Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

FLAIR registration
by K. Wagstyl 22 Feb '16

22 Feb '16

Hi all, We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial However for the other half the FLAIR registrations are either a bit off or completely flipped, including swapping axes. This then affects the generate surfaces. The problem line seems to be: bbregister --s <subjid> --mov mri/orig/FLAIRraw.mgz --lta mri/transforms/FLAIRraw.lta --init-fsl --T2 as the output registration of these files is incorrect. We've tried using mri_convert instead of dcm2nii. This does not solve the problem. Loading the FLAIR.nii in fslview, the image is upside down, but the letters indicating orientation are correct. Do you have any suggestions about how to solve this problem? Thanks, Konrad

2 3

Building from source -- [wishlist] please version the -packages.tar.gz
by Yaroslav Halchenko 21 Feb '16

21 Feb '16

ATM ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… has no versioned counterpart. Could you please provide some versioning e.g. by actually having centos6-x86_64-packages-0.0.20151104.tar.gz (based on its modification date, 0.0. to signal that it is not much of a real version), or following any other versioning scheme (e.g. base on version of freesurfer they were produced for) with centos6-x86_64-packages.tar.gz symlink pointing to it, so webserver (if FollowSymlinks) still resolving to that tarball Cheers, -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik

2 1

R: Re: R: Re: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 21 Feb '16

21 Feb '16

I have checked MRS_MASK.mg and all its voxels have a value=1. All voxels contains in the mask are well overlapped on f.nii. The registration is accurate: the MRS mask is located on the vmPFC and its is equally distributed on left and right hemisphere. The orig.nii.gz and f.nii.gz is well overlapped, as well the MRS mask. mri_convert $SUBJECTS_DIR/subj2/FS_space_MRS_voxel_maskFS_space_MRS_voxel_mask. nii.gz $SUBJECTS_DIR/subj2/mri/MRS_MASK.mgz mri_convert $SUBJECTS_DIR/subj2/FS_space_MRS_voxel_mask.nii.gz MRS_MASK.mgz fcseed-config -segid 1 -seg MRS_MASK.mgz -fsd rest -mean -cfg MRS_MASK.config - overwrite fcseed-sess -s subj2 -cfg MRS_MASK.config -overwrite -debug set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 0 == 0 ) then set SearchPathList = "." ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( subj2 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./subj2 if ( -d $stst ) then if ( -d ./subj2 ) then if ( ! -r $stst ) then if ( ! -r ./subj2 ) then pushd $stst > /dev/null ; pushd ./subj2 set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd > /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound > 1 ) then if ( 1 > 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /Applications/freesurfer/subjects/fMRI/subj2 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /Applications/freesurfer/subjects/fMRI/subj2 ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique && ! $AllowRedundant ) then if ( ! 1 && ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /Applications/freesurfer/subjects/fMRI/subj2 ) endif endif end end echo $SessPath echo /Applications/freesurfer/subjects/fMRI/subj2 exit $errs ; exit 0 set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#fcconfig == 0 ) then if ( 1 == 0 ) then set fcname = `cat $fcconfig | awk '{if($1 == "fcname") print $2}'` set fcname = `cat $fcconfig | awk '{if($1 == "fcname") print $2}'` cat MRS_MASK.config awk {if($1 == "fcname") print $2} set fsd = `cat $fcconfig | awk '{if($1 == "fsd") print $2}'` set fsd = `cat $fcconfig | awk '{if($1 == "fsd") print $2}'` cat MRS_MASK.config awk {if($1 == "fsd") print $2} set segstem = `cat $fcconfig | awk '{if($1 == "segstem") print $2}'` set segstem = `cat $fcconfig | awk '{if($1 == "segstem") print $2}'` cat MRS_MASK.config awk {if($1 == "segstem") print $2} set RegDOF = `cat $fcconfig | awk '{if($1 == "RegDOF") print $2}'` set RegDOF = `cat $fcconfig | awk '{if($1 == "RegDOF") print $2}'` cat MRS_MASK.config awk {if($1 == "RegDOF") print $2} set FillThresh = `cat $fcconfig | awk '{if($1 == "FillThresh") print $2}'` set FillThresh = `cat $fcconfig | awk '{if($1 == "FillThresh") print $2}'` cat MRS_MASK.config awk {if($1 == "FillThresh") print $2} set DoMean = `cat $fcconfig | awk '{if($1 == "DoMean") print $2}'` set DoMean = `cat $fcconfig | awk '{if($1 == "DoMean") print $2}'` cat