Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Tools for FreeSurfer group analysis in R
by Andreas Berger 21 Jul '14

21 Jul '14

Hello FreeSurfers, during the course of my diploma thesis i wrote a few R functions around FreeSurfer, mainly for group analysis of FreeSurfer surface data in R. I thought i'd just contribute the code here, on the off chance that someone may find it useful, and despite the code quality (i wrote this as part of me learning R, so it may actually set your house on fire and so on). It could be of use for someone already working in R and looking to bring FreeSurfer data into it, or someone looking for an alternative to QDEC and the plots created by QDEC. Hardware requirement is not entirely modest unfortunately; it eats up about 8G of memory and takes about 15 minutes around here. Here's an example of how it is used: ############################ BEGIN R CODE ############################## # Presupposing that you have a dataframe 'data' containing your group # description and that all subjects have been processed in ~/subjects ### Group analysis with lm ### # Run the model. This takes some time and memory. lm <- freesurfer.group.analysis.lm(data = data, formula = thickness ~ Age + Gender + Diagnosis, hemi = "lh", fwhm = 10, template = "fsaverage", freesurfer_subjects_dir = "~/subjects") # Extract t values from the model, do FDR correction t <- freesurfer.group.analysis.lm.stats(lm, type.of.value = "t", correction="fdr") # Write the t values to mgh files and open them in FreeSurfer's freeview freesurfer.group.analysis.lm.stats.to.mgh(t, hemi = "lh", template = "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.freeview = TRUE) # Write the t values to .dset ASCII files and open them in AFNI's SUMA freesurfer.group.analysis.lm.stats.to.suma(t, hemi = "lh", template = "fsaverage", freesurfer_subjects_dir = "~/subjects", launch.suma = TRUE) # Make nice plots for vertex #1000 freesurfer.group.analysis.lm.plot(lm, vertex = 1000, interactive = TRUE) ### Group analysis with QDEC ### # Call QDEC freesurfer.group.analysis.QDEC(data = data, freesurfer_subjects_dir = "~/subjects") ### Extract stats ### # Get segmentation stats segstats <- freesurfer.get.segstats(subjects = data$ID, freesurfer_subjects_dir = "~/subjects") ############################## END R CODE ############################## i uploaded the R package here, i called it freesurfR: https://www.nitrc.org/projects/freesurf_r/ thanks also goes to Heath Pardoe, whose code for reading and writing MGH files (also posted on this list) i was allowed to include. regards, Andreas

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Why conn't find subject in Segmentation of hippocampal subfields
by wang kangcheng 20 Jul '14

20 Jul '14

Dear experts When I do Segmentation of hippocampal subfields, it report that ERROR:connot find /nfs/preproc/muti_first/s.... What should I do next? THe scripts was following: SUBJECTS_DIR=/nfs/preproc/multi_first subject_list=${SUBJECTS_DIR}/scripts/check/hipp.list ## Get subjects to run subjects=$( cat ${subject_list} ) ## A. SUBJECT LOOP for subject in $subjects do echo -------------------------- echo running subject ${subject} echo -------------------------- recon-all -s ${subject} -hippo-subfields done echo All have finished Wangkangcheng

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R: Re: Yeo parcellation
by stdp82＠virgilio.it 20 Jul '14

