Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

stats on mgz's
by Michael Harms 30 Jan '12

30 Jan '12

Does FS have a generic binary for natively getting simple stats from mgz files -- e.g., min, max, range, percentiles, etc? i.e., something analogous to 'fslstats', but which works directly on mgz files? thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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control point guidance
by Michael Harms 30 Jan '12

30 Jan '12

Hi guys, We are currently trying to fix some errors in the white/pial surfaces where there are thin white matter strands by using control points, and are noticing a couple things: 1) The resulting WM surface in the area of the CPs can end up too far into the GM instead. Given that, is there any practical guidance for how to think about the surrounding spatial extent that is impacted by a given CP? i.e., How do CP's actually get used within mri_normalize in an algorithmic sense? 2) The surfaces are being impacted in places distant from the CPs. e.g., CP's placed in the left anterior temporal lobe are resulting in surface changes in the right anterior temporal lobe. And when I difference the original norm.mgz vs. the one obtained after using CP's, I'm seeing an odd pattern of intensity differences which is clearly not limited to just the area of the CP's (which would be my expectation). This is version 5.1. thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Re: [Freesurfer] qdec analysis
by Douglas N Greve 30 Jan '12

30 Jan '12

Does /8000_series/8000_series/qdec/example_contrast/y.mgh exist? doug Cat Chong wrote: > yes, it does exist.. > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Cat Chong <cavecreekcutter(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, January 26, 2012 9:34 AM > *Subject:* Re: [Freesurfer] qdec analysis > > Does y.mgh exist? y.mgh is the stack of data that should be created by > qdec. I think it's called y.mgh and I think that it is in the GLM dir, > but it might be in the directory just above it. > doug > > Cat Chong wrote: > > Hi Doug, > > I spoke too soon. I tried to follow your advice and run either command: > > > > > > In a terminal, cd to the GLM directory inside qdec directory and then > > cd to the folder of the contrast of interest and run > > mri_segstats --id 1 --slabel fsaverage lh yourlabel --i gamma.mgh > > --sum yourlabel.sum > > the output yourlabel.sum will have information about the label > > including the mean gamma (gamma is a map of the contrast values). > > > > Along those same lines, you can run > > > > mri_segstats --id 1 --slabel fsaverage lh yourlabel --i y.mgh --avgwf > > yourlabel.dat > > y.mgh should be there already and is a stack of thickness maps for all > > your subjects > > the output yourlabel.dat will be a single column with the average > > thicknesses for each subject > > > > ..... however the error message I receive is that y.mgh could not be > > opened...and I also don't seem to have a gamma.mgh file? > > > > Here is the error message, I received: > > > > mri_segstats --id 1 --slabel fsaverage lh lh.Temporal_lobe.label --i > > y.mgh --avgwf lh.Temporal_lobe.label.dat > > sysname Darwin > > hostname fmris-Mac-Pro-2.local > > machine x86_64 > > user fmri > > Constructing seg from label > > Loading y.mgh > > mghRead(/8000_series/8000_series/qdec/example_contrast/y.mgh , -1): > > could not open file. > > Filename extension must be .mgh, .mgh.gz or .mgz > > ERROR: loading y.mgh > > fmris-Mac-Pro-2:example_contrast fmri$ ls > > X.mat lh-Avg-Intercept-thickness qdec.fsgd > > Xg.dat lh-Avg-thickness-Age-Cor rstd.mgh > > beta.mgh lh-Diff-1-0-Cor-thickness-Age rvar.mgh > > contrasts lh-Diff-1-0-Intercept-thickness sar1.mgh > > contrasts.sig.mgh lh.Temporal_lobe.label surface > > dof.dat lh.Temporal_lobe.label.dat y.fsgd > > error.log mask.mgh y.mgh > > fwhm.dat mri_glmfit.log > > > > thanks so much for your help: > > cat > > > > > > > > > -- > 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 > Fax: 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> > > _______________________________________________ > 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

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Re: [Freesurfer] group wrfx error: MRInormWeights: value less than or eq to 0.
by Douglas N Greve 30 Jan '12