MRS_MASK.config awk {if($1 == "DoMean") print $2} set DoSVD = `cat $fcconfig | awk '{if($1 == "DoSVD") print $2}'` set DoSVD = `cat $fcconfig | awk '{if($1 == "DoSVD") print $2}'` cat MRS_MASK.config awk {if($1 == "DoSVD") print $2} set DoSqr = `cat $fcconfig | awk '{if($1 == "DoSqr") print $2}'` set DoSqr = `cat $fcconfig | awk '{if($1 == "DoSqr") print $2}'` cat MRS_MASK.config awk {if($1 == "DoSqr") print $2} if ( $#MakeMask == 0 ) set MakeMask = `cat $fcconfig | awk '{if($1 == "MakeMask") print $2}'` if ( 0 == 0 ) set MakeMask = `cat $fcconfig | awk '{if($1 == "MakeMask") print $2}'` set MakeMask = `cat $fcconfig | awk '{if($1 == "MakeMask") print $2}'` cat MRS_MASK.config awk {if($1 == "MakeMask") print $2} set WMErode = `cat $fcconfig | awk '{if($1 == "WMErode") print $2}'` set WMErode = `cat $fcconfig | awk '{if($1 == "WMErode") print $2}'` cat MRS_MASK.config awk {if($1 == "WMErode") print $2} set SVDSynth = `cat $fcconfig | awk '{if($1 == "SVDSynth") print $2}'` set SVDSynth = `cat $fcconfig | awk '{if($1 == "SVDSynth") print $2}'` cat MRS_MASK.config awk {if($1 == "SVDSynth") print $2} set DoWM = `cat $fcconfig | awk '{if($1 == "DoWM") print $2}'` set DoWM = `cat $fcconfig | awk '{if($1 == "DoWM") print $2}'` cat MRS_MASK.config awk {if($1 == "DoWM") print $2} set rlf = `cat $fcconfig | awk '{if($1 == "RunListFile") print $2}'` set rlf = `cat $fcconfig | awk '{if($1 == "RunListFile") print $2}'` cat MRS_MASK.config awk {if($1 == "RunListFile") print $2} set roicfg = `cat $fcconfig | awk '{if($1 == "roicfg") print $2}'` set roicfg = `cat $fcconfig | awk '{if($1 == "roicfg") print $2}'` cat MRS_MASK.config awk {if($1 == "roicfg") print $2} set tmp = `cat $fcconfig | awk '{if($1 == "segidlist") print $0}'` set tmp = `cat $fcconfig | awk '{if($1 == "segidlist") print $0}'` cat MRS_MASK.config awk {if($1 == "segidlist") print $0} if ( $#tmp ) set segidlist = ( $tmp[2-$#tmp] ) ; if ( 2 ) set segidlist = ( 1 ) set segidlist = ( 1 ) set UseB0DC = 0 ; set UseB0DC = 0 set tmp = `cat $fcconfig | awk '{if($1 == "UseB0DC") print $0}'` set tmp = `cat $fcconfig | awk '{if($1 == "UseB0DC") print $0}'` cat MRS_MASK.config awk {if($1 == "UseB0DC") print $0} if ( $#tmp ) set UseB0DC = $tmp[2] ; if ( 2 ) set UseB0DC = 0 set UseB0DC = 0 if ( $MakeMask ) set maskfile = $fcname.mask if ( 0 ) set maskfile = MRS_MASK.mask if ( $#roicfg ) then if ( 0 ) then if ( $#regfilename == 0 ) then if ( 0 == 0 ) then if ( ! $UseB0DC ) set regfilename = register.dof$RegDOF.dat if ( ! 0 ) set regfilename = register.dof6.dat set regfilename = register.dof6.dat if ( $UseB0DC ) set regfilename = register.dof$RegDOF.b0dc.dat if ( 0 ) set regfilename = register.dof6.b0dc.dat endif endif goto check_params_return ; goto check_params_return set ProjectDir = `pwd` ; set ProjectDir = `pwd` pwd if ( ! $nolog ) then if ( ! 0 ) then mkdir -p log mkdir -p log set LF = $ProjectDir/log/fcseed-sess.$fcname.log set LF = /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log if ( $#SessList == 1 ) then if ( 1 == 1 ) then set sessid = `basename $SessList` ; set sessid = `basename $SessList` basename /Applications/freesurfer/subjects/fMRI/subj2 set LF = $LF.$sessid set LF = /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 endif endif rm -f $LF rm -f /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 else else echo Logfile is $LF echo Logfile is /Applications/freesurfer/subjects/fMRI/log/fcseed-sess. MRS_MASK.log.subj2 Logfile is /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 date | tee -a $LF date tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 Sun Feb 21 12:21:37 CET 2016 uname -a | tee -a $LF uname -a tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 echo setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova echo "cd `pwd`" | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 echo cd `pwd` pwd cd /Applications/freesurfer/subjects/fMRI echo $0 | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 echo /Applications/freesurfer/fsfast/bin/fcseed-sess /Applications/freesurfer/fsfast/bin/fcseed-sess echo $cmdargs | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 echo -s subj2 -cfg MRS_MASK.config -overwrite -debug -s subj2 -cfg MRS_MASK.config -overwrite -debug cat $FREESURFER_HOME/build-stamp.txt | tee -a $LF cat /Applications/freesurfer/build-stamp.txt tee -a /Applications/freesurfer/subjects/fMRI/log/fcseed-sess.MRS_MASK.log. subj2 freesurfer-Darwin-lion-stable-pub-v5.3.0 