20 Jul '14

Hi list and Thomas, I'm running the first step to use Yeo's parcellation. The running is wrong. mri_surf2surf --s Control01 --hemi lh --sval-tal-xyz white --tval lh.white.Control01 --tval-xyz --trgsubject fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz Reading target surface reg $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.regMRISread( $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg): could not open fileNot a directorymri_surf2surf: could not read surface $SUBJECTS/fsaverage5/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz/surf/lh.sphere.reg Thanks, Stefano ----Messaggio originale---- Da: ythomas(a)csail.mit.edu Data: 7-feb-2014 9.49 A: <stdp82(a)virgilio.it> Cc: "freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Yeo parcellation Hi Stefano, A) From FreeSurfer 5.2 onwards, the Yeo parcellation files can be found inside $FREESURFER_HOME/subjects/fsaverage/label/, so you can simply use those files there instead of downloading from the wiki. B) You can use mri_surf2surf to transform the annot files from the fsaverage "subject" to the individual subjects' surface. There is an example of how to do it if you run "mri_surf2surf --help" C) Once you have created the subject's specific annot file from part B, I believe you must first run mris_anatomical_stats, and then run aparcstats2table. However, I am not sure about this, so someone on the list should correct me if I am wrong! Regards, Thomas On Fri, Feb 7, 2014 at 3:58 PM, <stdp82(a)virgilio.it> wrote: > Hi list, > > I have download the files of Yeo parcellation from > ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip. > > I have two questions, please. > > A- Which is the directory where I should put these files? > B-I have already run by recon-all -all all my subjects. How can I added to > them Yeo parcellation? > C-I'd like also calculate the cortical thickness for each Yeo's ROI. Is > possible with aparcstats2table? > > Thanks. > > Regards, > > > Stefano > > _______________________________________________ > 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

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Re: [Freesurfer] mri_cor2label revisited
by Douglas N Greve 20 Jul '14

20 Jul '14

Are you trying to view it in the volume or the surface? When I run freeview viewing the surface and load the label using the "Load Label" button (not File->LoadLabel), it works for me. Can you try the tksurfer command below? It runs for me. You can ignore the warning about 0 nonzero vertices since they are all set to 1. tksurfer fsaverage lh inflated -label ~/tmp/lh_binarymap_area_covar8.label subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /autofs/cluster/con_009/users/greve/ixi-subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/cluster/con_009/users/greve/ixi-subjects/ixi320/mri checking for nofix files in 'inflated' Reading image info (/autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage) Reading /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /autofs/cluster/con_009/users/greve/ixi-subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 surfer: curvature read: min=-0.673989 max=0.540227 surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) loading label /homes/4/greve/tmp/lh_binarymap_area_covar8.label reading white matter vertex locations... ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 surfer: using interface /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tksurfer.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_common.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkm_wrappers.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/lib/tcl/fsgdfPlot.tcl Reading /autofs/space/tanha_002/users/greve/fsdev.build/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... On 07/15/2014 09:04 AM, Lars M. Rimol wrote: > Hi, > > I go to File -> Label -> load label and there I pick > lh_binarymap_area_covar8.label and then I get the error message: > > > % ******************** 0 nonzero vertices found ******************** > label stat field identically zero - setting to 1 > > > That's it! > > I don't know, but it seems to be saying that all vertices are zero, > doesn't it? > > When I cat the file, I see this: > > 163839 -34.195 -22.897 -24.093 0.0000000000 > > 163840 -34.295 -23.062 -23.449 0.0000000000 > > 163841 -35.093 -23.358 -22.788 0.0000000000 > > The leftmost column surely is vertex number, I don't know what the > next two are (if this were a volume, I'd say x,y,z coordinates) and if > the final column is the value of each vertex, I would have to agree > with tksurfer that there are no nonzero vertices. > > When I load the mgh file, thogh, it has some zero vertices and 98877 > that are 100, that is they are larger than 99.999999999999992. > > >> size(find(gt(testing,99.999999999999992))) > > ans = > > 98877 1 > > > Here's the code I used to make the binary map and save it as an mgh file: > > log10pID = significance threshold > > binaryVLBWlhcovar8(find(gt(binaryVLBWlhcovar8,log10pID))) = 100; > binaryVLBWlhcovar8(find(lt(binaryVLBWlhcovar8,log10pID))) = 0; > > fs_save_mgh(binaryVLBWlhcovar8,'lh_binarymap_area_covar8.mgh',mri); > > > So mri_cor2label must be changing some of these vertices from > 99.99999etc. to 0, right? > > > LMR > > > > On Mon, Jul 14, 2014 at 7:33 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > It loads ok for me both in 5.1 and 5.3. Can you give more info on > what is going wrong with tksurfer? > > > On 07/13/2014 05:35 AM, Lars M. Rimol wrote: > > Hi Doug, > > I'm having some problems with the label creation again. When I > run mri_cor2label, it seems OK (please see below), but when I > try to open it in tksurfer, it gives me an error message (bottom). > > Would you mind taking a look at this label to see what's wrong > with it? I'm attaching the binary mgh file and the label. NB! > The binary .mgh file is from matlab, where I have set all > suprathreshold vertices to 100 and all others to 0. Of course, > Matlab doesn't really do this, it sets them to somewhere close > to 99.999999999999992. I don't suppose I could use "greater > than 99" in mri_cor2label? > > ######### > creating label: > > [LMR in ~ ] mri_cor2label --i > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh > --id 100 --l > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8 > --surf fsaverage lh > $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ > Loading mri > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8.mgh > Loading /home/lmr/subjects/fsaverage/surf/lh.white > Scanning the volume > Found 98877 label voxels > Writing label file > /home/lmr/ANALYSIS/STUDIER/VMI_Kam_103/OUTDIR/binary_pmaps/lh_binarymap_area_covar8 > Centroid: -28.93 -15.97 10.14 > mri_cor2label completed SUCCESSFULLY > > ####### > loading it in tksurfer: > > % ******************** 0 nonzero vertices found > ******************** > label stat field identically zero - setting to 1 > > > > Thank you! > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > > -- > yours, > > Lars M. Rimol, PhD > St. Olavs Hospital > Trondheim, > Norway -- 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/

