Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Dura too bright/thick: brain extraction
by octavian lie 31 Jan '12

31 Jan '12

Thank you. Unfortunately, we use a Phillips scanner for 3T scans: MPRAGE T1 TR 9.89; TE 4.60. If you have any suggestions, including which of the protocols comes closest, let mw know. Best, Octavian On 1/31/12, Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu> wrote: > Do you have a Siemens scanner? > > You can compare your protocols with the examples at > www.nmr.mgh.harvard.edu/~andre. > > On Tue, 31 Jan 2012, Bruce Fischl wrote: > >> Hi Octavian >> >> what kind of scanner are you using? Andre van der Kouwe and Dylan Tisdall >> (ccd) have developed a multi-echo mprage that allows one to identify dura >> by >> it's short T2*. They might be able to give it to you depending on your >> scanner and relationship with Siemens. Otherwise it can be difficult, as >> lenghtening your TE to reduce the dura signal also reduced gray/white >> contrast. >> >> cheers >> Bruce >> On Tue, 31 Jan 2012, octavian lie wrote: >> >>> Dear All, >>> >>> I am trying to perform brain extraction on T1 3D images, however the >>> dura appears too bright and thick compared to the underlying gray >>> matter. It seems that I have a hard time stripping the dura away. Do >>> you have any suggestions in terms of optimizing freesurfer parameters >>> to help with this problem, or alternatively, do you suggest a specific >>> T1 protocol (TE/TR) to dim the dura a bit? >>> Thank you, >>> >>> >>> Octavian Lie. >>> _______________________________________________ >>> 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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Dura too bright/thick: brain extraction
by octavian lie 31 Jan '12

31 Jan '12

Dear All, I am trying to perform brain extraction on T1 3D images, however the dura appears too bright and thick compared to the underlying gray matter. It seems that I have a hard time stripping the dura away. Do you have any suggestions in terms of optimizing freesurfer parameters to help with this problem, or alternatively, do you suggest a specific T1 protocol (TE/TR) to dim the dura a bit? Thank you, Octavian Lie.

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Installation
by Nooshin Zadeh 31 Jan '12

31 Jan '12

Hi, I am trying to install FS on the mini Mac. I downloaded the darwin leopard version of FS and it went to "Application". For setup configuration step, in tcsh terminal I wrote "setenv FREESURFER_HOME /Application/freesurfer " and then "source $FREESURFER_HOME/SetUpFreeSurfer.csh". It says no such file or directory, but I see SetUpFreeSurfer.csh in the FS folder on the "Application". Once I copied the FS on the desktop and then wrote "setenv" and "source" again. It worked temporarily but when I was done with all installation steps, it did not recognize tkmedit and tksurfer. Can you please guide me how can I fix the problem. Thanks, -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Re: [Freesurfer] re-running mri_glmfit-sim
by Douglas N Greve 31 Jan '12

31 Jan '12

That is a slight bug in that there is no default (you have to specify). Below is the text from running it with --help. If you have an apriori hypothesis that group1 > group2, then choose positive. If you don't know the sign, then use abs. Choosing a sign will yield stronger results (ie, smaller p-values), but you will lose the other sign. doug This is the sign of the threshold used to create the clusters for cluster-wise correction of multiple comparisons. Antonella Kis wrote: > Dear Doug, > > Thank you so much for your help. I still have one more question > please: WHEN i WAS TRYING TO RUN THE: > > mri_glmfit-sim \ > --glmdir Group_Analysis.glmdir \ > --sim neg perm 10000 3 permcsd\ > --cwpvalthresh .05 > > > as you recommended me so withouth --sim-sign I got the error that I > must specify the sign so I choose neg. I believe the default should be > abs but can you please shortly explain what exactly the --sim-sign means? > > Thank you very much. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, January 31, 2012 12:39 PM > *Subject:* Re: [Freesurfer] re-running mri_glmfit-sim > > You have to re-run > doug > > Antonella Kis wrote: > > dear All, > > > > I would like to know if I am running the > > mri_glmfit-sim \ > > --glmdir Group_Analysis.glmdir \ > > --sim perm 10000 3 permcsd \ > > --sim-sign neg \ > > --cwpvalthresh .05 > > > > and I want to change the --sim-sign from neg to positive if I need > to run again the whole simulation or I can just run: > > > > mri_glmfit-sim --glmdir Group_Analysis.glmdir \ --no-sim --sim-sign > pos or how exactly to edit the mri_glmfit in this case? > > > > Also if I need to add one more subject do I need to re-run the whole > simulation or for multiple comparison I can just use the --no-sim option? > > > > Thank you very much! > > Antonella > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 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> > > > > 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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How to visualize the group results after corrections by multiple comparison
by Antonella Kis 31 Jan '12

