Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Re: [Freesurfer] error in longitudinal processing "dimension mismatch"
by Bruce Fischl 01 May '13

01 May '13

> > Keith > > > On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Keith > > can you cc the list so that others can answer? Like Martin! > > thanks > Bruce > On Wed, 1 May 2013, Qi Wu wrote: > > Hi Bruce, > Thank you so much for your quick reply. > > I used the following script to do the first step > cross-sectional > preprossessing > > #!/bin/tcsh -ef > # add 'x' to '-ef' to trace code as it is executed > > ##### GO_FS1 - The "Easy" button ##### > ##### Usage: GO_FS-123 <subjects directory name> > ##### Feeds multiple subjects into autorecon1, autorecon2, > and autorecon3 > ##### Requires that original scan data be placed in > $SUBJECTS_DIR/_orig_ > ##### (Place each subject's anat series in separate > folders) > > > echo "\n <><><><><><><><><><><>< GO FreeSurfer! > ><><><><><><><><><><><> \n" > > ### Check if subjects directory specified ### > if ( "$1" != "" ) then > set subjdir = $1 > else > echo "\n ERROR: No subjects directory specified \n" > exit 1 > endif > > ### Set FREESURFER_HOME and SUBJECTS_DIR ### > > setenv FREESURFER_HOME /usr/local/freesurfer5.1 > > if ( -e > /data/keith/freesurferdata/subjects_longitudinal/$subjdir) > then > setenv SUBJECTS_DIR > /data/keith/freesurferdata/subjects_longitudinal/$subjdir > else > echo "\n ERROR: Specified subjects directory does not > exist \n" > exit 1 > endif > > ### Check if original scan data exists ### > > if ( ! -e /$SUBJECTS_DIR/_orig_ ) then > echo "\n ERROR: Original scan data not found. \n" > exit 1 > endif > > ### disable functional tools ### > > setenv NO_FSFAST > > ##### (To enable functional tools, disable the above line, > enable the > following:) > ##### (HAVE NOT TESTED THIS YET) (MAYBE BETTER IF > NO_FSFAST ANYWAYS) > #setenv FUNCTIONALS_DIR $FREESURFER_HOME/sessions > # echo "FUNCTIONALS_DIR = $FUNCTIONALS_DIR" > ##### (and add the following to ~/matlab/startup.m) > #fsfasthome = getenv('FSFAST_HOME'); > #fsfasttoolbox = sprintf('%s/toolbox',fsfasthome'); > #path(path,fsfasttoolbox); > > ### Set up FreeSurfer ### > > setenv prompt > source $FREESURFER_HOME/FreeSurferEnv.csh > echo "" > > > ### List out directories in _orig_ , set subj array, > prompt to continue ### > > echo "Found the following subjects: \n" > > set i = 0 > set subjID > > foreach d ($SUBJECTS_DIR/_orig_/*) > @ i++ > set subjID = ($subjID $d:t) > echo " Subject "$i": " $subjID[$i] > end > set subjCount = $i > > set response > while ($response != "n" && $response != "y") > echo -n "\n Process these $subjCount subjects? [y/n] > " > set response = $< > end > if ($response == "n") then > echo "\n Program ended by user \n" > exit 1 > endif > > > ### Prompt user for First Anat Filename's ### > > set firstAnatSame > while ($firstAnatSame != "y" && $firstAnatSame != "n") > echo -n "\n Are all the anat series named identically? > [y/n]: > " > set firstAnatSame = $< > end > switch ($firstAnatSame) > case [y]: > echo -n "\n Please enter the first filename (e.g. > p1_000.dcm) for all > anat series: > " > set firstAnat = $< > breaksw > case [n]: > echo "\n Please enter the first filename (e.g. > p1_000.dcm) in the anat > series for:" > set i = 0 > set firstAnat > while ($i < $subjCount) > @ i++ > echo -n " "$subjID[$i]": > " > set firstAnat = ($firstAnat $<) > end > breaksw > endsw > > > ### Run autorecon1 for each subject ### > > cd $SUBJECTS_DIR > > switch ($firstAnatSame) > case [y]: > set i = 0 > while ($i < $subjCount) > @ i++ > echo "\n<><><><><><><><><><><><| NOW