correct and register using the middle time point of each run.
This is the option that you should use.
-per-session
Motion correct and register using the first time point of the first
run. This is mainly for compatability with version 4.
-fwhm FWHM
Specify a full-width/half-max (in mm) when smoothing. If you do not
want to smooth, specify 0 (but you must specify something).
-update
Only perform a stage if the output is newer than the input or if the
output does not exist. This can be very convenient as you do not have to
keep track of what has been done. Just specify all the sessions and
and it will figure out what needs to be done. This is the default
behavior. See also -force.
-force
-noupdate
Force processing of all stages regardless of what has been done
before. This turns off -update
-sliceorder so
Perform slice-timing correction with the given slice order. Legal
values are siemens, up, down, odd, and even. Siemens slice order is
interleaved starting on the first slice for an odd number of slices or
the second slice for an even number. "up" is 1st, 2nd, 3rd,
etc. "down" is last, next to last, etc. odd is 1st, 3rd, 5th, , etc,
then 2nd, 4th, 6th, etc. "even" is 2nd, 4th, 6th, etc, then 1st, 3rd,
5th, etc. See also stc-sess.
-sdf slicedelayfile
Provide a text file that gives the slice delay of each slice in
fractions of TR rather than computing it analytically from up,
down, etc. Usually the middle of the TR has a value of 0. The
format should be the same as the output of the slicedelay program.
This allows for arbitrary slice orders.
-surface subject hemi
Sample raw data onto the surface of the hemisphere of the given
subject. Hemi should be lh, rh, or lhrh (for both). Both -surface and
-mni305can be specified (in which case it will do both).
-mni305
Sample raw data into the mni305 2mm space. Both -mni305 and -surface can be
specified (in which case it will do both).
-i instem
Explicitly specify input stem. Default is f.
EXAMPLE 1
To perform template creation, MC, registration, mask creation, sampling
to the lh and rh hemispheres of fsaverage and to the mni305 2mm space,
preproc-sess -sf sessidlist -df sessdirlist
-surface fsaverage lhrh -mni305 -fwhm 5
EXAMPLE 2
To perform template creation, MC, registration, mask creation,
sampling to the lh and rh hemispheres of native subject anatomy and
to the mni305 2mm space,
preproc-sess -sf sessidlist -df sessdirlist
-surface self lhrh -mni305 -fwhm 5
INPUTS AND OUTPUTS
Unless otherwise specified, the input stem is f, and the input stems
and output stems of the other stages are automatically determined as
follows:
Input to MC is instem (default is f) Output of MC is instem"mcpr" (ie,
the MC input stem with "mcpr" appended to the end, eg, "fmcpr"). When
per-session is used, the MC default stem will be instem"mc".
Input to STC is outstem of MC
Output of STC is stcinstem.SliceOrder where SliceOrder is the slice
order used (eg, "siemens", see -sliceorder above).
Input to smoothing is outstem of STC (or MC if no STC)
Output of smoothing is sminstem"smFWHM" (ie, the smoothing
input stem with "sm" appended to the end and then the specified
FWHM appended to that).
====================================================================
These options are obsolete but still functional
-vol-fwhm fwhm
Specify the fwhm for 3D spatial smoothing. There is no default. The
output will have "smFWHM" appened to it. Eg, for -vol-fwhm 5, then the
output will have "sm5" appened. If you do not want to perform
smoothing, use -nosmooth. See also spatialsmooth-sess. Cannot be run
with -surf-fwhm.
-surf-fwhm fwhm
Specify the fwhm for 2D (surface) spatial smoothing. The raw data are
resampled to the surface, smoothed, and then put back into the volume
(so that they can be analyzed in standard volumetric fashion). Values
not on the surface are not changed. Surface smoothing can be slow, so
be patient! Requires that registration have been performed
(spmregister-sess or fslregister-sess). The output will have
"smFWHMs" appened to it. Eg, for -surf-fwhm 5, then the output will
have "sm5s" appened. If you do not want to perform smoothing, use
-nosmooth. See also surfsmooth-sess. Cannot be run with -vol-fwhm.
Any per-run instruction will force surface smoothing to use
"register.dat" in each run directory. The registration file name can
be changed with -reg. By default, samples midway between the white and
pial surfaces (ie, projection fraction of 0.5), but this can be
changed with -projfrac. Or the average over the ribbon can be computed
with -projfrac-avg (but this will be slow).
-inorm
Not needed anymore. Turn on computing of intensity normalization
factor (creates stem.meanval). This was necssary for the old selxavg.
