Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

FSFAST TUTORIAL
by Danny Kim 02 Sep '10

02 Sep '10

Hello all, I've recently downloaded Freesurfer 5 and was going through the FSFAST tutorial. I keep on getting an error saying when I run "preproc-sess -s mgh-101.1 -fwhm 5 -per-run": -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- $Id: preproc-sess,v 1.31.2.4 2010/07/26 15:55:24 greve Exp $ fmri setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects Darwin copernicus.bcricwh.lan 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 /Applications/freesurfer/fsfast-tutorial/my-study /Applications/freesurfer/fsfast/bin/preproc-sess -s mgh-101.1 -fwhm 5 -per-run Thu 2 Sep 2010 11:03:13 PDT instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain mgh-101.1 Template ----------------------------- mktemplate-sess -s mgh-101.1 -d /Applications/freesurfer/fsfast-tutorial/my-study -fsd bold -update Session: /Applications/freesurfer/fsfast-tutorial/my-study/mgh-101.1 ---------------- Thu 2 Sep 2010 11:03:13 PDT find: illegal option -- m find: illegal option -- a find: illegal option -- e find: illegal option -- p find: illegal option -- t find: illegal option -- h find: 1: No such file or directory ERROR: no run directories found Anyone managed to encounter this problem in the past? Thanks in advance for your help! Best Regards, Danny Kim BC Children's Hospital

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getting polar/eccen retinotopy maps into matlab
by Finnegan Calabro 02 Sep '10

02 Sep '10

Hi Doug et al, I'm trying to import the polar and eccentricity maps resulting from a retinotopy analysis into Matlab for some additional manipulation. Specifically, what I'd like is to get something like the output from: surf-sess -s sessid -a rtopy -retinotopy polar/eccen -flat as polar and eccentricity values that I can use to compare to activation from another task (i.e. what are the polar visual field coordinates for all surface locations with significant activation in the other task). The surf-sess command above works and the rest of the field sign analysis looks good, so I think the analysis all went fine, but I'm not sure which files contain the data I'm looking for (seems like map-real/imag-?h.w, but if so, I'm not clear on how to combine the real and imaginary parts). Thanks! Finn

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intensity correction error
by Mareen Kussatz 02 Sep '10

02 Sep '10

Hi to all, thanks for your help, we could solve the autorecon2 problem! there is another problem with autorecon1... ncid 4: No space left on device mivarput1: MINC package entry point nu_evaluate: crashed while running mincresample (termination status=768) nu_correct: crashed while running nu_evaluate (termination status=768) ERROR: nu_correct Darwin RK2.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 The Intensity correction ist not running, after we had an error at talairach transformation step. I went to tkregister2 (talairach is not ok- and started again recon-all, finally get that error??? best Mareen -- 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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optseq2 polynomial order
by Leo Fernandino 01 Sep '10

01 Sep '10

Hi there, I noticed that when I include additional polynomials as nuisance variables, the efficiency of the design decreases. When should we include polynomials to account for scanner drift, and how do we decide the maximum order of the polynomials? Does it depend only on the length of the run? My runs are 8 min each, am I justified in having a quadratic polynomial? Thank you, Leo Fernandino ------------------- Leonardo Fernandino, Ph.D. Post-Doctoral Scholar Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7847 http://www.fmri.uchicago.edu/ "Those who cannot remember the past are condemned to repeat it." - George Santayana

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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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