PROCESSING > <"$subjID[$i]"> > |><><><><><><><><><><><>\n" > recon-all -i > $SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat -all -s > $subjID[$i] > end > breaksw > case [n]: > set i = 0 > while ($i < $subjCount) > @ i++ > echo "\n<><><><><><><><><><><><| NOW PROCESSING > <"$subjID[$i]"> > |><><><><><><><><><><><>\n" > recon-all -i > $SUBJECTS_DIR/_orig_/$subjID[$i]/$firstAnat[$i] -all -s > $subjID[$i] > end > breaksw > endsw > > > echo "" > date +"Finished $0 without error at %T on %a %b %d %Y" > echo "" > exit 0 > > ################### > ### Simple working loop > #set i = 0 > #while ($i < 10) > # echo $i > # @ i++ > #end > ####################### > > ############# > ### TO DO ### > ############# > # why don't env's remain 'set' after running this? (they > do after running > SetUpFreeSurfer.csh or FreeSurferEnv.csh) > # why can't FS_FAST be set up? > > > Then I did the "base" step and the "long" step with the > following > > recon-all -base kp5_base -tp kp5 -tp k5b -all > > recon-all -long kp5 kp5_base -all > recon-all -long kp5b kp5_base -all > > > Keith > > > On Wed, May 1, 2013 at 12:15 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Keith > > what were the recon-all command lines you ran? > Bruce > On Wed, 1 May 2013, Qi Wu wrote: > > Dear Freesurfer experts, > > I have a dataset of 2 time points. I ran into > problems > when I tried to use > the two-stage approach to pull out statistics such > as the > rate of change in > Freesurfer 5.1. > > I could not even get the first stage working. The > error > messages I got were > “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR > -11 : > mri_glmfit did > not work?” > > I did further trouble-shooting for this particular > message > "nv1 = 140942, > nv1 = 143525", and I found out that "143525" was in > the > "base" folder > (kp5_base), and "140942" was for the two > longitudinally > registered images > (kp5.long.kp5_base, and kp5b.long.kp5_base). > > The command line I used was : “long_mris_slopes > --qdec > ./qdec/AS_long_qdec.dat --meas thickness --hemi lh > --do-avg --do-rate > --do-pc1 --do-spc --do-stack --do-label --time weeks > –nosmooth”. > > The first three lines in the qdec file: > > “fsid fsid-base weeks age sex FSS avgPain > > kp5 kp5_base 0 48 0 4.1 7 > > kp5b kp5_base 20 48 0 8.6 6” > > This error was similar to what was in apreviouspost(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-Jun > e/024576 > .htm > l by joost janssen Jun 29, 2012). I tried to fix any > similar problems, but > still wasn’t able to get it working. > > What else could I have been doing wrong? > > The on screen error output is provided as follows > > Many thanks > > Keith > > Postdoctoral fellow > Toronto Western Hospital > Toronto, Ontario > Canada > > *********************************** > > Parsing the qdec table: ./qdec/AS_long_qdec.dat > > Working in SUBJECTS_DIR: > > /data/keith/freesurferdata/subjects_longitudinal_5.1_old > > Subject-Template: kp5_base > > INFO: 2 TPs in kp5_base , mean age: 10.0 > > =========================================================================== > > > ==== > > SUBJECT kp5_base Intersecting Within-Subject Cortex > Label > > cp/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_bas > > e/ > label/lh.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_o > > ld/kp5_base/label/lh. > long.cortex.label > > mris_label_calcintersect/data/keith/freesurferdata/subjects_longitudinal_5. > 1_old/kp5b.long > .kp5_base > /label/lh.