#! /bin/csh -f
#
# rawfunc2surf-sess
#
# Original Author: Doug Greve
#
# Copyright © 2021
# The General Hospital Corporation (Boston, MA).
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#
set VERSION = 'rawfunc2surf-sess @FS_VERSION@';
set inputargs = ($argv);
set fsd = bold;
set instem = ()
set mc = mc
set outstem = ();
set regfile = ();
set RegDOF = 6;
set trgsubject = fsaverage
set hemilist = ()
set ProjFrac = 0.5;
set interp = trilin
set PerRun = 1;
set maskname = brain
set maskdir = masks
set maskstem = ();
set RunListFile = ();
set volsurffwhm = (); # smooth in the volume, for testing
set fwhm = ();
set UpdateOnly = 0;
set nolog = 0;
set debug = 0;
set DoSelf = 0;
set PrintHelp = 0;
set SurfReg = sphere.reg
set ExpKey = ();
set ExpKeyNeeded = 0;
set SliceOrder = ();
set SliceDelayFile = ();
set SaveUnsmoothed = 0;
set UseB0DC = 0;
set b0dcmapstem = b0dcmap
set UseCortexLabel = 1;
set outfmt = nii
if($?FSF_OUTPUT_FORMAT) then
set outfmt = $FSF_OUTPUT_FORMAT
endif
## If there are no options, just print the usage ##
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
set n = `echo $argv | grep -e -help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
source $FREESURFER_HOME/sources.csh
goto parse_args;
parse_args_return:
set SessList = `getsesspath $inputargs`;
if($status || $#SessList == 0) then
getsesspath $inputargs
echo "ERROR: cannot find any sessions"
exit 1;
endif
goto check_params;
check_params_return:
# Create a string like lhrh
set hemistr = ();
foreach hemi ($hemilist)
set hemistr = $hemistr$hemi
end
set ProjectDir = `pwd`;
## Loop through each session ##
@ nthsess = 0;
foreach sess ($SessList)
set sessid = `basename $sess`
@ nthsess = $nthsess + 1;
##### Create a log file ######
set LF = /dev/null
if(! $nolog) then
set logdir = $ProjectDir/log;
mkdir -p $logdir
set LF = $logdir/rawfunc2surf-sess.$sessid.$fsd.$outstem.$hemistr$ExpKey.log
if(-e $LF) mv $LF $LF.old
endif
echo "rawfunc2surf-sess log file" >> $LF
echo $VERSION >> $LF
uname -a >> $LF
date >> $LF
pwd >> $LF
echo $0 $inputargs >> $LF
echo UpdateOnly $UpdateOnly >> $LF
echo "------------------------------ " |& tee -a $LF
echo "$nthsess/$#SessList $sessid" |& tee -a $LF
set subject = `cat $sess/subjectname`;
if($DoSelf) set trgsubject = $subject
set b0dcmap = ();
set pedir = 2; #2=row direction
if($UseB0DC) then
set b0dcmap = `stem2fname $sess/$fsd/$b0dcmapstem`;
if($status) then
echo "$b0dcmap"|& tee -a $LF
exit 1;
endif
set pedirfile = $sess/$fsd/$b0dcmapstem.pedir.txt
if(-e $pedirfile) then
set pedir = `cat $pedirfile`
echo "Setting PE direction so $pedir" | tee -a $LF
endif
endif
set RunList = `getrunlist $sess/$fsd $RunListFile`;
if($status) then
echo "$RunList" |& tee -a $LF
exit 1;
endif
# Handle masks first
foreach hemi ($hemilist)
if(! $PerRun) then
# Per-session
set reg = $sess/$fsd/$regfile
if(! -e $reg) then
echo "ERROR: cannot find $reg" | tee -a $LF
echo "Try running register-sess" | tee -a $LF
exit 1;
endif
set maskstempath = $sess/$fsd/$maskdir/$maskname
set mask = `stem2fname $maskstempath`
if($status) then
echo "$mask" | tee -a $LF
echo "Try running mkbrainmask-sess" | tee -a $LF
exit 1;
endif
set outmask = $sess/$fsd/$maskdir/$maskstem.$hemi$ExpKey.$outfmt
set UpdateNeeded = `UpdateNeeded $outmask $reg $mask $b0dcmap`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded) then
set cmd = (mri_vol2surf --mov $mask --reg $reg \
--trgsubject $trgsubject --interp nearest --projfrac $ProjFrac\
--hemi $hemi --o $outmask --noreshape)
if($UseCortexLabel) set cmd = ($cmd --cortex)
if($trgsubject != $subject) set cmd = ($cmd --surfreg $SurfReg)
if($UseB0DC) set cmd = ($cmd --vsm $b0dcmap $pedir)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
set cmd = (mri_binarize --i $outmask --min .00001 --o $outmask)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
else
echo "$outmask does not need updating" | tee -a $LF
endif
continue;
endif
# Must be per-run to get here
foreach Run ($RunList)
echo " $nthsess/$#SessList $sessid $Run $hemi ---------" |& tee -a $LF
echo " `date`" |& tee -a $LF
set funcdir = $sess/$fsd/$Run
set reg = $sess/$fsd/$Run/$regfile
if(! -e $reg) then
echo "ERROR: cannot find $reg" | tee -a $LF
