Freesurfer

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Update on mri_em_register_cuda
by Richard G. Edgar 01 Sep '10

01 Sep '10

Greetings, I've been running more extensive tests on mri_em_register_cuda, trying to determine why it sometimes gives substantially different results to mri_em_register. The problem appears to stem from the construction of the transform matrix on the CPU and GPU. This occurs slightly differently on each platform, leading to inevitable differences in output. These can be large enough to 'capture' the search to a different transform. If you are encountering problems with mri_em_register_cuda, I would suggest making the following changes to mri_em_register.c: At the start of the file (around line 48), there are two lines which read #define FAST_TRANSLATION 1 #define FAST_TRANSFORM 1 change these to #define FAST_TRANSLATION 0 #define FAST_TRANSFORM 0 and recompile. This will cause the program to compute all of the transforms on the CPU, and only evaluate the energy function on the GPU. Runtime will increase from around 30 seconds to around 4 minutes. Regards, Richard

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Re: [Freesurfer] Freesurfer 5.0.0 recon-all i/o load
by Martin Reuter 01 Sep '10

01 Sep '10

Hi David, there is a new robust motion correction used in 5.0 which is more accurate than the flirt, but it needs a lot of memory. You can go back to the old version by adding the parameter: -flirt-motioncor Best, Martin On Tue, 2010-08-31 at 18:01 -0700, David Mischel wrote: > We run our Freesurfer (recon-all) jobs on a grid (Sun Grid Engine) > which uses a single NFS file server for all data. Since we have begun > using Freesurfer 5.0.0 we have noticed very intense I/O activity as > soon as recon-all jobs begin. The level of activity is markedly > greater than we have seen in previous versions. The effective > cumulative impact on our file server, when scores of jobs are launched > at once, is significant and degrades the server's response. > > > > Has something changed about how data files are accessed at the > beginning of a recon-all job? If so, is there a way to "ease into it" > so that the initial activity is more distributed as processing > continues? > > > > < david > > > > > > David Mischel > > Manager of IT > > Center for Imaging of Neurodegenerative Diseases (CIND) > > http://www.cind.research.va.gov/ > > VA Medical Center > > 4150 Clement Street, 114M > > San Francisco, CA 94121 > > voice: 415-221-4810 x3864 > > fax: 415-668-2864 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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base processing error
by Derin Cobia 01 Sep '10

01 Sep '10

In creating the base template for two of our subjects, the superior portion of the volume somehow got cut off (see attached). The original volumes for both time points are fine (i.e., do not display this problem), and completed the cross-sectional stream without problem. Is this an issue with aligning volumes from both time points, can it be fixed? Thanks. CentOS 5.2 FS v4.5.0 -Derin

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standard deviation using mri_segstats
by corinna bauer 01 Sep '10

01 Sep '10

Hello, Is there a way to calculate standard deviation of PET data within each segmentation using mri_segstats? Corinna

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FSDG problem
by keepmoon 01 Sep '10

01 Sep '10

Dear all, I am using Freesurfer longitudinal analysis to detect the relationship between the change of thickness in patients and a clinical test (ex: MMSE). I just have MRI of patients at two time points (baseline and followup) without normal control subjects. I have already completed longitudinal analysis following Freesurfer instruction. Now I am not sure how to design the FSDG file and contrast vector. I want to measure whether the change of thickness of patients (from baseline to followup) has some relationship with MMSE. Mean thickness of the brain is a covariate. The following is the FSDG and contrast I designed. Can anyone help me have a look whether it is right? Thanks in advance! Joe FSGD: GroupDescriptorFile 1 Title MMSEandthickness Class Baseline Class Followup Variable MMSE mean_thickness Input subject1 Baseline 21 2.6 Input subject2 followup 18 2.7 . . . Contrast: 1 -1 0.5 0.5 0 0

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Freesurfer 5.0.0 recon-all i/o load
by David Mischel 31 Aug '10

31 Aug '10

We run our Freesurfer (recon-all) jobs on a grid (Sun Grid Engine) which uses a single NFS file server for all data. Since we have begun using Freesurfer 5.0.0 we have noticed very intense I/O activity as soon as recon-all jobs begin. The level of activity is markedly greater than we have seen in previous versions. The effective cumulative impact on our file server, when scores of jobs are launched at once, is significant and degrades the server's response. Has something changed about how data files are accessed at the beginning of a recon-all job? If so, is there a way to "ease into it" so that the initial activity is more distributed as processing continues? < david David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864

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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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