Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

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

2 1

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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How to validate custom-built FreeSurfer binaries?
by Malcolm Tobias 30 Jan '12

30 Jan '12

My foray into custom-built binaries looks promising. Using the distributed (CentOS4) build of 5.1, I'm running the Bert/Ernie benchmark in ~12 hours. If I build this myself (using 4.1.2 / Red Hat 4.1.2-51) I can run in ~10 hours. If I build the same code using the Intel compilers (12.0.0) with pretty generic options I can get this down to ~9 hours, which is the 10% speed-up that Nick suggested. Now the hard part: What steps should I take to validate these custom-built binaries before users start using them for production runs? It seems like at a minimum I should run and pass all of 'make check'. These seem to stop after the first error. I wonder if it would be better to have them run to completion to get an idea of what all passes/fails? -For gcc, it fails on the test for libg2c. I can understand why you need to test for this before releasing to the world, but is there some way for me to disable this particular test so it doesn't stop the rest of the tests from running? -For the Intel compilers, the environment doesn't seem to inherit my LD_LIBRARY_PATH so most of the tests fail early on because of missing libraries. Any thoughts on how to fix this? The 'make check' seems to test for basic functionality, not necessarily the consistency of the results (please correct me if I'm wrong). To test the validity of the processing, it seems the Bert/Ernie sample data is used. I'm not sure what parts of the results I should check? It's been suggested that I compare the results of the aseg.stats and aparc.stats files, possibly using asegstatsdiff and aparcstatsdiff. Does this seem reasonable? If so, what levels of differences would be considered acceptable? To put this all another way, what do you guys normally do to test out a build before releasing it? Cheers, Malcolm -- Malcolm Tobias 314.362.1594

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Performance questions
by Malcolm Tobias 30 Jan '12

30 Jan '12

Is there a standard benchmark for FreeSurfer? I've been using the data under subjects (Bert?/Ernie?) and running a recon- all: recon-all -s ernie -i ./sample-001.mgz -i ./sample-002.mgz -all On our hardware using the 5.1 distributed binary (freesurfer-Linux- centos4_x86_64-stable-pub-v5.1.0.tar.gz) it takes about 12 hours. I was surprised that 5.1 was running so much faster than 5.0. With 5.0 (freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0.tar.gz) it was taking about 18 hours. Did anyone else notice a big speed-up from 5.0 to 5.1? Maybe it's a difference between centos5 vs. centos4? If so, wouldn't you expect the former to be faster? If I back-port the changes Nick made to configure.in for the dev branch to the stable release of 5.1 and build from source on our systems, I'm able to run in ~10 hours. I'm guessing this is mostly due to the difference in the versions of gcc used on our system (4.1.2) vs. those used for the centos4 distributed binary? For the dev release, it's taking about ~11 hours. I'm guessing the dev branch is mostly focused on features/bug-fixes and performance is only looked at before a release? Besides GPUs, what else are people doing to increase performance? Cheers, Malcolm -- Malcolm Tobias 314.362.1594

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talairach_with_skull_2.lta missing
by cloud.ctrl＠me.com 30 Jan '12

30 Jan '12

In article http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix, it is mentioned that talairach_with_skull_2.lta is created during autorecon2, and that it can be useful when troubleshooting skull-strips, however I do not find talairach_with_skull_2.lta in the mri/transforms directory of any of my subjects. Has the processing been altered since the creation of this article or is my data incomplete? If incomplete, why?

2 1

ERROR with mri_glmfit-sim
by Antonella Kis 30 Jan '12

30 Jan '12

Hi, I was trying to run for my FA group study the following: mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --sim neg perm 10000 3 permcsd\ --cwpvalthresh .05 but I got an error: Flag permcsd unrecognized and then is asking me agout --sim sign. Can you please help? THANK YOU! Antonella

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Freesurfer January 2012