echo "Try running register-sess with -per-run" | tee -a $LF
exit 1;
endif
# Use only one mask for all runs so no pruning necessary
#set maskstempath = $sess/$fsd/$maskdir/$maskname
# This creates problems when there is motion or
# or removed and replace subject in scanner
# So go back to using run-based mask
set maskstempath = $sess/$fsd/$Run/$maskdir/$maskname
set mask = `stem2fname $maskstempath`
if($status) then
echo "$mask" | tee -a $LF
echo "Try running mkbrainmask-sess with -per-run" | tee -a $LF
exit 1;
endif
# Create a .pr mask here, then merge them together into a single mask
later
set outmask = $sess/$fsd/$Run/$maskdir/$maskstem.$hemi$ExpKey.pr.$outfmt
set UpdateNeeded = `UpdateNeeded $outmask $reg $mask $b0dcmap`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded) then
set cmd = (mri_vol2surf --mov $mask --reg $reg \
--trgsubject $trgsubject --interp nearest --projfrac $ProjFrac\
--hemi $hemi --o $outmask --noreshape)
if($UseCortexLabel) set cmd = ($cmd --cortex)
if($trgsubject != $subject) set cmd = ($cmd --surfreg $SurfReg)
if($UseB0DC) set cmd = ($cmd --vsm $b0dcmap $pedir)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
set cmd = (mri_binarize --i $outmask --min .00001 --o $outmask)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
else
echo "$outmask does not need updating" | tee -a $LF
endif
end # loop over runs
# Merge run-level masks and prune
set prmasklist = ()
foreach Run ($RunList)
set prmask = $sess/$fsd/$Run/$maskdir/$maskstem.$hemi$ExpKey.pr.$outfmt
set prmasklist = ($prmasklist $prmask)
end
set finalmask = $sess/$fsd/$maskdir/$maskstem.$hemi$ExpKey.pr.$outfmt
set UpdateNeeded = `UpdateNeeded $finalmask $prmasklist`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded) then
set cmd = (mri_concat --o $finalmask --mean $prmasklist)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
set cmd = (mri_binarize --i $finalmask --min 10e-10 --o $finalmask)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Now copy it to each run, remove the .pr
foreach Run ($RunList)
set prmask = $sess/$fsd/$Run/$maskdir/$maskstem.$hemi$ExpKey.$outfmt
cp $finalmask $prmask |& tee -a $LF
if($status) exit 1;
end
else
echo "$finalmask does not need updating" | tee -a $LF
endif
end # loop over hemi
# Now do time series data
foreach hemi ($hemilist)
foreach Run ($RunList)
echo " $nthsess/$#SessList $sessid $Run $hemi ---------" |& tee -a $LF
echo " `date`" |& tee -a $LF
set funcdir = $sess/$fsd/$Run
set invol = `stem2fname $funcdir/$instem`
if($status) then
echo "$invol" |& tee -a $LF
exit 1;
endif
# Get the mask and reg to use
if($PerRun) then
set outmask = $sess/$fsd/$Run/$maskdir/$maskstem.$hemi$ExpKey.$outfmt
set reg = $sess/$fsd/$Run/$regfile
else
set outmask = $sess/$fsd/$maskdir/$maskstem.$hemi$ExpKey.$outfmt
set reg = $sess/$fsd/$regfile
endif
set outvol = $funcdir/$outstem.$hemi$ExpKey.$outfmt
set UpdateNeeded = `UpdateNeeded $outvol $invol $reg $outmask`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded == 0) then
echo " $sessid $Run Update not needed" | tee -a $LF
continue
endif
set cmd = (mri_vol2surf --mov $invol --reg $reg \
--trgsubject $trgsubject --interp $interp --projfrac $ProjFrac\
--hemi $hemi --o $outvol --noreshape)
if($UseCortexLabel) set cmd = ($cmd --cortex)
if($trgsubject != $subject) set cmd = ($cmd --surfreg $SurfReg)
if($UseB0DC) set cmd = ($cmd --vsm $b0dcmap $pedir)
if($#volsurffwhm) set cmd = ($cmd --fwhm $volsurffwhm) # dont do for mask
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Smooth raw data within mask
if($fwhm != 0) then
if($SaveUnsmoothed) cp $outvol $funcdir/$outstem0.$hemi$ExpKey.$outfmt
set cmd = (mris_fwhm --s $trgsubject --hemi $hemi --smooth-only \
--i $outvol --fwhm $fwhm --o $outvol --mask $outmask --no-detrend)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
endif
end # Loop over runs
end # Loop over hemis
end # foreach sess ($SessList)
echo "" |& tee -a $LF
date |& tee -a $LF
echo "rawfunc2surf-sess completed " |& tee -a $LF
exit 0;
############--------------##################
parse_args:
set cmdline = "$argv";
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "-i":
case "-instem":
if ( $#argv == 0) goto arg1err;