cat $fcconfig >> $LF cat MRS_MASK.config foreach sess ( $SessList ) foreach sess ( /Applications/freesurfer/subjects/fMRI/subj2 ) set sessid = `basename $sess` ; set sessid = `basename $sess` basename /Applications/freesurfer/subjects/fMRI/subj2 set subject = `cat $sess/subjectname` set subject = `cat $sess/subjectname` cat /Applications/freesurfer/subjects/fMRI/subj2/subjectname set RunList = ( `getrunlist $sess/$fsd $rlf` ) ; set RunList = ( `getrunlist $sess/$fsd $rlf` ) getrunlist /Applications/freesurfer/subjects/fMRI/subj2/rest foreach Run ( $RunList ) foreach Run ( 002 ) set rundir = $sess/$fsd/$Run set rundir = /Applications/freesurfer/subjects/fMRI/subj2/rest/002 set LLF = $rundir/$fcname.log set LLF = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log rm -f $LLF rm -f /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log date | tee -a $LLF date tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log Sun Feb 21 12:22:08 CET 2016 uname -a | tee -a $LLF uname -a tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova echo "cd `pwd`" | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo cd `pwd` pwd cd /Applications/freesurfer/subjects/fMRI echo $0 | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo /Applications/freesurfer/fsfast/bin/fcseed-sess /Applications/freesurfer/fsfast/bin/fcseed-sess echo $cmdargs | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo -s subj2 -cfg MRS_MASK.config -overwrite -debug -s subj2 -cfg MRS_MASK.config -overwrite -debug cat $FREESURFER_HOME/build-stamp.txt | tee -a $LLF cat /Applications/freesurfer/build-stamp.txt tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log freesurfer-Darwin-lion-stable-pub-v5.3.0 echo "" | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo set outfile = $rundir/$fcname set outfile = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK set UpdateNeeded = 0 ; set UpdateNeeded = 0 if ( ! -e $outfile ) set UpdateNeeded = 1 ; if ( ! -e /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK ) set UpdateNeeded = 1 set UpdateNeeded = 1 if ( $UpdateNeeded == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $fcconfig` if ( 1 == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $fcconfig` if ( $#segidlist || $DoWM ) then if ( 1 || 0 ) then set f = `stem2fname $rundir/$funcstem` set f = `stem2fname $rundir/$funcstem` stem2fname /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr if ( $status ) then if ( 0 ) then set reg = $rundir/$regfilename set reg = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6. dat if ( $UpdateNeeded == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $f` if ( 1 == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $f` if ( $UpdateNeeded == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $reg` if ( 1 == 0 ) set UpdateNeeded = `UpdateNeeded $outfile $reg` else else if ( $UpdateOnly && ! $UpdateNeeded ) then if ( 0 && ! 1 ) then rm -f $outfile rm -f /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK set tmpdir = $rundir/tmp.fcseed-sess.$$ set tmpdir = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187 rm -rf $tmpdir rm -rf /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187 mkdir -p $tmpdir mkdir -p /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187 if ( $#segidlist || $DoWM ) then if ( 1 || 0 ) then set template = `stem2fname $rundir/template` set template = `stem2fname $rundir/template` stem2fname /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template if ( $DoWM ) then if ( 0 ) then set seganat = $SUBJECTS_DIR/$subject/mri/$segstem.mgz set seganat = /Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz endif endif set seg = $tmpdir/seg.$FSF_OUTPUT_FORMAT set seg = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/seg.nii.gz set pvf = $tmpdir/pvf.