Freesurfer

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30080 discussions

Make_average_subject
by Alexander Fornito 26 Nov '07

26 Nov '07

Hi all, I've been having problems with make_average_subject. The command and error are below. Below this is the same command with the output generated by the --debug flag. I am running version 4.0 (redhat) on Linux Debian. I'd appreciate any help on this. Thanks, Alex make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 cann53 cann54 cann55 cann56 --out testavg $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $ Fri Oct 26 11:03:31 EST 2007 /data/kang/work/struct/alex/freesurfer/subjects_cann setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003 make_average_subject --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 cann53 cann54 cann55 cann56 --out testavg --debug set verbose = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then if ( ! -e $FREESURFER_HOME ) then if ( ! -e /usr/local/freesurfer_4.0 ) then if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR if ( 0 == 0 ) set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann set outdir = $sdout/$average_subject set outdir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg if ( -e $outdir && ! $Force ) then if ( -e /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg && ! 0 ) then echo "ERROR: $outdir already exists, select a new average subject name" echo ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg already exists, select a new average subject name ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg already exists, select a new average subject name echo " or delete and rerun" echo or delete and rerun or delete and rerun exit 1 ; exit 1

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Re: [Freesurfer] loading data to matlab?
by Maryam Vaziri 26 Nov '07

26 Nov '07

Hi Cameron, I want to run a classification analysis on my functional data from all of the cortex using matlab. It is not something complicated but the very fist step is to run a PCA on all the data from all the voxels in the cortex. I am trying to reduce my data set as much as I can as the computation will b every extensive if I have huge files and Hardware-wise impossible to do. So vertex based data the way it is in the surfaces is very big for my purpose. I need volume data. I read my functional volumes to matlab using MRIread and reading the bhdr files in my BOLD directory (I can also read it using fmri_ldbvolume). But the problem with these files is that It is still too big. For reducing it I have to get rid of everything but the cortex. The problem is that I want the whole cortex data, and thus I cannot read just a label. I also need volume data so I cannot read a surface. Moreover I need to reduce my data set so I cannot read the whole brain volume. I also need all the time points so I cannot read the w files from a contrast analysis. What I finaly want is a N*T*4 matrix, containing x,y,z coordinates and values of all (N) voxels in the cortex, in all(T) time points. I figured that if I can somehow relate the voxels in the ribbon.mgz to the functional volumes I will be all set. But is this impossible? What does the contents of register.dat mean? Is there anyway that I can relate the two files using register.dat? Or maybe somebody has a totally different suggestion? Bests, Maryam. On Nov 20, 2007, at 10:32 AM, Cameron Ellis wrote: > Hi Maryam, > What type of analysis are you trying to do? It sounds like you are > trying > to do something unique and not simply follow the fs-fast surface based > analysis. Were you able to read the entire functional volume into > matlab? > It will be hard to limit this matrix to "active" voxels (not 0) > because it > is unlikely that any voxel in your functional will have a value of > 0. I > think you should be able to restrict the functional volume to the > cortex > but I am not sure how to do this. The register.dat file contains the > matrix used to relate the anatomic volume to the functional volume > but I > am also unsure if how to apply this to the ribbon.mgz or the raw > functional data and I am not sure that this is the best way to > obtain the > information you want. I wish I could be more help. I am just not > sure of > how that data is organized when it is read into matlab (according to > scanner coordinates/tal coordinates etc.) Are you sure there is not > a way > to do what you would like to do without reading the data into matlab? > Cameron > >> Hi again, >> >> I found a file named ?h.ribbon.mgz among the structural files which >> contains the cortical part of the volume that I want. But I do not >> know how to relate this structural volume to my functional volumes to >> get only cortical voxels from my functional volumes. I think that I >> should use the file register.dat, but I do not know what does the >> information inside the register.dat mean. What I basically want to do >> is to read voxels in my functional data, which their corresponding >> voxel in the ribbon.mgz is not zero and get rid of the voxels that >> their corresponding voxels in ribbon,mgz is zero. >> >> Bests, >> Maryam. >> >> On Nov 16, 2007, at 12:28 AM, Cameron Ellis wrote: >> >>> Hi Maryam, >>> do you know about the matlab toolbox for freesurfer? it is >>> located at: >>> $FREESURFER_HOME/matlab. all of these scripts are intended to read >>> fmri >>> data into matlab. I think the script you are looking for is >>> MRIread.m or >>> maybe load_analyze.m, load_cor.m or load_dicom.m I think you may be >>> able >>> to load a surface volume using cortical_labeling_tabel.m I actually >>> haven't used these so i could be completely off the mark that these >>> would >>> be useful. Hope this helps. >>> Cameron >>> >>>> Hi, >>>> >>>> I am a newbie in using freesurfer so sorry if this is a very >>>> trivial >>>> question. I want to load my fMRI data into matlab. I want to make a >>>> matrix containing coordinates and values of all the voxels in the >>>> brain at all timepoints. I also only want the voxels that are in >>>> the >>>> gray matter and not the voxels that are in the white matter or >>>> outside the brain. Where can I get this data and how can I load >>>> it to >>>> matlab? I have already managed to import all the voxels using MRI- >>>> ldbvolume, but this includes white matter and skull. How can I get >>>> rid of the rest of the brain and just get the surface? >>>> >>>> Bests, >>>> Maryam. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> >> >>