set instem = $argv[1]; shift;
breaksw
case "-fsd":
if ( $#argv == 0) goto arg1err;
set fsd = $argv[1]; shift;
breaksw
case "-runlistfile":
case "-rlf":
if ( $#argv == 0) goto arg1err;
set RunListFile = $argv[1]; shift;
breaksw
case "-per-run":
case "-perrun":
set PerRun = 1;
breaksw
case "-per-session":
case "-no-per-run":
case "-no-perrun":
set PerRun = 0;
#set ExpKeyNeeded = 1;
breaksw
case "-surfreg":
if ( $#argv == 0) goto arg1err;
set SurfReg = $argv[1]; shift;
set ExpKeyNeeded = 1;
breaksw
case "-expkey":
if($#argv < 1) goto arg1err;
set ExpKey = $argv[1]; shift;
set ExpKey = (.$ExpKey); # prepend a dot
breaksw
case "-update":
set UpdateOnly = 1;
breaksw
case "-force":
set UpdateOnly = 0;
breaksw
case "-nearest":
set interp = "nearest"e
set ExpKeyNeeded = 1;
breaksw
case "-trilin":
set interp = "trilin"
breaksw
case "-trgsubject":
if($#argv < 1) goto arg1err;
set trgsubject = $argv[1]; shift;
breaksw
case "-stc":
case "-sliceorder":
case "-so":
if ( $#argv == 0) goto arg1err;
set SliceOrder = $argv[1]; shift;
if($SliceOrder != siemens && $SliceOrder != up && $SliceOrder != down && \
$SliceOrder != odd && $SliceOrder != even && $SliceOrder != none) then
echo "ERROR: -stc is $SliceOrder, must be siemens, up, down, odd,
even, or none"
exit 1;
endif
breaksw
case "-sdf":
if ( $#argv == 0) goto arg1err;
set SliceDelayFile = $argv[1]; shift;
set DoSTC = 1;
breaksw
case "-reg":
if($#argv < 1) goto arg1err;
set regfile = $argv[1]; shift;
set ExpKeyNeeded = 1;
breaksw
case "-dof":
if ($#argv < 1) goto arg1err;
set RegDOF = $argv[1]; shift;
breaksw
case "-b0dc":
case "-b0dcor":
case "-vsm":
set UseB0DC = 1;
set ExpKey = ".b0dc"
breaksw
case "-projfrac":
if($#argv < 1) goto arg1err;
set ProjFrac = $argv[1]; shift;
set ExpKeyNeeded = 1;
breaksw
case "-fwhm":
if($#argv < 1) goto arg1err;
set fwhm = $argv[1]; shift;
breaksw
case "-volsurffwhm":
if($#argv < 1) goto arg1err;
set volsurffwhm = $argv[1]; shift;
breaksw
case "-hemi":
if($#argv < 1) goto arg1err;
set hemi = $argv[1]; shift;
set hemilist = ($hemilist $hemi);
breaksw
case "-lh":
set hemilist = ($hemilist lh);
breaksw
case "-rh":
set hemilist = ($hemilist rh);
breaksw
case "-self":
set DoSelf = 1;
breaksw
# should not use either of these
case "-o":
case "-outstem":
if ( $#argv == 0) goto arg1err;
set outstem = $argv[1]; shift;
breaksw
case "-mask":
# output mask stem
if ( $#argv == 0) goto arg1err;
set maskstem = $argv[1]; shift;
breaksw
case "-save-unsmoothed":
set SaveUnsmoothed = 1;
breaksw
case "-no-mc":
set mc = ""
breaksw
case "-no-cortex-label":
set UseCortexLabel = 0;
breaksw
case "-cortex-label":
set UseCortexLabel = 1;
breaksw
case "-nolog":
set nolog = 1;
breaksw
case "-debug":
set debug = 1;
set verbose = 1;
set echo = 1;
breaksw
case "-cwd":
breaksw
case "-s":
case "-sf":
case "-df":
case "-d":
case "-g":
shift;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#fwhm == 0) then
echo "ERROR: you must enter a FWHM. Use 0 for no smoothing."
exit 1;
endif
if($ExpKeyNeeded && $#ExpKey == 0) then
echo "ERROR: experts key needed (-expkey)"
exit 1;
endif
if($#instem == 0) then
# Note that if no MC, then there will be no "pr" appended
set instem = f${mc}
if($mc != "" && $PerRun) set instem = fmcpr
if($#SliceOrder != 0) set instem = $instem.$SliceOrder
if($#SliceDelayFile != 0) set instem = $instem.sdf
endif
if($DoSelf) then
set subjstr = self
else
set subjstr = $trgsubject
endif
if($#outstem == 0) set outstem = $instem
set outstem0 = $outstem.sm0.$subjstr; # for saving unsmoothed
if($#volsurffwhm == 0) then
set outstem = $outstem.sm$fwhm.$subjstr; # hemi appended later
else
set outstem = $outstem.vsm$volsurffwhm.sm$fwhm.$subjstr; # hemi appended
later
endif
if($#maskstem == 0) set maskstem = $maskname
set maskstem = $maskstem.$subjstr # hemi appended later
if($#hemilist == 0) set hemilist = (lh rh);
echo "instem $instem"
echo "outstem $outstem.hemi"
if($#regfile == 0) then
if(! $UseB0DC) set regfile = register.dof$RegDOF.lta
if($UseB0DC) set regfile = register.dof$RegDOF.b0dc.lta
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo "rawfunc2surf-sess"
echo ""
echo " Session Arguments (some required)"
echo " -sf sessidfile ..."
