Freesurfer

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30132 discussions

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?

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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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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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