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Re: [Freesurfer] Error with mc-sess
by lreddy＠MIT.EDU 26 Nov '07

26 Nov '07

Hi, I've tried a few more things since posting my last message but have still not been able to solve the problem with mc-sess where it hangs. I got rid of the Matlab process manager error by using Matlab 6, but the motion correction process still hangs after opening Matlab and printing >> >>INFO: northog = 6, pct=100. I also tried to use the bert dataset and had the same output and then it hanged. The exact command I used was mc-sess -sf sessid -df sesspar I use the PowerPC version of freesurferv4.0.1. Any help would be appreciated. I attach the log file generated by mc-sess with this email. Leila --------------------------------------------------------------------- FREESURFER_HOME: /Software/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.10.0 Power Macintosh --------------------------------------------------------------------- ------------------------------ Message: 3 Date: Tue, 13 Nov 2007 22:08:45 -0500 From: Leila Reddy <lreddy(a)MIT.EDU> Subject: [Freesurfer] Error with mc-sess To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <20071113220845.pkqf8xeylhs8ggg8(a)webmail.mit.edu> Content-Type: text/plain; charset=ISO-8859-1 Hi, I recently installed freesurfer, AFNI etc but am having problems with mc-sess. The script runs and gets to the stage in each run where it calls up matlab, enters the MRIwrite command but then gives the message below. It then hangs. >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2007-11-13 18:44:51.464 MATLAB[6569] Process manager already initialized -- can't fully enable headless mode. I can kill the process (e.g.6569 in the example above) and it moves on to the next run, but without saving anything for the current run. Does anyone know what I can do to fix it? Thanks, Leila ------------------------------

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DODS or DOSS?
by Juergen Haenggi 26 Nov '07

26 Nov '07

Dear FS experts We have done a group analysis with FS, but we are not absolutely sure which is the most adequate design matrix to describe our data. We compared two groups and used one covariate of no interest (mean thickness, total area, etc.). Because there are two different options to create the design matrix (dods and doss), we run the analysis twice, one time with dods and the other time with doss, and unfortunately, we got two quite different patterns of structural brain differences. Is there any theoretical and/or empirical recommendation/clues in order to decide which type of design matrix is more appropriate for our data? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Error with mc-sess
by Leila Reddy 26 Nov '07

26 Nov '07

Hi, I recently installed freesurfer, AFNI etc but am having problems with mc-sess. The script runs and gets to the stage in each run where it calls up matlab, enters the MRIwrite command but then gives the message below. It then hangs. >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2007-11-13 18:44:51.464 MATLAB[6569] Process manager already initialized -- can't fully enable headless mode. I can kill the process (e.g.6569 in the example above) and it moves on to the next run, but without saving anything for the current run. Does anyone know what I can do to fix it? Thanks, Leila

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How to register a subject surface to average surface?
by Jiefeng Jiang 23 Nov '07