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_ > > old/kp5_base/label/lh. > long.cortex.label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/k > > p5_base/label/lh. > long.cortex.label > > LabelWrite:savingto/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/l > abel/l > h. > long.cortex.label > > =========================================================================== > > > ==== > > SUBJECT kp5_base Stackinbg Within-Subject Maps > > mri_concat/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long > > .kp5_base/ > surf/lh.thickness/data/keith/freesurferdata/subjects_longitudinal_5.1_old/k > > p5b.long.kp5_base > /surf/lh.thickness--o/data/keith/freesurferdata/subjects_longitudinal_5.1_o > ld/kp5_base/surf/l > h.l > ong.thickness-stack.mgh > > ninputs = 2 > > Checking inputs > > nframestot = 2 > > Allocing output > > Done allocing > > nframes = 2 > > Writingto/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/ > surf/lh > .l > ong.thickness-stack.mgh > > =========================================================================== > > > ==== > > SUBJECT kp5_base Running Within-Subject GLM > > Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ... > > mri_glmfit--y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_b > ase/surf/l > h.l > ong.thickness-stack.mgh --X > ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat > --allow-zero-dof --no-contrasts-ok --surf kp5_baselh--label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/ > la > bel/lh. > long.cortex.label --glmdir > ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > Readingsourcesurface/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_b > ase/su > rf/lh.w > hite > > Number of vertices 143525 > > Number of faces 287046 > > Total area 91438.851562 > > AvgVtxArea 0.637094 > > AvgVtxDist 0.873064 > > StdVtxDist 0.245806 > > $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve > Exp $ > > cwd > /data/keith/freesurferdata/subjects_longitudinal_5.1_old > > cmdlinemri_glmfit--y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_b > ase/surf/l > h.l > ong.thickness-stack.mgh --X > ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat > --allow-zero-dof --no-contrasts-ok --surf kp5_baselh--label/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/ > la > bel/lh. > long.cortex.label --glmdir > ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > sysname Linux > > hostname davissvr1.uhnres.utoronto.ca > > machine x86_64 > > user qwu > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh. > > l > ong.thickness-stack.mgh > > logyflag 0 > > X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat > > usedti 0 > > labelmask/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/ > > label/lh. > long.cortex.label > > maskinv 0 > > glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > Loadingyfrom/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf > / > lh.l > ong.thickness-stack.mgh > > Saving design matrix to > ./tmp-kp5_base_lh_thickness_6PR2rH/glm/Xg.dat > > Normalized matrix condition is 1 > > Matrix condition is 10 > > Found 131455 points in label. > > ERROR: mri_reshape: number of elements cannot change > > nv1 = 143525, nv1 = 140942 > > Pruning voxels by thr: 0.000000 > > Found 134956 voxels in mask > > Saving mask to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/mask.mgh > > Reshaping mriglm->mask... > > ERROR: mri_reshape: number of elements cannot change > > nv1 = 140942, nv1 = 143525 > > search space = 91439.090793 > > DOF = 0 > > Starting fit and test > > Fit completed in 0.0042 minutes > > Computing spatial AR1 on surface > > ERROR: MRISar1: Surf/Src dimension mismatch. > > ERROR -11 : mri_glmfit did not work? > > > > > > 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. > > > > > >