$FSF_OUTPUT_FORMAT ; set pvf = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/pvf.nii.gz set cmd = ( mri_label2vol --seg $seganat --reg $reg --temp $template -- fillthresh $FillThresh --o $seg --pvf $pvf ) ; set cmd = ( mri_label2vol --seg /Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz -- fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp. fcseed-sess.32187/seg.nii.gz --pvf /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf. nii.gz ) echo $cmd | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo mri_label2vol --seg /Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz -- fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp. fcseed-sess.32187/seg.nii.gz --pvf /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf. nii.gz mri_label2vol --seg /Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz -- fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp. fcseed-sess.32187/seg.nii.gz --pvf /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf. nii.gz $cmd | tee -a $LLF mri_label2vol --seg /Applications/freesurfer/subjects/subject_prova/subj2/mri/MRS_MASK.mgz --reg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat --temp /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz -- fillthresh .5 --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp. fcseed-sess.32187/seg.nii.gz --pvf /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/pvf. nii.gz tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log PVF /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Applications/freesurfer/subjects/fMRI/subj2/rest/002/template.nii.gz Outut Volume: /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/seg.nii.gz Registration File: /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -0.278 0.000 0.000 32.000; -0.000 -0.000 -0.278 32.000; -0.000 0.200 0.000 10.500; 0.000 0.000 0.000 1.000; Template Voxel Volume: 64.5752 nHits Thresh: 32.2876 Loading registration from /Applications/freesurfer/subjects/fMRI/subj2/rest/002/register.dof6.dat RegMat: -------- -0.998 0.003 0.070 1.814; 0.070 -0.089 0.994 -26.255; -0.009 -0.996 -0.088 -3.555; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- 0.278 -0.001 -0.020 31.495; 0.003 0.277 0.025 32.989; 0.014 -0.018 0.199 5.249; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 0 (0 filled) ASeg2Vol: done PVF /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/pvf.nii.gz Computing PVF 64.5752 if ( $status ) exit 1 ; if ( 0 ) exit 1 if ( $#maskfile ) then if ( 0 ) then set mask = $tmpdir/mask.$FSF_OUTPUT_FORMAT set mask = /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz endif endif set cmd = ( mri_binarize --i $seg --o $mask ) set cmd = ( mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg. nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz ) foreach id ( $segidlist ) foreach id ( 1 ) set cmd = ( $cmd --match $id ) set cmd = ( mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg. nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz --match 1 ) end end echo $cmd | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg. nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz --match 1 mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp. fcseed-sess.32187/seg.nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/mask.nii.gz --match 1 $cmd | tee -a $LLF mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp. fcseed-sess.32187/seg.nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/mask.nii.gz --match 1 tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /Applications/freesurfer/subjects/fMRI cmdline mri_binarize --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess.32187/seg. nii.gz --o /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz --match 1 sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano input /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/seg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done if ( $status ) exit 1 ; if ( 0 ) exit 1 else else if ( $DoMean ) then if ( 1 ) then set cmd = ( mri_segstats --i $f --seg $mask --id 1 --sum $tmpdir/junk.sum -- avgwfvol $tmpdir/avgwf.mgh ) set cmd = ( mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/avgwf.mgh ) echo $cmd | tee -a $LLF tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log echo mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/avgwf.mgh mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr. nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/avgwf.mgh $cmd | tee -a $LLF mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr. nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/avgwf.mgh tee -a /Applications/freesurfer/subjects/fMRI/subj2/rest/002/MRS_MASK.log $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz --seg /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/mask.nii.gz --id 1 --sum /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/junk.sum --avgwfvol /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/avgwf.mgh sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano UseRobust 0 Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed-sess. 