Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Freesurfer tool to automatically generate label surrounding a given vertex?
by Martha Shiell 22 Feb '16

22 Feb '16

Hello Freesurfer community, I am looking for a way to automatically generate a surface label file of a specific dimension (e.g. a circle with a specific diameter, or a square), given a specific vertex and some measure of the desired size. I have considered to do so by starting with a label file consisting of a single vertex, and then expanding this label with the mri_label2label tool, using the --dilate option. I wanted to know though if anyone has any better suggestions. Thank you, Martha -- Martha M. Shiell, PhD

8 15

Longitudinal results questions
by Hutton, Seth 22 Feb '16

22 Feb '16

Hello FreeSurfers, My lab has been using the longitudinal processing stream for our data set and seem to be getting some potentially troublesome results. The attached images present a snap shot of the issues we are encountering. As you can see in the left image, there seems to be some kind of shifting going on. However, when you view each individual T1 with their corresponding boundary maps they look spot on. My question is whether or not this will have any major implication when we are trying to do a longitudinal analysis of cortical thickness? The more troublesome issue which is shown on the right is an overall "messiness" that seems to occur in some scans. When looking back at the template and the original FreeSurfer images there doesn't appear to be any issue. It's only when the longitudinal image is constructed that there seems to be some exaggerated blur as well as some over inclusions of dura (this isn't shown in the image but has happened in a handful of our subjects). Has anyone else experienced these kinds of issues? Only a quarter of our subjects that look as good "quality wise" as the examples posted on your wiki. Thanks, Seth Hutton ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

2 1

Use of gcs altlas with freesurfer on T1 image
by Thomas Jacquemont 22 Feb '16

22 Feb '16

Dear FreeSurfer experts, I would like to use the P. Hagmann atlas (Lausanne 2008 available here https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs) on my subjects. I ran Recon all on their T1 images and then these two commands to get the Hagmann parcellation for my subject: mris_ca_label -dir ../subject_dir/003_S_2374 rh sphere.reg /aramis/home/jacquemont/DataAramis/Atlas/Hagmann/myatlas_250_rh.gcs ./test_sub_003_S_2374.rh.Hagmann500.annot mri_label2vol --subject 003_S_2374 --hemi rh --annot ./test_sub_003_S_2374.rh.Hagmann500.annot --temp ../subject_dir/003_S_2374/mri/orig/001.mgz --o annoted_volume_Hagmann500_003_S_2374.mgz --identity I have two questions. First, looking at the recon all log file I saw that the command is used this way: #@# Cortical Parc lh mardi 19 janvier 2016, 23:32:45 (UTC+0100) mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NameSubject_M0 lh ../surf/lh.sphere.reg /path/to/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot I would like to know what is the "seed" option? Do I need it? Secondly, By surperimposed the resulting parcellation file (output of the mri_label2vol command) to the repective T1 image it seems that they are not in the same space. How could I have the pacellated file in the same space as the T1 image? Is the way I am using these two command good? What inputs should I change? The sphere file (for mris_ca_label), the --temp (for mri_label2vol), etc... Thank you for your help, Yours faithfully, Thomas

4 4

Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?
by Karas, Marta 22 Feb '16

22 Feb '16

H! I am working with data which is an output from the FreeSurfer processing. I would like to kindly ask you to refer me to materials / precise "mathematical" definitions that could help to understand what are the following parameters: * ?MeanCurv - Integrated Rectified Mean Curvature, * GausCurv - Integrated Rectified Gaussian Curvature, * FoldInd - Folding Index, * CurvInd - Intrinsic Curvature Index. (I have been trying to google but not been successful, unfortunately.) Kind regards, Marta Karas, M.S. Research Assistant, Department of Biostatistics Richard M. Fairbanks School of Public Health and School of Medicine Indiana University tel: 317-665-4551 email: mkaras(a)iu.edu<mailto:harezlak@iu.edu>

4 4

comparison between two hemisphere in single
by Ashkan Faghiri 22 Feb '16

22 Feb '16

Thank you doug for you answer. So now I have two other question. 1- how can I check the inter hemisphere registration quality? e.g. can I check if the parcellation for the two hemisphere are matched well? or there is other ways? 2- how can I correct for multiple correction for single subject? calculate the p vale for each vertex (to find significant difference between the two hemisphere) and correct these for multiple correction. Regards, Ashkan > What is your mris_preproc command line? If you run mris_preproc with > --xhemi, it should give you two frames (left hemi and right hemi). If > you want to compute left-right, then add --paired-diff to the command > line. The output will be on the lh of fsaverage_sym. This can be > displayed on the white, pial, or inflated of fsaverage_sym. You can use > mris_apply_reg to map this back to the subject's native surface if you > want to display it there. > doug > > On 2/19/16 9:18 AM, Ashkan Faghiri wrote: > > Hello, > > > > sorry for asking this again > > > > I want to calculate the difference between the thickness of one > > subjects different hemispheres and show this on pial (left or right or > > even fsaverage_sys). so I have ran : > > > > surfreg --s $subject --t fsaverage_sym --lh > > surfreg --s $subject --t fsaverage_sym --lh --xhemi > > > > for my one subject. now I have two .reg files: > > shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg > > shahi/surf/lh.fsaverage_sym.sphere.reg > > > > If I am understanding this right, these two are the transform matrix > > for both hemisphere of my one subject to fsaverage_sym (*right?*) > > > > if I run mris_preproc with xhemi option I will get a vector which have > > the length equal to number of vertexes. it's values are left-right > > (*or right-left?*). how can I convert this vector to pial or inflated > > surface? and how can I use lh.fsaverage_sym.sphere.reg to register my > > pial directly to fsaverage_sym? > > > > Regards, > > Ashkan > > -- > > -- > > Ashkan Faghiri > > MSc student of Bioelectrical Engineering > > Department of Electrical Engineering > > Sharif University of Technology > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

2 1

longitudinal analysis Repeated Measures ANOVA 2x2
by María Díez Cirarda 22 Feb '16

22 Feb '16

Dear FS experts, I am trying to do a longitudinal analysis with a Repeated Measures ANOVA 2x2, with two groups (experimental and control group) and two times (pre and post treatment). First, I have followed the Longitudinal Processing Tutorial: 1) I have 2 acquisitions per subject so, I created a subject template (BASE) for each pair of subjects 2) I created the two longitudinal runs Now I am confused, because I don´t know wether I have to: 1) do a Longitudinal QDEC table with two columns (time and group) or 2) create a FSGD File, (or a DOSS file?) and create the contrasts. If I have to create the FSGD file, Would this be OK? GroupDescriptorFile 1 Class Subject 1 Class Subject 2 Variables Tp1vsTp2.Gr1Exp Tp1vsTp2.Gr2Control Input Subject1-tp1 Subject1 1 0 Input Subject1-tp2 Subject1 -1 0 Input Subject2-tp1 Subject2 0 1 Input Subject2-tp2 Subject2 0 -1 Contrasts: Mtx file: 0 0 1 0 0 0 0 -1 0 0 1 -1 Were do I have to create the FSGD file? In subjects folder or inside qdec folder? The group descriptor file must be "subject1" "subject2", or should I introduce the specific names of the folders from the subjects of my study? Thank you in advance, Maria.

2 3

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

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