Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

how do I register rh.dpial.ribbon.mgz to rawavg.mgz
by John Herrington 31 Aug '10

31 Aug '10

I have successfully run a subject through recon-all --all using freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0. I am trying to spatially align and overlay rh.dpial.ribbon.mgz onto rawavg.mgz. Based on info from prior posts, I've tried the following commands: mri_convert rh.dpial.ribbon.mgz -rl rawavg.mgz rh_dpial_ribbon_rawavespace.nii.gz ...and... mri_vol2vol --mov rh.dpial.ribbon.mgz --targ rawavg.mgz --o rh_dpial_ribbon_rawavespace.nii.gz --regheader --interp nearest These commands had identical outputs: the rh_dpial_ribbon_rawavespace.nii.gz file was in the same general orientation as rawavg.mgz, but misaligned. It looks like the rh.dpial.ribbon.mgz is in a different coordinate space than rawavg.mgz (i..e, not native), but I could not find documentation on which space that is, or where to find the transformation file(s) for it. Could someone send me an example command for how to transform rh.dpial.ribbon.mgz into the same space as rawavg.mgz? Thanks, John

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EEG source localization?
by Andrea Seisler 31 Aug '10

31 Aug '10

I have used freesurfer in the past for functional imaging data. Can source localization also be completed for EEG data utilizing the available anatomic MR images? Thanks, Andrea -- Andrea R. Seisler Laboratory Manager Human Electrophysiology Facility Social, Life, & Engineering Sciences Imaging Center 120 Chandlee Laboratory The Pennsylvania State University University Park, PA USA 16802 Phone: 814-865-6774 Email: ars17(a)psu.edu

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retinotopy - Freesurfer 5.0 problem
by Katie Bettencourt 31 Aug '10

31 Aug '10

I was trying to do retinotopic analysis on a dataset using the new Freesurfer v5.0.0 on a 64bit Linux (Red Hat 4.1.2-48 CentOS 5.5) computer and have run across a problem. I set up the analysis using mkanalysis-sess as suggested in an earlier email to the list, but when I try to run selxavg3-sess it errors out. The commands I ran were: mkanalysis-sess -analysis retino26-lh -surface self lh -fwhm 0 -retinotopy 55.467 -paradigm retino.par -TR 2.6 -runlistfile polar_runs.txt selxavg3-sess -a retino26-lh -s spicyrobin -df retino-dirfile It gets through all the preprocessing and then this is the output (the matlab error is one I know about, if that is causing the problem I can talk to our IT here about getting it fixed): preproc-sess done ------------------------------------------- /home/kcb/mri-space/spicyrobin Tue Aug 31 15:29:38 EDT 2010 anadir = /home/kcb/mri-space/spicyrobin/bold/retino26-lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2010 The MathWorks, Inc. Version 7.10.0.499 (R2010a) 64-bit (glnxa64) February 5, 2010 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:TooManyInputs Too many input arguments. > In matlabrc at 227 >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $ outtop = /home/kcb/mri-space Extension format = nii nruns = 4 autostimdur = outanadir = /home/kcb/mri-space/spicyrobin/bold/retino26-lh Found 117359/125110 (93.8) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 1024, nX = 36, DOF = 988 Saving X matrix to /home/kcb/mri-space/spicyrobin/bold/retino26-lh/Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 247 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n thanks, Katie

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Question on freesurfer statistical values output
by Daniel Goldberg 31 Aug '10

31 Aug '10

Hi, I have processed about 50 subjects using freesurfer (freesurfer_stable4.4.0). I'm now taking out the values for cortical thickness from the STATS and have been noticing the following problem. I'm opening the files /stats/lh.aparc.a2005s.stats and /stats/rh.aparc.a2005s.stats. Those files should have 78 values of cortical thickness for different areas of the brain, however in some cases (half from those I have open so far) for the left hemisphere (only happening in the left hemisphere but not in the right so far) there are only 77 values and it is the "S_subcentral_ant" the value who is missing (completely missing from the list, not even a zero value assigned) in all those cases. Is this something that I should expect or is this an error/bug? At the end of the recon-all-status.log file, it says it finished without error. Thanks, Daniel