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incomplete tracts
by stdp82＠virgilio.it 01 May '13

01 May '13

Hi Bruce, trac-all -prep -c $FREESURFER_HOME/dmrirc_single_subject_d11_NEW.I'm also attaching dmrirc files. Thank you very much. Stefano ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 1-mag-2013 15.39 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu>, <ayendiki(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: incomplete tracts Hi Stefano you need to tell us what command you were running. cheers Bruce On Wed, 1 May 2013, stdp82(a)virgilio.it wrote: > > I have this error: > > writing registered surface to/Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_av > g35.sphere.reg... > expanding nbhd size to 1 > 1109: 1 negative triangles > mris_resample: Command not found. > > Thanks, > > Stefano > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 30-apr-2013 21.12 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: incomplete tracts > > > Like I said in my previous email to you, please do not specify the CVS > template. This means delete the cvstempdir line from your configuration > file, or comment it out. > > On Tue, 30 Apr 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > when I run the configuration file (which I'm attaching) > > ERROR: Could not find CVS template > > > > I apologize but which is the correct directory of CVS template? > > > > Thanks, > > > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 26-apr-2013 20.08 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > Hi Stefano - Just use the default for that, you don't need to specify the > > location. > > > > a.y > > > > On Sun, 21 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Hi Anastasia, > > > I apologize but I do not find CVS template? Where it should be located? > > > > > > Thank you very much, > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 9-apr-2013 17.50 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: incomplete tracts > > > > > > > > > Hi Stefano - Did you try CVS for the inter-subject registration? It > > > doesn't look like it from the configuration file. > > > > > > a.y > > > > > > On Tue, 9 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi Anastasia, > > > > yes, I tried.I'm attacking the last configuration file that I used. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 9-apr-2013 1.42 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > What registration methods are you using for the intra-subject and > > > > inter-subject registration? Have you tried the different options? > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely > fminor. > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 5-apr-2013 18.57 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > > > > > > > > > > What you say "again" you mean with 5.2? > > > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > Hi Anastasia, > > > > > > yes, for some subject the low-b volume is in the end. > > > > > > Some subjects have again incomplete tracts. > > > > > > I'm attacking an example of configuration file that I'm using. > > > > > > I hope that you can check it please. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > Data: 5-apr-2013 18.45 > > > > > > A: <stdp82(a)virgilio.it> > > > > > > Cc: > "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > > > > > > > Hi Stefano - In your case we determined that the ones that had the > low-b > > > > > > volume in the end didn't run correctly, right? In that case, I > didn't > > > > need > > > > > > to see anything, you were going to try running 5.2. > > > > > > > > > > > > a.y > > > > > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > Hi Anastasia, > > > > > > > could I send you the data of a subject that I don't run > correctly? > > > > > > > > > > > > > > I still have some subjects with tracts incomplete and I do not > know if > > > > > it depends > > > > > > from > > > > > > > my analysis or whether the images are not good. > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > Data: 5-apr-2013 17.37 > > > > > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > > > > > Cc: > "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but > instead a > > > > > > > tractography initialization issue, I strongly recommend running > 5.2 > > > > with > > > > > > > bbregister for the registration (which is the default in 5.2 > anyway). > > > > > > > > > > > > > > You can also upload an example data set with issues (include: > dmri, > > > > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a > look: > > > > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > > > > > > > > > Hope this helps, > > > > > > > a.y > > > > > > > > > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > > > > > thanks for the help. There is also a line option in freeview. > > > > However > > > > > we still > > > > > > have > > > > > > > > brains with missing tracks, I rerun them with increasing the > ncpts > > > > and > > > > > registering > > > > > > > to > > > > > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > > > > > confident that our > > > > > > > bvel > > > > > > > > and bvac are correct, since we have roughly 20 cases out of 90 > > > > > processed brains > > > > > > > where > > > > > > > > there are no missing tracts. Further sometimes only one tract > is > > > > > missing, > > > > > > sometimes > > > > > > > it > > > > > > > > is more severe. We could not find any correlation with > recon-all > > > > > problems or DTI > > > > > > raw > > > > > > > > data issues (all but one were without moving artefacts). Since > we > > > > are > > > > > running > > > > > > > bedpostx > > > > > > > > outside of trac-all (i.e. trac-prep then bedpostx then > trac-path) > > > > > might it be an > > > > > > > issue > > > > > > > > that is solved with installing the 5.2. version? Would that > run in > > > > > freesurfer > > > > > > 5.1.0? > > > > > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > > > > > > > > > Kind regards > > > > > > > > Gerit Pfuhl > > > > > > > > > > > > > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > > > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the > lines > > > > in > > > > > the corpus > > > > > > > > callosum follow the curvature of the corpus callosum, > and in a > > > > > sagittal > > > > > > > > view to see if the lines in the cingulum follow the > curvature > > > > of > > > > > the > > > > > > > > cingulum. Does this make sense? > > > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA > because > > > > > our > > > > > > > > gradient table is wrong but I am not really sure how to > > > > analyse > > > > > > > > these informations. You wrote to Stefano the lines have > to > > > > point > > > > > in > > > > > > > > the right direction and that the eigenvectors are not > pointing > > > > > along > > > > > > > > his corpus callosum. Can you give me a more detailed > > > > description > > > > > > > > what I have to do when I dislpay dtifit_V1 as lines, > overlaid > > > > on > > > > > > > > dtifit_FA. > > > > > > > > > > > > > > > > Thanks and kind regards > > > > > > > > Benjamin > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > http://gerit-orientation.blogspot.com > > > > > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > 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 > > > > > > > > > > > > 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 > > > > > > > > > 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 > > > > > > 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 > > > 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 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