32187/mask.nii.gz Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/002/fmcpr.nii.gz Voxel Volume is 64.5752 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Applications/freesurfer/subjects/fMRI/subj2/rest/002/tmp.fcseed- sess.32187/avgwf.mgh Segmentation fault if ( $status ) exit 1 ; if ( 139 ) exit 1 exit 1 >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 18.04 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: FS-FAST using MRS voxel or .label as seed > > >Make sure that the MRS_MASK.mgz itself has some voxels with value=1, and >make sure that there are enough of them to fit into at least one >functional voxel. > >Make sure that the registration is accurate. > >When you run run fcseed-sess, add -debug, capture the output, and send >it to me. > > >On 02/18/2016 06:43 PM, stdp82(a)virgilio.it wrote: >> The problem persist. >> >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >>> Data: 19-feb-2016 0.25 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed >>> >>> >>> I think it may be our fcseed-config command line >>> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >>> rest -mean -cfg MRS_MASK.config –overwrite >>> >>> It should be -seg MRS_MASK.mgz >>> >>> They way you have it, fcseed will use the segmentation for Subj for all >>> subjects, which is why it works for one and not for others >>> >>> >>> On 02/18/2016 06:10 PM, stdp82(a)virgilio.it wrote: >>>> Hi list, >>>> >>>> I'm having problem to use FS-FAST fMRI connectivity using as seed a >>>> mask of a MRS voxel or .label obtained by drawing it from surface. In >>>> order to resolve my concern, I'm reporting step by step the command >>>> lines which I have used. The mask, f.nii.gz, orig.nii.gz and >>>> aparc+aseg.nii.gz showed a good overlap. >>>> >>>> These are the features of each one: >>>> >>>> fslinfo orig.nii.gz >>>> >>>> data_type UINT8 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 2 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.010747 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> fslinfo aparc+aseg.nii.gz >>>> >>>> data_type INT32 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 8 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.010747 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> fslinfo MRS_MASK.nii.gz >>>> >>>> data_type FLOAT32 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 16 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.000000 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> I’m using MNI2mm for subcortical analysis. >>>> >>>> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >>>> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >>>> >>>> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >>>> rest -mean -cfg MRS_MASK.config –overwrite >>>> >>>> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh >>>> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >>>> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >>>> -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh >>>> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >>>> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >>>> -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask >>>> -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 >>>> -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >>>> MRS_MASK -o my-group >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >>>> MRS_MASK -o my-group >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >>>> MRS_MASK -o my-group >>>> >>>> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >>>> it seem to be functioning for the first subj, but the next subj2 show >>>> this error >>>> >>>> Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii. gz >>>> >>>> Voxel Volume is 64.5752 mm^3 >>>> >>>> Generating list of segmentation ids >>>> >>>> Found 1 segmentations >>>> >>>> Computing statistics for each segmentation >>>> >>>> 0 1 0 0.000 >>>> >>>> MRIalloc(0, 1, 1): bad parm >>>> >>>> Reporting on 0 segmentations >>>> >>>> Computing spatial average of each frame >>>> >>>> Writing to >>>> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess. >> 28328/avgwf.mgh >>>> Segmentation fault >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 Partners Compliance HelpLine >> at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >>> but does not contain patient information, please contact the sender and >> properly >>> dispose of the e-mail. >>> >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