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Freesurfer v5.0.0 longitudinal processing error
by Simmons, Andy 31 Aug '10

31 Aug '10

Dear All, I have run into problems with a longitudinal analysis using v5.0.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) that seemed to work fine under v4.5.0. For both analyses I processed the raw data from scratch since they were run on different clusters. Following the instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing I initially processed all images using the cross sectional stream, eg recon-all -s PATIENT016_TIMEPOINT1 -i PATIENT016_TIMEPOINT1 then created a template from all time points for each subject, eg recon-all -base PATIENT016 -tp PATIENT016_TIMEPOINT1 -tp PATIENT016_TIMEPOINT2 -tp PATIENT016_TIMEPOINT3 -all Finally I tried to run the longitudinal processing stream, eg recon-all -long PATIENT016_TIMEPOINT1 PATIENT016 -all where I ran into the following error message "ERROR: longitudinal base ID cannot be the same as a timepoint subject ID (in /home/asimmons/images/FREESURFER/PATIENT016/base-tps) Find more info at: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing" The longitudinal base ID is however not the same as any of the timepoints in /home/asimmons/images/FREESURFER/LNDMCI016/base-tps which just contains a list of the time points as expected - PATIENT016_TIMEPOINT1 PATIENT016_TIMEPOINT2 PATIENT016_TIMEPOINT3 Best wishes, Andy Simmons ---- Dr Andy Simmons Reader in Neuroimaging & Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simmons(a)kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-… ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116

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make_average_surface error?
by Jeff Sadino 31 Aug '10

31 Aug '10

Hello, I issued this command to make an average subject: make_average_subject --subjects 2101 2102 2103 --out uh3 I wanted to verify the average thickness file is what it sounds like. I used the recon-all -qcache on each subject individually, read the fwhm0 thickness files into matlab, and averaged vertex #100. However, when I look at vertex #100 from the uh3 surf folder, the numbers don't match. What is the reason for this? I am using freesurfer 4.3.1. Thank you, Jeff Sadino

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Notes on CUDA Acceleration
by Richard G. Edgar 31 Aug '10

31 Aug '10

Greetings, I've been asked to provide some extra information about GPU support in Freesurfer (being the one guilty of mri_em_register_cuda...). Firstly, there are no immediate plans for OpenCL support. It would be very nice to have - with ATI, NVIDIA _and_ x86 multicore backends. However, it's far less mature than CUDA. The good news is that the really 'hard' bit is restructuring the algorithms to fit well on a GPU. The syntax of CUDA and OpenCL is very similar (strange that....), but OpenCL is more verbose. As for cards..... for what is in the current release, any GeForce GTX-200 series or Tesla 10 series (i.e. C1060 and S1070) card should work (I don't know the Quadro model numbers - CUDA architecture 1.3 is the key feature). I think that everything should actually work on somewhat older cards, but the compile flags will have to be tweaked. So long as that threshold is reached, the only issue is the amount of RAM needed. Currently, I expect that any card with at least 1 GiB of RAM will have plenty, and the threshold for mri_em_register_cuda will be much lower than that. Going forward, I would strongly recommend purchasing 'Fermi' class cards. These are the GTX 400 series, and Tesla 20 series. The new architecture lifts some hardware limits on GPU kernels which are crippling for portions of mri_ca_register. With a more accelerated mri_ca_register, RAM limits may also come into play, until I can come up with a suitably cunning GPU implementation of the Gaussian Classifier Array (right now, I'm going to burn around 2 GiB on a single GCA, to make implementation simple). However, I have bigger fish to fry first. One final thing: Nick and I found last week that the accelerated mri_em_register_cuda doesn't seem to work prior to skull stripping. I'm going to work on this this week, but if you want to continue using the GPU accelerated binary, you'll have to turn off the FAST_TRANSLATION and FAST_TRANSFORM flags in mri_em_register.c, and recompile. This will increase the runtime to around 4 minutes on ernie, but will give results identical to the CPU code. I hope this is helpful, Richard