30 Jan '12

Yes, that does look excessive. There should be a "masks" volume that gets created. This will have the individual masks for each subject. You can load this something like tksurfer fsaverage lh inflated -overlay masks.mgh -fthresh 0.5 -t masks.mgh ie, load it as an overlay and timecourse. When you click on a point, the time course will show your the value at each subject, and you can look for subjects where it is 0. You should also do this with the cesvar map (that's probably where your problem is). doug Sid Kundu wrote: > Hi Doug, > > Thanks for the help, was able to get the group analysis to work. > However, I went back and looked at the mask that was being created and > passed into the glmfit and got what's shown in the attached pictures. > The ammount of zero valued voxels seems really high. Not sure if this > is out of the ordinary or not, but might indicate a problem somewhere > else in my analysis. > _________________________________ > Sid Kundu > Biomedical Engineering > Boston University > > > > On Thu, Jan 26, 2012 at 11:59 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Try the version here > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_concat > doug > > Sid Kundu wrote: > > Hi Doug, > > The --prune argument doesn't work with mri_concat in the > version of freesurfer I am using. Any other way to accomplish > this? > _________________________________ > Sid Kundu > Biomedical Engineering > Boston University > > > > On Wed, Jan 25, 2012 at 3:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > I'm guessing that there is a voxel (or more) in cesvar that > is 0 > for a subject (or more). Usually such voxels are masked out by > pruning the input ces. You can create your own mask with > > mri_concat tal.cs.nii tal.cesvar.nii --prune --o junk.mgh > mri_binarize --i junk.mgh --min .00000000000001 --o newmask.mgh > > Then pass this mask to mri_glmfit with the --mask option. > > doug > > Finnegan Calabro wrote: > > Hi Doug et al, > > We're running into a problem doing a wrfx group > analysis using > FreeSurfer 4.5. Looks like the glmfit is having > trouble with > the weights. We tried running it for different subsets > of our > subjects, and get the same thing, so it's not one subject > contaminating the analysis. Any guess where we should look > for tracking this down? Presumably the cesvar files are > screwed up somehow, which would imply something went > wrong in > the individual selxavg3's. But any ideas about what could > lead to this? The individual overlays all seem to look ok. > > > > [sidkundu@brodmann all-vs-null]$ mri_glmfit --y tal.ces.nii > --osgm --glmdir tal.wrfx.osgm --nii --mask ../tal.mask.nii > --wls tal.cesvar.nii > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 > greve Exp $ > cwd > > /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null > cmdline mri_glmfit --y tal.ces.nii --osgm --glmdir > tal.wrfx.osgm --nii --mask ../tal.mask.nii --wls > tal.cesvar.nii sysname Linux > hostname brodmann.bu.edu <http://brodmann.bu.edu> > <http://brodmann.bu.edu> > <http://brodmann.bu.edu/> > > machine x86_64 > user sidkundu > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 1 > y > /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii > logyflag 0 > usedti 0 > mask ../tal.mask.nii > maskinv 0 > glmdir tal.wrfx.osgm > IllCondOK 0 > DoFFx 0 > wFile tal.cesvar.nii > weightinv 1 > weightsqrt 1 > Creating output directory tal.wrfx.osgm > Loading y from > > /home/sidkundu/freesurfer/sessions/Heading-TTP/1-24-12-TTP/TTP_analysis/all-vs-null/tal.ces.nii > Saving design matrix to tal.wrfx.osgm/Xg.dat > Matrix condition is 1 > Pruning voxels by thr: 0.000000 > Found 260736 voxels in mask > Saving mask to tal.wrfx.osgm/mask.nii > search space = 2.08589e+06 > ERROR: MRInormWeights: value less than or eq to 0. > c=34, r=2, s=33, v=0 > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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 <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> > > -- 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

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configure fsfast to use octave instead of matlab
by Kiley 30 Jan '12

30 Jan '12

Hi, I am currently using my macbook to carryout the analysis steps of my retinotopy data. Since I was having problems with running selxavg3 with the version of matlab installed here (matlab: No MATLAB bin directory for this machine architecture), I installed octave to circumvent the problem. I assume I need to configured the terminal in order to use octave instead of matlab, because currently I still get the matlab error (above) when I run selxavg3. I am new to macs and freesurfer, and I am sure it is a matter simply setting a path to octave, but so far I have had no luck working out how to do this. Your help would be very much appreciated! Thanks in advance Kiley

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Save segmentation results as nifi files
by Fellhauer, Iven 30 Jan '12

30 Jan '12

Dear all, I run recon-all with the -autorecon1 and -autorecon2 options. Now I want to store the segmentation results in a spm like way. One nifti file for each matter. Can I do this with freesurfer? And how can I do this with freesurfer? Best regards, Iven Fellhauer ---------------------------------------------------------------- Universitätsklinikum Heidelberg Zentrum für Psychosoziale Medizin Klinik für Allgemeine Psychiatrie Sektion für Gerontopsychiatrie Voßstr. 4 69115 Heidelberg Tel.: +49 (0) 6221 - 56 7578 Email: iven.fellhauer(a)med.uni-heidelberg.de

