Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

Re: [Freesurfer] tracula fibers display question
by Anastasia Yendiki 08 Apr '13

08 Apr '13

Hi Sal - I'm cc-ing the list since this is of general interest. In 5.2 there's also a path.pd.trk file in the tracula output directory, which contains all the sample splines that were added up to create the probabilistic distribution in path.pd.nii.gz. The .trk format can be displayed in freeview or trackvis. These are still not like the pretty streamlines that you see visualized in deterministic tractography tools, simply b/c they haven't been smoothed. Hope this helps, a.y On Sun, 7 Apr 2013, Salil Soman wrote: > Dear Anastasia, > > Is there a way to display the merged_avg33_mni_flt.mgz file as a set of streamlines, rather > than the clay appearing structures generated by using freeview -tv /merged_avg33_mni_flt.mgz ? > I ask primarily because my collaborators in surgery and neurology are becoming increasingly > used to DTI fiber tracking images that give the appearance of multiple fibers (I recognize > that the modeling of white matter tracts using probabilities does not support delineation of > specific individual fibers, however, I think I am having a hard time even introducing > collaborators to the DTI data generated by Tracula due to the unusual appearance of its > output). > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS > >

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Re: [Freesurfer] Tracula the inverse of TBSS results
by Sean Hatton 08 Apr '13

08 Apr '13

This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: > Hi Freesurfer gurus, > > I have been using Tracula to investigate white matter abnormalities in a patient > cohort (n=20) compared to matched controls (n=40). In line with the literature, we > expected to see reductions in FA in the patients' tracts but instead they have > significantly higher FA means. To double-check, we ran TBSS over the same cohorts and > got the results as per the literature (I.e. reduced FA in the patient group). The FA, > RD, AD, MD and volume outputs are normally distributed and there are no extreme > outliners. So wondering: > 1. The patient group had significantly reduced tract volumes. If this volume > calculation is incorrect I expect it could influence the calculation of the mean > FA, RD, AD etc. Is there a way of checking the volume and subsequent > calculations? > 2. Yendiki et al 2011 had no corrections – do I need corrections? > 3. Should I be thresholding tract stats? > Thank you in advance, > > Sean Hatton > Brain and Mind Research Institute > University of Sydney > > > > > > > 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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Problem running Tracula longitudinal analysis
by Dylan Nielson 08 Apr '13

08 Apr '13

I am trying to run Tracula on a single subject with two time points. I get the following Error below. I suspect it is because I am not setting my dmrirc file up correctly, but I cannot figure out what the error is. I've copied my dmrirc file below as well. Thanks, Dylan Command: trac-all -prep -nocorr -nointra -c dmrirc.long.RP0603 Error: trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp1002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/tp2002.long.002/scripts/trac-all.cmd ; trac-preproc -c /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/dmrirc.local -log /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.log -cmd /home/dylan/fmri/RP0629_3T/freesurfer/002/scripts/trac-all.cmd ; dmrirc.long setenv SUBJECTS_DIR ~/fmri/RP0629_3T/freesurfer set dtroot = ~/fmri/RP0629_3T/freesurfer set subjlist = ( tp1002.long.002 \ tp2002.long.002 ) set baselist = ( 002 002 ) set dcmroot = ~/fmri/RP0629_3T/freesurfer/ set dcmlist = ( tp1002.long.002/dmri/dwi.nii. gz \ tp2002.long.002/dmri/dwi.nii.gz ) set bvecfile = ( tp1002.long.002/dmri/bvec \ tp2002.long.002/dmri/bvec ) set bvalfile = ( tp1002.long.002/dmri/bval \ tp2002.long.002/dmri/bval ) set dob0 = 0 set doeddy = 0 set thrbet = 0.5 set doregflt = 0 set doregbbr = 1 set doregmni = 0 set doregcvs = 1 set cvstemp = cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects set usemaskanat = 1 set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS \ lh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 7 7 5 5 5 5 4 4 5 5 5 5) set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt set nstick = 2 set nburnin = 200 set nsample = 7500 set nkeep = 5 set reinit = 0

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incomplete tracts
by stdp82＠virgilio.it 08 Apr '13

08 Apr '13

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.

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BA that are the begin and target of each tracts obtained in TRACULA
by stdp82＠virgilio.it 08 Apr '13

08 Apr '13

Hi list and Anastasia, how can I identify which are the Brodmann areas that are the begin and target of each tracts obtained in TRACULA analysis. Thanks, Stefano

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mri_normalize control in FS 5.2
by Michael Harms 08 Apr '13

08 Apr '13

Hi guys, I see that the recon-all for FS 5.2 now has flags for setting the -b and -n arguments to mri_normalize separately for the two different Normalization stages. Was that just for increased control/flexibility, or did you find that it was actually detrimental to use say "-b 20 -n 5" in the first Normalization stage, if for example using an expert options file for mri_normalize? thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu

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Fwd: [FSL] Neuro Bureau Announces the BRAIN-ART COMPETITION 2013
by MCLAREN, Donald 08 Apr '13

08 Apr '13

In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the third annual Brain-Art Competition. Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The Brain-Art Competition aims to recognize this often unappreciated aspect of the publication process, and highlight the artistic creativity of our community. We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have five award categories: – Best Representation of the Human Connectome – Best Abstract Brain Illustration – Best Humorous Brain Illustration – Best Video Illustration of the Brain – Special Topic: Best Visualization of Probabilistic Connectivity The 'Special Topic' is a new addition to this year’s competition that highlights an important challenge in current connectomics research: visualizing the uncertainty of 3D connections in tractography and functional connectivity data. Submission Deadline: 11:59PM CDT, Wednesday, June 5th, 2013 Award Notification: June 17th during the Neuro Bureau gala event, held at the OHBM Annual Meeting in Seattle. For more information, check out the competition details and submission form at: www.neurobureau.org

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R: Re: cortical thickness normalization
by stdp82＠virgilio.it 08 Apr '13

08 Apr '13

Hi list and Michael, is there a paper that you advise me to cite for mean thickness? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 15.45 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] cortical thickness normalization If you're studying thickness, I'm a fan of using mean cortical thickness as the covariate (since thickness is what you're studying). I've posted on this in the past. cheers,-MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 7:21 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] cortical thickness normalization Hi list, I'm reading a lot of post on this list about cortical thickness normalization. I' m noting very different results on my data when I use mean thickness or ICV as nuisance factor than no factor. I'm confuse on this topic, could you advise the best way, please? Thanks, 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.

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Hacks needed to build freesurfer
by Chris Roat 08 Apr '13

08 Apr '13

I thought I'd share the changes I needed in order to build from the current stable5 source in the repo. I have a Raring Ubuntu distribution, and I tried to install all the necessary libraries. (Independent of building, I still see https://bugzilla.redhat.com/show_bug.cgi?id=905638 in chklc.c of stable5, but I've also commented that out in order to proceed.) Needed updates (diffs below): - Pulled missing unwarpGradientNonlinearity.{h,c} files from somewhere in Google's cache - Updates to configure.in: Bypass gcc 4.4 decision so that libtool is used correctly (Raring has uses 4.7) Correct the MNI libraries link order Change GL include directory Do not create glut Makfile/library (use glut from system) - Update several Makefile.am files to use glut from system - Configure options that I used: --disable-Werror --with-mni-dir=/usr --with-vxl-dir=/usr --with-tcl-include=/usr --with-gl-dir=/usr --x-libraries=/usr/lib/X11 --x-includes=/usr/include/X11 ? include/unwarpGradientNonlinearity.h ? utils/unwarpGradientNonlinearity.c Index: configure.in =================================================================== RCS file: /usr/fscvsroot/dev/configure.in,v retrieving revision 1.519.2.39 diff -b -r1.519.2.39 configure.in 203,210c203,210 < ac_have_gcc_44="no" < if test "${CC}" = "gcc"; then < gcc --version | head -n 1 | awk '{print $2 $3}' | grep "(GCC)4.4." >& /dev/null < if test "$?" = "0"; then < AC_MSG_NOTICE(Have gcc 4.4) < ac_have_gcc_44="yes" < fi < fi --- > ac_have_gcc_44="yes" > # if test "${CC}" = "gcc"; then > # gcc --version | head -n 1 | awk '{print $2 $3}' | grep "(GCC)4.4." >& /dev/null > # if test "$?" = "0"; then > # AC_MSG_NOTICE(Have gcc 4.4) > # ac_have_gcc_44="yes" > # fi > #fi 1229c1229 < LIBS_MNI="-lnetcdf -lhdf5 -lvolume_io2 -lminc2" --- > LIBS_MNI="-lvolume_io2 -lminc2 -lnetcdf -lhdf5" 2748c2748 < [ ac_gl_includes="$withval"/include --- > [ ac_gl_includes="$withval"/include/GL 3472d3471 < glut/Makefile Index: fsgdf/fsgdf_wrap.c =================================================================== RCS file: /usr/fscvsroot/dev/fsgdf/fsgdf_wrap.c,v retrieving revision 1.18 diff -b -r1.18 fsgdf_wrap.c 110c110 < #include <tcl.h> --- > #include <tcl8.5/tcl.h> Index: Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/Makefile.am,v retrieving revision 1.224.2.13 diff -b -r1.224.2.13 Makefile.am 13d12 < glut \ Index: mri_probedicom/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/mri_probedicom/Makefile.am,v retrieving revision 1.7 diff -b -r1.7 Makefile.am 5c5 < AM_CFLAGS=-I$(top_srcdir)/glut $(GL_CFLAGS) \ --- > AM_CFLAGS=$(GL_CFLAGS) \ 14c14 < $(X_LIBS) $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a --- > $(X_LIBS) $(LIBS_OPENGL) -lglut Index: mris2rgb/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/mris2rgb/Makefile.am,v retrieving revision 1.8 diff -b -r1.8 Makefile.am 14d13 < -I$(top_srcdir)/glut \ 26,27c25 < $(LIBS_OPENGL) -lGL $(LIBTIFF) \ < $(top_builddir)/glut/libglut.a --- > $(LIBS_OPENGL) -lGL -lX11 $(LIBTIFF) -lglut Index: mris_show/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/mris_show/Makefile.am,v retrieving revision 1.7 diff -b -r1.7 Makefile.am 6d5 < -I$(top_srcdir)/glut \ 15c14 < $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a --- > $(LIBS_OPENGL) -lglut Index: nmovie/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/nmovie/Makefile.am,v retrieving revision 1.11.4.3 diff -b -r1.11.4.3 Makefile.am 10,11c10 < -I$(top_srcdir)/unix \ < -I$(top_srcdir)/glut --- > -I$(top_srcdir)/unix 16,17c15 < -I$(top_srcdir)/unix \ < -I$(top_srcdir)/glut --- > -I$(top_srcdir)/unix 27c25 < $(top_builddir)/glut/libglut.a --- > -lglut 31c29 < $(top_builddir)/glut/libglut.a --- > -lglut Index: stim_polar/Makefile.am =================================================================== RCS file: /usr/fscvsroot/dev/stim_polar/Makefile.am,v retrieving revision 1.9 diff -b -r1.9 Makefile.am 7c7 < -I$(top_srcdir)/glut $(GL_CFLAGS) --- > $(GL_CFLAGS) 14c14 < $(X_LIBS) $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a --- > $(X_LIBS) $(LIBS_OPENGL) -lglut