echo " -df srchdirfile ..."
echo " -s sessid ..."
echo " -d srchdir ..."
echo ""
echo " -fwhm FWHMmm : smooth by FWHM mm (enter 0 for no smoothing)"
echo ""
echo "Optional Arguments"
echo " -i instem : fmcpr (default is fmcpr)"
echo " -fsd dir : functional subdirectory ($fsd)"
echo " -self : map to native subject surface instead of fsaverage"
echo ""
echo "Expert Options"
echo " -reg regfile : default is register.dof$RegDOF.lta"
echo " -nearest : use nearest neighbor interp (default is trilin)"
echo " -surfreg SurfReg : change from $SurfReg"
echo " -per-session : use session-level registration and mask instead of
-per-run"
echo " -no-cortex-label : do not use cortex label for masking"
echo " -dof DOF"
echo ""
echo "Other options"
echo " -save-unsmoothed : save sm0 in addition to smoothed data"
echo " -update : only run if update is needed"
echo " -force : force an update (default)"
echo " -version : print version and exit"
echo " -debug"
echo ""
if(! $PrintHelp ) exit 1;
echo " "
echo "$VERSION "
echo " "
cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;
#---- Everything below here is printed out as part of help -----#
BEGINHELP
Resamples raw functional data onto the cortical surface.
#! /bin/csh -f
#
# rawfunc2tal-sess
#
# Original Author: Doug Greve
#
# Copyright © 2021
# The General Hospital Corporation (Boston, MA).
# All rights reserved.
#
# Distribution, usage and copying of this software is covered under the
# terms found in the License Agreement file named 'COPYING' found in the
# FreeSurfer source code root directory, and duplicated here:
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense
#
# General inquiries: freesurfer@nmr.mgh.harvard.edu
# Bug reports: analysis-b...@nmr.mgh.harvard.edu
#
set VERSION = 'rawfunc2tal-sess @FS_VERSION@';
set inputargs = ($argv);
set fsd = bold;
set instem = ();
set outstem = ();
set regfile = ();
set RegDOF = 6;
set target = mni305
set res = 2;
set talxfm = talairach.xfm
set interp = trilin
set PerRun = 1;
set maskname = brain
set maskdir = masks
set maskstem = ();
set fwhm = ();
set MaskedSmoothing = 1;
set RunListFile = ();
set UpdateOnly = 0;
set ExpKey = ();
set ExpKeyNeeded = 0;
set SliceOrder = ();
set SliceDelayFile = ();
set UseB0DC = 0;
set b0dcmapstem = b0dcmap
set ApplySubCortMask = 1;
set UseCVS = 0;
set mc = mc
set nolog = 0;
set debug = 0;
set PrintHelp = 0;
set outfmt = nii
if($?FSF_OUTPUT_FORMAT) then
set outfmt = $FSF_OUTPUT_FORMAT
endif
## If there are no options, just print the usage ##
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -version | wc -l`
if($n != 0) then
echo $VERSION
exit 0;
endif
set n = `echo $argv | grep -e -help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
endif
source $FREESURFER_HOME/sources.csh
goto parse_args;
parse_args_return:
set SessList = `getsesspath $inputargs`;
if($status || $#SessList == 0) then
getsesspath $inputargs
echo "ERROR: cannot find any sessions"
exit 1;
endif
goto check_params;
check_params_return:
set ProjectDir = `pwd`;
## Loop through each session ##
@ nthsess = 0;
foreach sess ($SessList)
set sessid = `basename $sess`
@ nthsess = $nthsess + 1;
##### Create a log file ######
set LF = /dev/null
if(! $nolog) then
set logdir = $ProjectDir/log;
mkdir -p $logdir
set LF = $logdir/rawfunc2tal-sess.$sessid.$fsd.$outstem$ExpKey.log
if(-e $LF) mv $LF $LF.old
endif
echo "rawfunc2tal-sess log file" >> $LF
echo $VERSION >> $LF
uname -a >> $LF
date >> $LF
pwd >> $LF
echo $0 $inputargs >> $LF
echo UpdateOnly $UpdateOnly >> $LF
set subject = `cat $sess/subjectname`
echo "------------------------------ " |& tee -a $LF
echo "$nthsess/$#SessList $sessid $subject" |& tee -a $LF
## Make sure the functional subdirectory exists ##
if(! -e $sess/$fsd) then
echo "ERROR: $sess/$fsd does not exist" |& tee -a $LF
exit 1;
endif
set b0dcmap = ();
set pedir = 2; #2=row direction
if($UseB0DC) then
set b0dcmap = `stem2fname $sess/$fsd/$b0dcmapstem`;
if($status) then
echo "$b0dcmap"|& tee -a $LF
exit 1;
endif