31 Jan '12

Hi Doug, Sorry I forgot to ask one more question: after I am getting my clusters for my FA group study should I use the fsaverage (which is not on the CVS space) or the concatenated file GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz (registered over the CVS space) or I should use the CVS space to visualize my results, I mean should I use: tkmedit fsaverage orig.mgz \ -ov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh \ -seg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.anat.mgh \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.lut \ -fminmax 1.3 5 or freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/Group_Analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh:colormap=heat Also do I need to use the average value GroupAnalysis.Average-fa-masked.ANAT+CVS-to-avg35.mgz when I run the mri_glmfit or just the concatenated file GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz? THANKS SO MUCH! Antonella

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re-running mri_glmfit-sim
by Antonella Kis 31 Jan '12

31 Jan '12

dear All, I would like to know if I am running the mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign neg \ --cwpvalthresh .05 and I want to change the --sim-sign from neg to positive if I need to run again the whole simulation or I can just run: mri_glmfit-sim --glmdir Group_Analysis.glmdir \ --no-sim --sim-sign pos or how exactly to edit the mri_glmfit in this case? Also if I need to add one more subject do I need to re-run the whole simulation or for multiple comparison I can just use the --no-sim option? Thank you very much! Antonella

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Error with mri_glmfit permcsd
by Antonella Kis 31 Jan '12

31 Jan '12

Hi Doug, I wonder how many hours it can take the mri_glmfit-sim with perm option. This is what I was running yesterday from 2 pm and is still not completed. It can take so long or there may be something wrong? I did not get any error but I have the same number of files as yesterday in my GroupAnalysis.glmdir. I also attached my log file. mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim perm 10000 3 permcsd \ --sim-sign neg \ --cwpvalthresh .05 Thank you for any suggestion and help. Antonella

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About FsFast volume output
by Robert Boldt 31 Jan '12

31 Jan '12

Thank you for a beautiful program. I'm using freesurfer to preprocess fMRI images (using a command similar to that in your manual): preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I want my preprocessed fMRI data to be sampled into 'Common space', but need the data as volume files, not surface file. I solved this by simply deleting fsaverage/mri.2mm/subcort.mask.mgz, and renaming the fsaverage/mri.2mm/brainmask.mgz as subcort.mask.mgz. This resulted in fmcpr.up.sm5.mni305.2mm.nii.gz containing the whole volume instead of only subcortical structures. I made the assumption that the whole brain is sampled to 'Common space', but that all cortical structure are masked out, so that information contained in the surface files would not be replicated. My results are fine, but I'm afraid that I violated some assumption done for the volume files. I'm very grateful for your program, as I would be for an answer Best regards Robert Boldt

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extract beta values ROI
by Lúcia Garrido 31 Jan '12

31 Jan '12

Hello, I'm trying to extract beta values in cortical thickness analysis. For example, if I use qdec to look at the association between cortical thickness and variables A and B, can I extract the vertex-wise parameter estimates corresponding to the association between A and cortical thickness across subjects for a certain ROI? This ROI could be one of the regions from freesurfer parcellation or another saved ROI. I can visualize the beta values by looking at beta.mgh in tksurfer but I'd like to be able to extract them in 'table' format. I think I know how to do extract summary statistics for an ROI, but I'd like instead to extract the betas for each vertex. Many thanks for your help! Lucia

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trying to compile Freesurfer error: '::conj' has not been declared
by Starr Hazard 30 Jan '12

30 Jan '12

Folks, Even when I use gcc-3.4.6 the compilation error recurs. This problem is referred from line 405 of templates.MatrixSpec.cc in the /mni/EBTKS-1.4-src directory. Here is the error again 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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