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Group analysis tutorial
by Vilde 19 Jul '14

19 Jul '14

Dear mailing list, I am doing the group analysis freesurfer tutorial. When I try to open the significance map, I get the error message "unrecognized sub-opton flag 'overlay_threshold'. " The command is freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d I get the same error message doing the tutorial on my mac os x and on a linux, so I doubt there is a problem with the tutorial data. All files needed seem to be in the directory. I very much appreciate any help Best, Vilde

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Tracula AD weighted average
by Cat Chong 18 Jul '14

18 Jul '14

Dear Anastasia, Another quick question: We found significant differences in two subject groups for the AD_AVG as well as the AD_AVG_Weight, which is stated as the "weighted average over the entire path distribution'. Could you tell me how the average weight is calculated and why it would be better to use than the AD_AVG perhaps? Thank you very much, Cat

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Re: [Freesurfer] recon-all ERROR, no idea why
by Remy Wahnoun 18 Jul '14

18 Jul '14

Thanks Douglas, I definitely appreciate your help. Here is what it Spit out, *Rémy Wahnoun, PhD* Biomedical Research Group Manager Barrow Neurological Institute at Phoenix Children's Hospital Adjunct Faculty, Arizona State University *www.NeuralControl.net <http://www.neuralcontrol.net/>* set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = --n shift switch ( $flag ) switch ( --n ) if ( $#argv == 0 ) goto arg1err ; if ( 10 == 0 ) goto arg1err set nIters = $argv[1] ; shift ; set nIters = 1 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = --proto-iters shift switch ( $flag ) switch ( --proto-iters ) if ( $#argv == 0 ) goto arg1err ; if ( 8 == 0 ) goto arg1err set nProtoIters = $argv[1] ; shift ; set nProtoIters = 1000 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = --distance shift switch ( $flag ) switch ( --distance ) if ( $#argv == 0 ) goto arg1err ; if ( 6 == 0 ) goto arg1err set Distance = $argv[1] ; shift ; set Distance = 50 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = --no-rescale shift switch ( $flag ) switch ( --no-rescale ) set DoRescale = 0 ; set DoRescale = 0 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = --i shift switch ( $flag ) switch ( --i ) if ( $#argv == 0 ) goto arg1err ; if ( 3 == 0 ) goto arg1err set InVol = $argv[1] ; shift ; set InVol = orig.mgz shift breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = --o shift switch ( $flag ) switch ( --o ) if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set OutVol = $argv[1] ; shift ; set OutVol = orig_nu.mgz shift 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 ( $#InVol == 0 ) then if ( 1 == 0 ) then if ( ! -e $InVol ) then if ( ! -e orig.mgz ) then if ( $#OutVol == 0 ) then if ( 1 == 0 ) then goto check_params_return ; goto check_params_return set OutDir = `dirname $OutVol` ; set OutDir = `dirname $OutVol` dirname orig_nu.mgz mkdir -p $OutDir ; mkdir -p . if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log set LF = ./mri_nu_correct.mni.log if ( -e $LF ) mv $LF $LF.bak if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak pwd | tee -a $LF pwd tee -a ./mri_nu_correct.mni.log /media/sf_Imagery/FreeSurfer/xx/mri which mri_nu_correct.mni | tee -a $LF which mri_nu_correct.mni tee -a ./mri_nu_correct.mni.log /usr/local/freesurfer/bin/mri_nu_correct.mni echo $cmdargs | tee -a $LF echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz tee -a ./mri_nu_correct.mni.log --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz echo "nIters $nIters" | tee -a $LF echo nIters 1 tee -a ./mri_nu_correct.mni.log nIters 1 echo $VERSION | tee -a $LF tee -a ./mri_nu_correct.mni.log echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ uname -a | tee -a $LF uname -a tee -a ./mri_nu_correct.mni.log Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux date | tee -a $LF date tee -a ./mri_nu_correct.mni.log Mon Jun 23 15:32:45 EDT 2014 nu_correct -version | tee -a $LF nu_correct -version tee -a ./mri_nu_correct.mni.log Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$ if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745 set tmpdir = ./tmp.mri_nu_correct.mni.1745 mkdir -p $tmpdir mkdir -p ./tmp.mri_nu_correct.mni.1745 echo "tmpdir is $tmpdir" | tee -a $LF echo tmpdir is ./tmp.mri_nu_correct.mni.1745 tee -a ./mri_nu_correct.mni.log tmpdir is ./tmp.mri_nu_correct.mni.1745 set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc ) if ( $UseFloat ) set cmd = ( $cmd -odt float ) if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float ) pwd | & tee -a $LF pwd tee -a ./mri_nu_correct.mni.log /media/sf_Imagery/FreeSurfer/xx/mri echo $cmd | & tee -a $LF echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float tee -a ./mri_nu_correct.mni.log mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float $cmd | & tee -a $LF mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float tee -a ./mri_nu_correct.mni.log mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=25.00, TE=5.36, TI=0.00, flip angle=30.00 i_ras = (-1, 1.49012e-08, 0) j_ras = (0, 0, -1) k_ras = (-1.30385e-08, 1, -5.96046e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc... if ( $status ) then if ( 0 ) then @ nthIter = 1 ; @ nthIter = 1 while ( $nthIter < = $nIters ) while ( 1 < = 1 ) echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log echo "--------------------------------------------------------" | & tee -a $LF echo -------------------------------------------------------- tee -a ./mri_nu_correct.mni.log -------------------------------------------------------- echo "Iteration $nthIter `date`" | & tee -a $LF echo Iteration 1 `date` tee -a ./mri_nu_correct.mni.log date Iteration 1 Mon Jun 23 15:32:49 EDT 2014 @ m = $nthIter - 1 @ m = 1 - 1 set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ; set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ) if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ; if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 ) if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop ) if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ; if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 ) if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ; if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm ) echo $cmd | & tee -a $LF echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 tee -a ./mri_nu_correct.mni.log nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 $cmd | & tee -a $LF nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 tee -a ./mri_nu_correct.mni.log [fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) if ( $status ) then if ( 0 ) then rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp @ nthIter = $nthIter + 1 ; @ nthIter = 1 + 1 echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log end end while ( $nthIter < = $nIters ) while ( 2 < = 1 ) echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log echo " " | & tee -a $LF echo tee -a ./mri_nu_correct.mni.log set numnc = $tmpdir/nu$nIters.mnc set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc if ( $DoRescale ) then if ( 0 ) then if ( ! -e $numnc ) then if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then echo "ERROR: file $numnc does not exist!" | & tee -a $LF echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! tee -a ./mri_nu_correct.mni.log ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist! exit 1 ; exit 1 ------------------------------ This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. Any unauthorized review, use, copying, disclosure, or distribution is prohibited. If you are not the intended recipient, or the person responsible for delivering this to an addressee, you should notify the sender immediately by telephone or by reply e-mail, and destroy all copies of the original message.