5 9

autorecon2
by Mareen Kussatz 30 Aug '10

30 Aug '10

> Hi to all, > > there are still correction problems after recon-all! > > After recon-all not all of the corrections are visible??????? > > I corrected e.g. 10 slices. I deleted some voxels in wm.mgz as aux volume, non-white matter classified as white matter. I saved the aux volume and i startet recon-all! > After running without errors, i checked in tkmedit. There were 5 of 10 slices corrected, but not the others???? With means there are still 5 slices of the previous corrected including some non-white matter classified as white matter! When i open the cor files for these slice, the corrections are visible!! > > > please help to find the bug > > Best Mareen > > > > -------- Original-Nachricht -------- >> Datum: Fri, 13 Aug 2010 11:38:01 -0400 (EDT) >> Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> An: Mareen Kussatz <mareenkussatz(a)gmx.de> >> CC: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] autorecon2 > >> Hi Maureen, >> >> if you exit tkmedit and reload the wm.mgz before rerunning recon-all are >> your edits in it? It shouldn't matter whether you edit/save in the main or >> aux volume. >> >> cheers >> Bruce >> >> On Wed, 11 Aug 2010, Mareen Kussatz wrote: >> >>> Hi to all, >>> >>> after correcting white matter problems, we saved the wm as aux volume >> and we tried also to save it as main volume. And than, we started recon-all >> -autorecon2-wm -subjid (subject file name). The process ends without any >> error for both conditions but after checking the tkmedit, there weren´t any >> corrections visible and actually there were no change at all.??? >>> >>> We just want to know if it is a syntax problem or if there is something >> wrong with the freesurfer itself. >>> >>> thanks and best regards. >>> >>> Mareen Kussatz >>> > > 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. -- GMX DSL SOMMER-SPECIAL: Surf & Phone Flat 16.000 für nur 19,99 ¿/mtl.!* http://portal.gmx.net/de/go/dsl

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FS5 Longitudinal broken
by Martin Reuter 30 Aug '10

30 Aug '10

Dear FreeSurfer user, we are sorry to let you know that the longitudinal stream in FreeSurfer Release 5.0 is broken due to some last minute improvements to mri_robust_register. It shares some of it's code with mri_robust_template, where the 'improvements' break the processing, which leads to blurry average images in some cases. We are working on a fix and will let you know immediately when it is ready. Until then you can keep processing your longitudinal data with 4.5 which does not have the bug. Best regards, Martin Reuter -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Web : http://reuter.mit.edu

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Re: [Freesurfer] PALS-B12-based ROIs in fsaverage in v5.0.0
by Nick Schmansky 30 Aug '10

30 Aug '10

yes, it can be used with subjects processed prior to v5. there is nothing v5 specific about the rois (it just happened that they became available in this release). the fsaverage subject is the same as v4. n. On Mon, 2010-08-30 at 09:37 -0700, Wayne Su wrote: > Hi Nick, > > Can I use this atlas on subjects processed by the earlier version? > > Regards, > Wayne > > > On 27/08/10 9:42 AM, "Nick Schmansky" <nicks(a)nmr.mgh.harvard.edu> wrote: > > > there is one new feature in the new v5.0.0 which was missing from the > > early release notes, but that which some people might have an interest. > > the Van Essen Lab created some ROIs on their PALS-B12 atlas, and then > > mapped them to the freesurfer fsaverage subject. some basic info is > > here: > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12 > > > > it will take a bit of freesurfer expertise on your part to make use of > > these, as you would need to: > > > > 1) identify which labels (ROIs) are of interest to you (by viewing > > the .annot file on fsaverage) > > 2) use mri_annotation2label to extract the labels > > 3) use mri_label2label to map from fsaverage to your subject > > 3) optionally use mri_anatomical_stats to get stats about those labels > > > > n. > > > > > > _______________________________________________ > > 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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Freesurfer August 2010