Re: [Freesurfer] Use our own training subjects?
by Anastasia Yendiki 01 May '13

01 May '13

Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is described in the online documentation for trackvis. The priors are generated by trac-all on the fly, given the .trk files and aparc+aseg for each of the training subjects. So once the manual labeling is done, it's just about transforming these files to the template space and passing the list to trac-all. I'm happy to document this part. The hard work is the manual labeling! Hope this helps, a.y On Wed, 1 May 2013, Susan Kuo wrote: > Hi Anastasia, I would like to add several tracts of interest to our priors, e.g. the IFO and sections of > the corpus callosum. Would it be possible for you to document how your group created your priors? Are we > constrained to trackvis as a program? I know this is a lot of documentation, but I would be happy to help. > I'm located on the NIH campus, and can travel up to help with the documentation if you'd like. It would be > a good learning process for me. Thank you! > > > Susan Kuo > > > On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Susie - If you can label the connection that you want in trackvis consistently in a set of > subjects, then yes, it'd be possible to create your own mini atlas. You'd have to map the .trk > files with the trackvis streamlines and the aparc+aseg's from all the training subjects to > either the MNI or the CVS template. Then there's a trainfile variable that you can set in the > configuration file that tells trac-all where to find the training data. If you decide to go > through with this, I can try to document it in more detail on the wiki. > > a.y > > On Mon, 15 Apr 2013, Susan Kuo wrote: > > Hi Anastasia, > We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that > the tract did not reach > Broca's area. While there exists literature that now challenges this > neuroanatomical convention, I would > like to investigate the possibility of creating and inputting on our own training > subjects as priors. Do > you know if we can try this? Thank you! > > -- > Susie Kuo > > Mediocrity knows nothing higher than itself, but talent instantly recognizes > genius. - Sir Arthur Conan > Doyle, Sherlock Holmes- Valley of Fear > > > > > 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. > > > > > -- > Susie Kuo > > Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan > Doyle, Sherlock Holmes- Valley of Fear > >

2 1

Which space is TRACULA statistics in?
by Susan Kuo 01 May '13

01 May '13

Hi FreeSurfing researchers, I am looking at the pathstats.overall.txt, and wanted to see if anybody knew which space these voxels are in - I assume MNI space (given that I used the MNI template) and not individual diffusion space, but would like to confirm. Does anybody know for certain what space this data is reported in? Thanks! -- Susie Kuo

2 2

How to flip L/R image in the freeview?
by Glen Lee 01 May '13

01 May '13

Freesurfer users, I'm a newbie for FS and have a rudimentary question for you. I have to overlay the group map for right hemisphere onto the lh.inflated (due to using sym space, where left surface map became symmetrical to the right), but I wonder if there is any way of reverting it back to rh.inflated after the overlay using the freeview software. Your help would be appreciated. -Glen

2 1

Visualize a fixed number of voxels using Tksurfer
by Martin Bleichner 01 May '13

01 May '13

Hi all, is there a way to visualize a fixed number of voxesl using TKsurfer. I want to display the 200 most active voxels (i.e. highest beta values) on the inflated surface. Is there a possibility within tksurfer or do I have to determine the corresponding threshold beforehand? Thanks Martin