set pedirfile = $sess/$fsd/$b0dcmapstem.pedir.txt
if(-e $pedirfile) then
set pedir = `cat $pedirfile`
echo "Setting PE direction so $pedir" | tee -a $LF
endif
endif
if(! $PerRun) then
set reg = $sess/$fsd/$regfile
if(! -e $reg) then
echo "ERROR: cannot find $reg" | tee -a $LF
echo "Try running register-sess" | tee -a $LF
exit 1;
endif
set maskstempath = $sess/$fsd/$maskdir/$maskname
set mask = `stem2fname $maskstempath`
if($status) then
echo "$mask" | tee -a $LF
echo "Try running mkbrainmask-sess" | tee -a $LF
exit 1;
endif
# Create the mask in the mni305/CVS space, create .pr then merge later
set outmask = $sess/$fsd/$maskdir/$maskstem$ExpKey.$outfmt
set UpdateNeeded = `UpdateNeeded $outmask $reg $mask $b0dcmap`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded) then
if($UseCVS == 0) then
set cmd = (mri_vol2vol --mov $mask --reg $reg \
--tal --talres $res --talxfm $talxfm --nearest \
--no-save-reg --o $outmask)
if($UseB0DC) set cmd = ($cmd --vsm $b0dcmap $pedir)
else
set gcam =
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
if(! -e $gcam) then
echo "ERROR: cannot find $gcam" | tee -a $LF
exit 1;
endif
set dstreg =
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
set cmd = (mri_vol2vol --vsm-pedir $pedir --gcam $mask $reg $gcam
$dstreg)
if($UseB0DC) set cmd = ($cmd $b0dcmap)
if(! $UseB0DC) set cmd = ($cmd 0)
set cmd = ($cmd 0 $outmask)
endif
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Take intersection with whole brain or subcort mask
set mask = $brainmask
if($ApplySubCortMask) set mask = $subcortmask
set cmd = (mri_mask $outmask $mask $outmask)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
else
echo "$outmask does not need updating" | tee -a $LF
endif
endif
set RunList = `getrunlist $sess/$fsd $RunListFile`;
if($status) then
echo "$RunList" |& tee -a $LF
exit 1;
endif
# Build masks for each run
if($PerRun) then
foreach Run ($RunList)
echo " $nthsess/$#SessList $sessid $Run ----------------" |& tee -a $LF
echo " `date`" |& tee -a $LF
set funcdir = $sess/$fsd/$Run
set reg = $sess/$fsd/$Run/$regfile
if(! -e $reg) then
echo "ERROR: cannot find $reg" | tee -a $LF
echo "Try running register-sess with -per-run" | tee -a $LF
exit 1;
endif
set maskstempath = $sess/$fsd/$Run/$maskdir/$maskname
set mask = `stem2fname $maskstempath`
if($status) then
echo "$mask" | tee -a $LF
echo "Try running mkbrainmask-sess with -per-run" | tee -a $LF
exit 1;
endif
# Create the mask in the mni305/CVS space, create .pr then merge later
set outmask = $sess/$fsd/$Run/$maskdir/$maskstem$ExpKey.pr.$outfmt
set UpdateNeeded = `UpdateNeeded $outmask $reg $mask $b0dcmap`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded) then
if($UseCVS == 0) then
set cmd = (mri_vol2vol --mov $mask --reg $reg \
--tal --talres $res --talxfm $talxfm --nearest \
--no-save-reg --o $outmask)
if($UseB0DC) set cmd = ($cmd --vsm $b0dcmap $pedir)
else
set gcam =
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
if(! -e $gcam) then
echo "ERROR: cannot find $gcam" | tee -a $LF
exit 1;
endif
set dstreg =
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
set cmd = (mri_vol2vol --vsm-pedir $pedir --gcam $mask $reg $gcam
$dstreg)
if($UseB0DC) set cmd = ($cmd $b0dcmap)
if(! $UseB0DC) set cmd = ($cmd 0)
set cmd = ($cmd 0 $outmask)
endif
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Take intersection with whole brain
set mask = $brainmask
if($ApplySubCortMask) set mask = $subcortmask
set cmd = (mri_mask $outmask $mask $outmask)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
else
echo "$outmask does not need updating" | tee -a $LF
endif
end # Loop over runs
# Merge run-level masks and prune
set prmasklist = ()
foreach Run ($RunList)
set prmask = $sess/$fsd/$Run/$maskdir/$maskstem$ExpKey.pr.$outfmt
set prmasklist = ($prmasklist $prmask)
end
set finalmask = $sess/$fsd/$maskdir/$maskstem$ExpKey.$outfmt
set UpdateNeeded = `UpdateNeeded $finalmask $prmasklist`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded) then