2 5

Tracula trac-all -stat flag -stat unrecognized
by Cat Chong 18 Jul '14

18 Jul '14

Hello Anastasia, I have just converted pathstas.overall.txt files to a table for group analyses. Now, I am trying to convert pathstats.byvoxel.txt files to a table for group analyses using the command: trac-all -stat -c I am receiving the error message: ERROR: flag -stat unrecognized I am working on a mac using bash script using Freesurfer version 5.3 Do you have any ideas? Cheers, Cat

2 2

transforming Base surfaces to Cross space
by prasser 18 Jul '14

18 Jul '14

Dear All, For longitudinal data sets, is there a way that the lh.pial surface from the Base can be transformed into the brainmask.mgz space of a Cross so that it can be viewed with tkmedit on the Cross brainmask.mgz? Thanks, Paul

2 2

Group differences in pc1 (longitudinal stage2)
by Tudor Popescu 18 Jul '14

18 Jul '14

Dear FS list, (dear Martin!) I have a longitudinal design, 3 groups, 2 timepoints, and I created three different QDEC tables (two groups at a time) in order to be able to compare each pair of groups in terms of percentage change from pre to post (what's referred to as "pc1" in the first stage of the two-stage-model). I look at thickness, area and lGI as dependent variables. Group is a categorical factor of interest, gender as the other categorical factor (not interested in its effect), and age as (continuous) nuisance. I'm interested in the contrast "Does the average ..., accounting for gender, differ between G1 and G2?" Say that, for some analysis (e.g. group 1 vs group 2, thickness, LH) I get a certain cluster that survives the MonteCarlo Null-Z correction. If the cluster is redish, I take it to mean that group 1 has a higher signed value of pc1 than group 2, and vice-versa if the cluster is blueish. However, because pc1 is (I think) a signed statistic, i.e. is negative for thickness decrease and positive for thickness increase, this makes me unsure how to interpret the stage2 (cross-sectional) result. As I understand it, having a significant red cluster in the group comparison can mean either of these 3 scenarios: 1. Both groups have pc1>0 2. G1 has pc1>0 and G2 has pc1<0 3. Both groups have pc1<0 ..but that the pc1 of G1 is always greater, as a signed number, than that of G2, since that is what defines the cluster. The problem is that, when I run the same analysis but keeping only subjects of one group in at one time, i.e. for each group separately and looking at the contrast "Does the average ... differ from zero?", in most cases I don't get the same cluster that appeared in the group comparison. My question is therefore: can a cluster appearing in the between-groups analysis be trusted if the same (or similar) cluster does *not *appear in each of the two within-groups (one-sample test) analyses? And if the latter analysis produces null results but the former does have sig clusters, does it still make sense to look at the sign of each group's mean pc1 in order to find the effect of the longitudinal treatment (atrophy or increase), even if that group in fact did not have a pc1 that was significantly different from zero? Many thanks for your help! Tudor

2 1

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