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Caudate segmentation and exporting ROIs
by Paula Banca 29 Jan '12

29 Jan '12

Dear Freesurfer's, I'm wondering if it is possible to use FreeSurfer to do the caudate segmentation automatically. I'm asking that because I did all my fMRI data analysis in BrainVoyager and currently I need to run more statistical analysis in this specific region (caudate). For that I need to have this ROI. However, to create it manually in BV I would need a lot of time. I'd like to check if there is a possibility to create this ROI automatically,using Freesurfer, and then export it to BV in order to finish my functional analysis there. Do you think this can be done ? Thanks in advance! All the best, Paula

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mris_anatomical_stats: no smoothing effect when using ?h.area file as target
by Jürgen Hänggi 29 Jan '12

29 Jan '12

Dear FS experts I have done group comparisons wrt thickness, surface area and volume. The found clusters were written out as annotations, transformed into each individual space, and then the corresponding values were extracted. When using mris_anatomical_stats, values are different for thickness and volume maps depending whether I used the --nsmooth 15 option or not. So good so far. However, when using the same command (see below) for ?h.area files, extracted values are the same whether or not I used the --nsmooth 15 option. mris_anatomical_stats -a rh_area_parietal_insular.annot -t rh.area -nsmooth 15 -f subject/stats/output.stats subject rh It seems that the --nsmooth 15 option in mris_anatomical_stats does not affect (smooth) the area maps that were used to extract the values. Is this what one has to be expected? Or is it something like a bug? Thanks in advance Best regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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'::conj' has not been declared
by Hazard, E. Starr 28 Jan '12

28 Jan '12

Folks, I am doing my best to follow these instructions from : http://surfer.nmr.mgh.harvard.edu/fswiki/Devel My gcc is 4.4.6 Is there a way to avoid the error below or must I install gcc 3.4.6 as per the MNI readme? cd EBTKS-1.4-src; \ make; \ make install; make[1]: Entering directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make all-am make[2]: Entering directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' if /bin/sh ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF ".deps/Matrix.Tpo" \ -c -o Matrix.lo `test -f 'templates/Matrix.cc' || echo './'`templates/Matrix.cc; \ then mv ".deps/Matrix.Tpo" ".deps/Matrix.Plo"; \ else rm -f ".deps/Matrix.Tpo"; exit 1; \ fi g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF .deps/Matrix.Tpo -c templates/Matrix.cc -o Matrix.o In file included from templates/Matrix.cc:3567: templates/MatrixSpec.cc: In member function 'Mat<Type>& Mat<Type>::conj() [with Type = std::complex<double>]': templates/MatrixSpec.cc:405: error: '::conj' has not been declared make[2]: *** [Matrix.lo] Error 1 make[2]: Leaving directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make[1]: Entering directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' if /bin/sh ./libtool --mode=compile g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF ".deps/Matrix.Tpo" \ -c -o Matrix.lo `test -f 'templates/Matrix.cc' || echo './'`templates/Matrix.cc; \ then mv ".deps/Matrix.Tpo" ".deps/Matrix.Plo"; \ else rm -f ".deps/Matrix.Tpo"; exit 1; \ fi g++ -DHAVE_CONFIG_H -I. -I. -I. -I./include -I./templates -DUSE_COMPMAT -DUSE_DBLMAT -msse2 -mfpmath=sse -MT Matrix.lo -MD -MP -MF .deps/Matrix.Tpo -c templates/Matrix.cc -o Matrix.o In file included from templates/Matrix.cc:3567: templates/MatrixSpec.cc: In member function 'Mat<Type>& Mat<Type>::conj() [with Type = std::complex<double>]': templates/MatrixSpec.cc:405: error: '::conj' has not been declared make[1]: *** [Matrix.lo] Error 1 make[1]: Leaving directory `/home/hazards/COMPILE3/FreeSurf_Support/mni/EBTKS-1.4-src' make: *** [ebtks] Error 2

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Unable to open tkmedit
by Daniel R. O'Young 28 Jan '12

28 Jan '12

I've been trying to open tkmedit but am continually getting an error ("GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found"). I'm using a machine with Ubuntu 11.04 that formerly ran tkmedit. The only suggestion I could find so far was this (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-May/014433.html) Has anyone else run into this error or solutions for it? Daniel O'Young droyoung(a)umd.edu<mailto:droyoung@umd.edu> DSCN Lab

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Freesurfer January 2012