R: Re: R: Re: R: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 20 Feb '16

20 Feb '16

I'm sorry but I do not understand my error. Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 18.05 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: FS-FAST using MRS voxel or .label as seed > >Yes, that is expected given your command line. > >On 02/18/2016 06:52 PM, stdp82(a)virgilio.it wrote: >> By running >> mri_cor2label --i $SUBJECTS_DIR/mri/MRS_MASK.nii.gz --id 1 --l MRS.label >> >> and opening the MRS.label by tksurfer fsaverage rh inflate -aparc -overlay MRS. >> label >> the inflate is empty. >> >> >> Stefano >> >> >> >>> ----Messaggio originale---- >>> Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >>> Data: 19-feb-2016 0.34 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: FS-FAST using MRS voxel or .label as seed >>> >>> That is an incorrect usage of mri_cor2label. MRS_MASK.nii.gz is a >>> volume, not a surface overlay. By using --surf, you are indicating that >>> it is a surface overlay >>> >>> On 02/18/2016 06:30 PM, stdp82(a)virgilio.it wrote: >>>> Furthermore, if I use mir_cor2label in order to show the location of >>>> MRS voxel (in native space) this error occurs: >>>> >>>> mri_cor2label --c $SUBJECTS_DIR/subj/MRS_MASK.nii.gz --id 1 --l >>>> MRS.label --surf fsaverage lh >>>> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >>>> Loading mri >>>> /Applications/freesurfer/subjects/subject_dir/subj/MRS_MASK.nii.gz >>>> Loading >>>> /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.white >>>> ERROR: dim mismatch between surface (163842) and input (16777216) >>>> >>>> ----Messaggio originale---- >>>> Da: stdp82(a)virgilio.it >>>> Data: 19-feb-2016 0.10 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: [Freesurfer] FS-FAST using MRS voxel or .label as seed >>>> >>>> Hi list, >>>> >>>> I'm having problem to use FS-FAST fMRI connectivity using as seed >>>> a mask of a MRS voxel or .label obtained by drawing it from >>>> surface. In order to resolve my concern, I'm reporting step by >>>> step the command lines which I have used. The mask, f.nii.gz, >>>> orig.nii.gz and aparc+aseg.nii.gz showed a good overlap. >>>> >>>> These are the features of each one: >>>> >>>> fslinfo orig.nii.gz >>>> >>>> data_type UINT8 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 2 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.010747 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> fslinfo aparc+aseg.nii.gz >>>> >>>> data_type INT32 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 8 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.010747 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> fslinfo MRS_MASK.nii.gz >>>> >>>> data_type FLOAT32 >>>> >>>> dim1 256 >>>> >>>> dim2 256 >>>> >>>> dim3 256 >>>> >>>> dim4 1 >>>> >>>> datatype 16 >>>> >>>> pixdim1 1.000000 >>>> >>>> pixdim2 1.000000 >>>> >>>> pixdim3 1.000000 >>>> >>>> pixdim4 0.000000 >>>> >>>> cal_max 0.0000 >>>> >>>> cal_min 0.0000 >>>> >>>> file_type NIFTI-1+ >>>> >>>> I’m using MNI2mm for subcortical analysis. >>>> >>>> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >>>> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >>>> >>>> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >>>> -fsd rest -mean -cfg MRS_MASK.config –overwrite >>>> >>>> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage >>>> lh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >>>> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >>>> -per-run -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage >>>> rh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >>>> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >>>> -per-run -overwrite >>>> >>>> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 >>>> -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 >>>> -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >>>> >>>> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >>>> MRS_MASK -o my-group >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >>>> MRS_MASK -o my-group >>>> >>>> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >>>> MRS_MASK -o my-group >>>> >>>> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >>>> it seem to be functioning for the first subj, but the next subj2 >>>> show this error >>>> >>>> Loading >>>> /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >>>> >>>> Voxel Volume is 64.5752 mm^3 >>>> >>>> Generating list of segmentation ids >>>> >>>> Found 1 segmentations >>>> >>>> Computing statistics for each segmentation >>>> >>>> 0 1 0 0.000 >>>> >>>> MRIalloc(0, 1, 1): bad parm >>>> >>>> Reporting on 0 segmentations >>>> >>>> Computing spatial average of each frame >>>> >>>> Writing to >>>> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed- sess. >> 28328/avgwf.mgh >>>> Segmentation fault >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 Partners Compliance HelpLine >> at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >>> but does not contain patient information, please contact the sender and >> properly >>> dispose of the e-mail. >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