2 1

R: Re: R: Re: R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 01 May '13

01 May '13

I have this error: writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff01/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 11109: 1 negative trianglesmris_resample: Command not found. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 30-apr-2013 21.12 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: incomplete tracts Like I said in my previous email to you, please do not specify the CVS template. This means delete the cvstempdir line from your configuration file, or comment it out. On Tue, 30 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > when I run the configuration file (which I'm attaching) > ERROR: Could not find CVS template > > I apologize but which is the correct directory of CVS template? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 26-apr-2013 20.08 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > Hi Stefano - Just use the default for that, you don't need to specify the > location. > > a.y > > On Sun, 21 Apr 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > I apologize but I do not find CVS template? Where it should be located? > > > > Thank you very much, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 9-apr-2013 17.50 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: incomplete tracts > > > > > > Hi Stefano - Did you try CVS for the inter-subject registration? It > > doesn't look like it from the configuration file. > > > > a.y > > > > On Tue, 9 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > Hi Anastasia, > > > yes, I tried.I'm attacking the last configuration file that I used. > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 9-apr-2013 1.42 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > What registration methods are you using for the intra-subject and > > > inter-subject registration? Have you tried the different options? > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor. > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 5-apr-2013 18.57 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] R: Re: R: Re: incomplete tracts > > > > > > > > > > > > What you say "again" you mean with 5.2? > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Hi Anastasia, > > > > > yes, for some subject the low-b volume is in the end. > > > > > Some subjects have again incomplete tracts. > > > > > I'm attacking an example of configuration file that I'm using. > > > > > I hope that you can check it please. > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 5-apr-2013 18.45 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > > > > Hi Stefano - In your case we determined that the ones that had the low-b > > > > > volume in the end didn't run correctly, right? In that case, I didn't > > > need > > > > > to see anything, you were going to try running 5.2. > > > > > > > > > > a.y > > > > > > > > > > On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > Hi Anastasia, > > > > > > could I send you the data of a subject that I don't run correctly? > > > > > > > > > > > > I still have some subjects with tracts incomplete and I do not know if > > > > it depends > > > > > from > > > > > > my analysis or whether the images are not good. > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > Data: 5-apr-2013 17.37 > > > > > > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > > > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: [Freesurfer] incomplete tracts > > > > > > > > > > > > > > > > > > Hi Gerit - If it's not an issue with the gradient table but instead a > > > > > > tractography initialization issue, I strongly recommend running 5.2 > > > with > > > > > > bbregister for the registration (which is the default in 5.2 anyway). > > > > > > > > > > > > You can also upload an example data set with issues (include: dmri, > > > > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > > > > > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > > > > > > > > > > > Hope this helps, > > > > > > a.y > > > > > > > > > > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > > > thanks for the help. There is also a line option in freeview. > > > However > > > > we still > > > > > have > > > > > > > brains with missing tracks, I rerun them with increasing the ncpts > > > and > > > > registering > > > > > > to > > > > > > > bbr (since that is default in Tracula 5.2.). We are reasonable > > > > confident that our > > > > > > bvel > > > > > > > and bvac are correct, since we have roughly 20 cases out of 90 > > > > processed brains > > > > > > where > > > > > > > there are no missing tracts. Further sometimes only one tract is > > > > missing, > > > > > sometimes > > > > > > it > > > > > > > is more severe. We could not find any correlation with recon-all > > > > problems or DTI > > > > > raw > > > > > > > data issues (all but one were without moving artefacts). Since we > > > are > > > > running > > > > > > bedpostx > > > > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) > > > > might it be an > > > > > > issue > > > > > > > that is solved with installing the 5.2. version? Would that run in > > > > freesurfer > > > > > 5.1.0? > > > > > > > I guess we need to change the dcmrirc files only a bit. > > > > > > > > > > > > > > Kind regards > > > > > > > Gerit Pfuhl > > > > > > > > > > > > > > > > > > > > > On 3 April 2013 16:59, Anastasia Yendiki > > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > > > > > > > Hi Benjamin - I'd look in a coronal view to see if the lines > > > in > > > > the corpus > > > > > > > callosum follow the curvature of the corpus callosum, and in a > > > > sagittal > > > > > > > view to see if the lines in the cingulum follow the curvature > > > of > > > > the > > > > > > > cingulum. Does this make sense? > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > > > > > > > > > > > Dear Anastasia, > > > > > > > > > > > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because > > > > our > > > > > > > gradient table is wrong but I am not really sure how to > > > analyse > > > > > > > these informations. You wrote to Stefano the lines have to > > > point > > > > in > > > > > > > the right direction and that the eigenvectors are not pointing > > > > along > > > > > > > his corpus callosum. Can you give me a more detailed > > > description > > > > > > > what I have to do when I dislpay dtifit_V1 as lines, overlaid > > > on > > > > > > > dtifit_FA. > > > > > > > > > > > > > > Thanks and kind regards > > > > > > > Benjamin > > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > http://gerit-orientation.blogspot.com > > > > > > > http://team-arzgebirg.blogspot.com > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > 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 > > > > > > > > > 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 > > > > > > 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 > > > 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 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

setting up FS
by Ash Rafea 01 May '13

01 May '13

Hi there, I am totally a begginer in the Neurodebian "world" so please be patient :( I installed FS but I don't know how to setup freesurfer? I don't know how to locate my FS home Simply, I'm stuck at this step: setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh attached is a screen shot of whats in my computer!

2 1

Begginer!
by Ash Rafea 01 May '13

01 May '13

1 0

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Freesurfer May 2013