set cmd = (mri_concat --o $finalmask --mean $prmasklist)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
set cmd = (mri_binarize --i $finalmask --min 10e-10 --o $finalmask)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Now copy it to each run, remove the .pr
foreach Run ($RunList)
set prmask = $sess/$fsd/$Run/$maskdir/$maskstem$ExpKey.$outfmt
cp $finalmask $prmask |& tee -a $LF
if($status) exit 1;
end
else
echo "$finalmask does not need updating" | tee -a $LF
endif
endif
# Convert the native functional space data to mni305/cvs
foreach Run ($RunList)
echo " $nthsess/$#SessList $sessid $Run ----------------" |& tee -a $LF
echo " `date`" |& tee -a $LF
set funcdir = $sess/$fsd/$Run
# Get the mask and reg to use
if($PerRun) then
set outmask = $sess/$fsd/$Run/$maskdir/$maskstem$ExpKey.$outfmt
set reg = $sess/$fsd/$Run/$regfile
else
set outmask = $sess/$fsd/$maskdir/$maskstem$ExpKey.$outfmt
set reg = $sess/$fsd/$regfile
endif
set invol = `stem2fname $funcdir/$instem`
if($status) then
echo "$invol" |& tee -a $LF
exit 1;
endif
set outvol = $funcdir/$outstem$ExpKey.$outfmt
set UpdateNeeded = `UpdateNeeded $outvol $invol $reg $outmask`;
if(! $UpdateOnly) set UpdateNeeded = 1;
if($UpdateNeeded == 0) then
echo " $sessid $Run Update not needed" | tee -a $LF
continue
endif
if($UseCVS == 0) then
set cmd = (mri_vol2vol --mov $invol --reg $reg \
--tal --talres $res --talxfm $talxfm --interp $interp \
--no-save-reg --o $outvol)
if($UseB0DC) set cmd = ($cmd --vsm $b0dcmap $pedir)
else
set gcam =
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
if(! -e $gcam) then
echo "ERROR: cannot find $gcam" | tee -a $LF
exit 1;
endif
set dstreg =
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta
set cmd = (mri_vol2vol --vsm-pedir $pedir --gcam $invol $reg $gcam
$dstreg)
if($UseB0DC) set cmd = ($cmd $b0dcmap)
if(! $UseB0DC) set cmd = ($cmd 0)
set cmd = ($cmd 0 $outvol)
endif
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Smooth if desired
if($fwhm > 0) then
set cmd = (mri_fwhm --i $outvol --o $outvol --smooth-only)
if($#fwhm) set cmd = ($cmd --fwhm $fwhm); # 3D smoothing
if($MaskedSmoothing) set cmd = ($cmd --mask $outmask)
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
end # Loop over runs
end # foreach sess ($SessList)
echo "" |& tee -a $LF
date |& tee -a $LF
echo "rawfunc2tal-sess completed " |& tee -a $LF
exit 0;
############--------------##################
parse_args:
set cmdline = "$argv";
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "-i":
case "-instem":
if ( $#argv == 0) goto arg1err;
set instem = $argv[1]; shift;
breaksw
case "-fsd":
if ( $#argv == 0) goto arg1err;
set fsd = $argv[1]; shift;
breaksw
case "-runlistfile":
case "-rlf":
if ( $#argv == 0) goto arg1err;
set RunListFile = $argv[1]; shift;
breaksw
case "-fwhm":
if ( $#argv == 0) goto arg1err;
set fwhm = $argv[1]; shift;
breaksw
case "-cvs"
set target = cvs_avg35_inMNI152;
set UseCVS = 1;
set res = 2;
breaksw
case "-no-masked-smooth":
set MaskedSmooth = 0;
set ExpKeyNeeded = 1;
breaksw
case "-per-run":
case "-perrun":
set PerRun = 1;
breaksw
case "-per-session":
case "-no-per-run":
case "-no-perrun":
set PerRun = 0;
#set ExpKeyNeeded = 1;
breaksw
case "-update":
set UpdateOnly = 1;
breaksw
case "-force":
set UpdateOnly = 0;
breaksw
case "-nearest":
set interp = "nearest"
set ExpKeyNeeded = 1;
breaksw
case "-subcort-mask":
case "-subcort":
set ApplySubCortMask = 1;
breaksw
case "-no-subcort-mask":
case "-no-subcort":
set ApplySubCortMask = 0;
breaksw
case "-trilin":
set interp = "trilin"
breaksw
case "-1mm":
set res = 1;
breaksw
case "-xfm":
if($#argv < 1) goto arg1err;
set talxfm = $argv[1]; shift;
set ExpKeyNeeded = 1;
breaksw
case "-stc":
case "-sliceorder":
case "-so":
if ( $#argv == 0) goto arg1err;
set SliceOrder = $argv[1]; shift;
if($SliceOrder != siemens && $SliceOrder != up && $SliceOrder != down && \
$SliceOrder != odd && $SliceOrder != even && $SliceOrder != none) then
echo "ERROR: -stc is $SliceOrder, must be siemens, up, down, odd,
even, or none"
exit 1;
endif
breaksw
case "-sdf":