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Re: [Freesurfer] Fwd: Error with experimental design using FSGD
by Douglas N Greve 08 Apr '13

08 Apr '13

Hi Joshua, you do not have samples for all of your groups (eg, group0bp2-2-1). doug On 04/04/2013 11:59 PM, Joshua deSouza wrote: > Hello Douglas, > > I have done as you have suggested and have created 16 classes with 2 > different groups, and 3 discreet variables. However, I seem to be > getting the same error but with a a different condo. The error is : > matrix is ill-conditioned or bad scaled, condo = 1e+08. The only 2 > continous variables are age and TIV. There is no strong correlation > between either continous variable. I also used another group instead > because the sample size was larger and I thought it might help. > > The FSGD file = thomas6.txt > The design matrix = Xg.dat > The contrast matrix = t6.txt > > Please let me know on what should be done or if I have overlooked > anything. I have done the necessary processing according to the steps > in the tutorial. Please let me know if you require any morer files > such as the .mgh files. > > Thank you for your time in this matter. > Joshua > > > On Thu, Apr 4, 2013 at 11:47 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Joshua, you should start by not coding gender and handedness as > continuous variables. In doing this, you are saying that you expect > right handers to have 2x the thickness as left handers (or females to > have 2x the thickness as males). You need 8 classes. If your "voxel" > variable is discrete, then you will need 16 classes. > doug > > > > > On 04/04/2013 05:22 AM, Joshua deSouza wrote: > > > > Hello Sir/Madam, > > > > I am currently running a statistical test using the FSGD method. > I am > > encountering a problem in relation to the creation of the glmdir > > folder when I run the mri_glmfit function. I recieve an ERROR > message > > that tells me that the design matrix (automatically generated) > is ill > > conditioned or badly scaled, condo = 10565.7. All the steps before > > creating the glmdir folder have been done in accordance with the > FSGD > > group analysis tutorial on the freesurfer wiki. > > > > The command line is : mri_glmfit --y lh.thomas4.10.mgh --fsgd > > thomas4.txt dods --C t4.txt --surf fsaverage lh --cortex --glmdir > > lh.thomas4.glmdir > > > > The FSGD file = thomas4.txt ( contains 2 groups and 5 variables) > > The data matrix = Xg.dat > > The contrast matrix = t4.txt > > > > There are 3 columns of variables that have discreet values of > either 1 > > or 2. However I have tried this with another FSGD file (thomas3.txt) > > that contained 4 variables of which 2 were continous and the > other 2 > > were in 1s' and 2s'. > > > > The contrast matrix of thomas3.txt = C.dat > > The design matrix of thomas3.txt = Xg1.dat > > > > I was able to generate a glmdir using mri_glmfit with > thomas3.txt and > > generate a surface for tksurfer to use. The file created was the > > sig.mgh file which was then compared with the fsaverage files. > However > > once I added another variable titled "voxel" in thomas4.txt, I > > received the error message. > > > > I did a correlation of the columns containing 1s and 2s in the FSGD > > file thomas4.txt using Matlab and have not found any significant > > correlation with each other. > > > > Please do advise on how to solve this issue and also from where the > > problem could stem from as I am unsure as to the nature of the > problem. > > > > Thank You for your patience and assistance > > > > Joshua > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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: 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the 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. > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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