1.5T GE dicom images into FreeSurfer
by pdavis＠westol.com 20 Feb '16

20 Feb '16

Hi, We would like to process 1.5 T GE dicom scans for over 200 individuals. It is unclear how to import these into FreeSurfer and process in batch. Each subject folder consists of several subfolders. Each subfolder consists of all the images of a single pulse sequence, e.g. sagittal spgr, axial T2, etc. The images in the subfolders are files labeled I.001.dcm, I.002.dcm, ... . Each image is a valid dicom image which can be individually opened in other dicom viewing programs. However, the entire series of images in the subfolder is not automatically recognized as a 3D set. Thank you, Peter Davis -------------------------------------------------------------------- mail2web.com ? What can On Demand Business Solutions do for you? http://link.mail2web.com/Business/SharePoint

2 1

Error in surface-based interhemispheric registration
by Ilaria Mazzonetto 20 Feb '16

20 Feb '16

Hi Freesurfer experts, I'm using freesurfer v5.2.0. If I use surfreg --s $subject --t fsaverage_sym --lh, I have this error: ERROR: cannot find /home/T1/fsaverage_sym/lh.reg.template.tif. Does anyone know how can I fix this? Thanks a lot. Ilaria

2 2

Fwd: Job Offer in Madrid
by José Ángel Pineda 20 Feb '16

20 Feb '16

We are pleased to offer a 2-year post-doctoral position at the Reina Sofia Foundation Alzheimer's Disease Centre in Madrid, Spain. The successful applicant will be involved in neuroimaging analyses of a 5-year longitudinal study (currently in year 4) of 1200 healthy elderly individuals (aged 70-85) to determine neuronal markers in the healthy state which predict subsequent development of mild cognitive impairment and dementia. In addition, the Reina Sofia Alzheimer's Centre offers: - A research-dedicated MRI facility attached to a 140-bed residence for patients with Alzheimer’s disease. - A brain-bank providing post-mortem histopathological confirmation of dementia diagnosis for patients scanned pre-mortem. - Ex-vivo MRI scanning. A strong background in neuroimaging techniques is required. Applicants must have a PhD in neuroscience, cognitive neuroscience, biomedical engineering, neuropsychology or related field. Experience in dementia research is a plus. Spanish language skills are NOT required. Competitive annual salary depending on experience. SUBMISSION Interested candidates should send CV and a cover letter (including contact details of 2 referees), to the following email address: bryan.strange(a)upm.es DEADLINE FOR SUBMISSION OF APPLICATIONS March 4, 2016 Any questions, please feel free to contact me.

1 0

Re: [Freesurfer] Building from source -- autoconf error
by Z K 20 Feb '16

20 Feb '16

Hello Yaroslav, Ive built freesurfer on Debian "Jessie" platform. It was just a matter of adding "libtool-bin" and "tcsh" to the list of packages that need to be installed. Ive update the wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out. -Zeke On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote: > Gotcha, thanks! > > On February 18, 2016 3:27:21 PM EST, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: >> >>> I would be infinitely grateful if freesurfer could build natively on >> Debian >>> stable! ;) Thanks for trying. In my case I am trying the build >> under jessie >>> chroot (using schroot helper), so I could quickly setup/enter such >> environment >>> while maintaining user/directory. I will do the same now for 14.04. >> If you >>> would like more -- let me know I could give a bit more detailed >>> instructions. >>> >> >> I have a debian jessie system just setup, but I have a high priority >> project due Monday, so I would be able to begin determining the exact >> build procedure on Debian jessie until beginning of next week. It is >> something I have been meaning to do so I plan on getting to it. If you >> dont hear from me by Tuesday/Wedensday feel free to shoot me an email >> for an update. Thanks. >> >> -Zeke >> >> >> 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 Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >

3 4

R: Re: R: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 19 Feb '16

19 Feb '16

By running mri_cor2label --i $SUBJECTS_DIR/mri/MRS_MASK.nii.gz --id 1 --l MRS.label and opening the MRS.label by tksurfer fsaverage rh inflate -aparc -overlay MRS. label the inflate is empty. Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 0.34 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: FS-FAST using MRS voxel or .label as seed > >That is an incorrect usage of mri_cor2label. MRS_MASK.nii.gz is a >volume, not a surface overlay. By using --surf, you are indicating that >it is a surface overlay > >On 02/18/2016 06:30 PM, stdp82(a)virgilio.it wrote: >> Furthermore, if I use mir_cor2label in order to show the location of >> MRS voxel (in native space) this error occurs: >> >> mri_cor2label --c $SUBJECTS_DIR/subj/MRS_MASK.nii.gz --id 1 --l >> MRS.label --surf fsaverage lh >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri >> /Applications/freesurfer/subjects/subject_dir/subj/MRS_MASK.nii.gz >> Loading >> /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.white >> ERROR: dim mismatch between surface (163842) and input (16777216) >> >> ----Messaggio originale---- >> Da: stdp82(a)virgilio.it >> Data: 19-feb-2016 0.10 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: [Freesurfer] FS-FAST using MRS voxel or .label as seed >> >> Hi list, >> >> I'm having problem to use FS-FAST fMRI connectivity using as seed >> a mask of a MRS voxel or .label obtained by drawing it from >> surface. In order to resolve my concern, I'm reporting step by >> step the command lines which I have used. The mask, f.nii.gz, >> orig.nii.gz and aparc+aseg.nii.gz showed a good overlap. >> >> These are the features of each one: >> >> fslinfo orig.nii.gz >> >> data_type UINT8 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 2 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo aparc+aseg.nii.gz >> >> data_type INT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 8 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo MRS_MASK.nii.gz >> >> data_type FLOAT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 16 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.000000 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> I’m using MNI2mm for subcortical analysis. >> >> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> >> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> -fsd rest -mean -cfg MRS_MASK.config –overwrite >> >> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage >> lh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >> -per-run -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage >> rh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >> -per-run -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 >> -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 >> -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >> MRS_MASK -o my-group >> >> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >> it seem to be functioning for the first subj, but the next subj2 >> show this error >> >> Loading >> /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >> >> Voxel Volume is 64.5752 mm^3 >> >> Generating list of segmentation ids >> >> Found 1 segmentations >> >> Computing statistics for each segmentation >> >> 0 1 0 0.000 >> >> MRIalloc(0, 1, 1): bad parm >> >> Reporting on 0 segmentations >> >> Computing spatial average of each frame >> >> Writing to >> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess. 28328/avgwf.mgh >> >> Segmentation fault >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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 Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

2 1

R: Re: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 19 Feb '16

19 Feb '16

The problem persist. Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 0.25 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed > > >I think it may be our fcseed-config command line >fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >rest -mean -cfg MRS_MASK.config –overwrite > >It should be -seg MRS_MASK.mgz > >They way you have it, fcseed will use the segmentation for Subj for all >subjects, which is why it works for one and not for others > > >On 02/18/2016 06:10 PM, stdp82(a)virgilio.it wrote: >> >> Hi list, >> >> I'm having problem to use FS-FAST fMRI connectivity using as seed a >> mask of a MRS voxel or .label obtained by drawing it from surface. In >> order to resolve my concern, I'm reporting step by step the command >> lines which I have used. The mask, f.nii.gz, orig.nii.gz and >> aparc+aseg.nii.gz showed a good overlap. >> >> These are the features of each one: >> >> fslinfo orig.nii.gz >> >> data_type UINT8 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 2 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo aparc+aseg.nii.gz >> >> data_type INT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 8 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo MRS_MASK.nii.gz >> >> data_type FLOAT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 16 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.000000 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> I’m using MNI2mm for subcortical analysis. >> >> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> >> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >> rest -mean -cfg MRS_MASK.config –overwrite >> >> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh >> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >> -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh >> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >> -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask >> -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 >> -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >> MRS_MASK -o my-group >> >> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >> it seem to be functioning for the first subj, but the next subj2 show >> this error >> >> Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >> >> Voxel Volume is 64.5752 mm^3 >> >> Generating list of segmentation ids >> >> Found 1 segmentations >> >> Computing statistics for each segmentation >> >> 0 1 0 0.000 >> >> MRIalloc(0, 1, 1): bad parm >> >> Reporting on 0 segmentations >> >> Computing spatial average of each frame >> >> Writing to >> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess. 28328/avgwf.mgh >> >> Segmentation fault >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)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 Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

2 1

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