if ( $#argv == 0) goto arg1err;
set SliceDelayFile = $argv[1]; shift;
set DoSTC = 1;
breaksw
case "-reg":
if($#argv < 1) goto arg1err;
set regfile = $argv[1]; shift;
set ExpKeyNeeded = 1;
breaksw
case "-expkey":
if($#argv < 1) goto arg1err;
set ExpKey = $argv[1]; shift;
set ExpKey = (.$ExpKey); # prepend a dot
breaksw
case "-dof":
if ($#argv < 1) goto arg1err;
set RegDOF = $argv[1]; shift;
breaksw
case "-b0dc":
case "-b0dcor":
case "-vsm":
set UseB0DC = 1;
set ExpKey = ".b0dc"
breaksw
# these should not be used
case "-o":
case "-outstem":
if ( $#argv == 0) goto arg1err;
set outstem = $argv[1]; shift;
breaksw
case "-mask":
# output mask stem
if ( $#argv == 0) goto arg1err;
set maskstem = $argv[1]; shift;
breaksw
case "-no-mc":
set mc = ""
breaksw
case "-nolog":
set nolog = 1;
breaksw
case "-debug":
set debug = 1;
set verbose = 1;
set echo = 1;
breaksw
case "-cwd":
breaksw
case "-s":
case "-sf":
case "-df":
case "-d":
case "-g":
shift;
breaksw
default:
echo ERROR: Flag $flag unrecognized.
echo $cmdline
exit 1
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($#fwhm == 0) then
echo "ERROR: you must enter a FWHM. Use 0 for no smoothing."
exit 1;
endif
if($ExpKeyNeeded && $#ExpKey == 0) then
echo "ERROR: experts key needed (-expkey)"
exit 1;
endif
if($#instem == 0) then
# Note that if no MC, then there will be no "pr" appended
set instem = f${mc}
if($mc != "" && $PerRun) set instem = fmcpr
if($#SliceOrder != 0) set instem = $instem.$SliceOrder
if($#SliceDelayFile != 0) set instem = $instem.sdf
endif
if($#outstem == 0) set outstem = $instem
set outstem = $outstem.sm$fwhm.$target.$res"mm"
if($#maskstem == 0) set maskstem = $maskname
set maskstem = $maskstem.$target.$res"mm"
if($#regfile == 0) then
if(! $UseB0DC) set regfile = register.dof$RegDOF.lta
if($UseB0DC) set regfile = register.dof$RegDOF.b0dc.lta
endif
if($UseCVS == 0) then
if($res == 2) then
set subcortmask =
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
set brainmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/brainmask.mgz
else
set subcortmask =
$FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz
set brainmask = $FREESURFER_HOME/subjects/fsaverage/mri/brainmask.mgz
endif
else
set subcortmask =
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz
set brainmask =
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/brainmask.mgz
endif
if($ApplySubCortMask && ! -e $subcortmask) then
echo "ERROR: cannot find $subcortmask"
exit 1;
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo "rawfunc2tal-sess"
echo ""
echo " Session Arguments (some required)"
echo " -sf sessidfile ..."
echo " -df srchdirfile ..."
echo " -s sessid ..."
echo " -d srchdir ..."
echo ""
echo " -fwhm FWHMmm : smooth by FWHM mm (enter 0 for no smoothing)"
echo ""
echo " Optional Arguments"
echo " -1mm : set output resolution to 1mm (default is 2mm)"
echo " -i instem : default is fmcpr"
echo " -fsd dir : functional subdirectory ($fsd)"
echo " -rlf RLF : run-list file"
echo ""
echo "Expert Options"
echo " -no-masked-smooth : do not mask when smoothing"
echo " -nearest : use nearest neighbor interp (default is trilin)"
echo " -xfm tal.xfm : xfm file found in subject/mri/transforms (default is
$talxfm)"
echo " -reg regfile : default is register.dof$RegDOF.lta"
echo " -per-session : use session-level registration and mask instead of
-per-run"
echo " -no-subcort-mask : do not apply subcortical mask"
echo " -cvs : use cvs_avg35_inMNI152 instead of MNI305 (res fixed at 2mm)"
echo " -dof DOF"
echo ""
echo "Other options"
echo " -update : only run if update is needed"
echo " -force : force an update (default)"
echo " -version : print version and exit"
echo " -debug"
echo ""
if(! $PrintHelp ) exit 1;
echo " "
echo "$VERSION "
echo " "
cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;
#---- Everything below here is printed out as part of help -----#
BEGINHELP
Resamples raw data into "talairach" space. This is MNI305 space
sampled at 2mm isotropic.
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