23 Nov '07

Hi, I used make_average_subject to create an average subject, and I want to register a subjects's pial surface to the average subject's pial surface. I used mris_make_template lh pial average lh.pial.tif to create a template, and used mris_register -curv lh.pial $SUBJECTS_DIR/average/surf/lh.pial.tif lh.pial.avg.reg but the result was a sphere. Could anyone tell me how to do the registration? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278

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Re: The results of your email commands
by l.gutierrez＠ion.ucl.ac.uk 22 Nov '07

22 Nov '07

> > > > Hi, > > I fixed talairach manually (as website says), and this command is > not > > working. Could it be because now I am using the last version and I > used > > before other version? > > thanks in advance > > Leticia > > > > [leticia@triton ~/subjects]1% recon-all -all -subjid sukma > > INFO: SUBJECTS_DIR is /mounts/auto/leticia-freesurfer/subjects > > Actual FREESURFER_HOME > > /export/local/fc5_x86_64_usr2/mrtools/freesurfer/4.0.1 > > -rw-rw-r--+ 1 leticia news 1279831 Nov 22 14:37 > > /mounts/auto/leticia-freesurfer/subjects/sukma/scripts/recon-all.log > > Linux triton.nmr.ion.ucl.ac.uk 2.6.18-1.2257.fc5 #1 SMP Fri Dec 15 > > 16:07:14 EST 2006 x86_64 x86_64 x86_64 GNU/Linux > > #-------------------------------------------- > > #@# MotionCor Thu Nov 22 14:37:55 GMT 2007 > > ERROR: no run data found in > > /mounts/auto/leticia-freesurfer/subjects/sukma/mri. Make sure to > > have a volume called 001.mgz in > > /mounts/auto/leticia-freesurfer/subjects/sukma/mri/orig. > > If you have a second run of data call it 002.mgz, etc. > > See also: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion > > Linux triton.nmr.ion.ucl.ac.uk 2.6.18-1.2257.fc5 #1 SMP Fri Dec 15 > > > 16:07:14 EST 2006 x86_64 x86_64 x86_64 GNU/Linux > > > > > > recon-all exited with ERRORS at Thu Nov 22 14:37:55 GMT 2007 > > > > >

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POSTDOCTORAL FELLOWSHIP IN SPEECH PERCEPTION AND THE STRUCTURE AND FUNCTION OF HUMAN AUDITORY CORTEX
by David L. Woods 21 Nov '07

21 Nov '07

POSTDOCTORAL FELLOWSHIP IN SPEECH PERCEPTION AND THE STRUCTURE AND FUNCTION OF HUMAN AUDITORY CORTEX A postdoctoral fellowship is available in Martinez, CA (in the San Francisco Bay Area) to study the relationship between age-related changes in speech perception and anatomical and functional changes in human auditory cortex. Speech processing will be tested with nonsense syllables and sentences and correlated with tests of basic auditory discrimination abilities and auditory short-term verbal memory. Subject with impaired speech processing will then undergo PC-based adaptive training designed to improve speech processing in noise and force beneficial neuroplastic changes in auditory cortex. Brain structure will be imaged using multimodal structural brain imaging (including high-resolution T1, diffusion tensor, and magnetization transfer imaging) and analyzed using advanced cortical surface mapping as well as automated techniques to analyze subcortical structures and white matter tracts. In selected subjects, functional activations to speech and non-speech stimuli will be studied using fMRI. The job involves close collaboration with international scientists, graduate students, and post-docs. Job Availability: Immediate. Job duration: 2-4 years. Salary: $40,000-$65,000 depending on experience. QUALIFICATIONS. Successful candidates should have a strong background in auditory perception, physiology and/or anatomy (PhD or MD required), a good publication record, familiarity with Windows and Linux operating systems, and some programming experience. Knowledge of psychophysics, neuropsychology, and neuroimaging methods including ERPs, fMRI, or TMS is desirable. US citizenship preferred. Interested candidates should email a C.V., letter of intent, and the names of three references to: Professor David L. Woods, Dept. of Neurology, UC Davis and VANCHCS (127E), 150 Muir Rd., Martinez CA 94553. Email: <file:///dlwoods@ucdavis.edu>dlwoods(a)ucdavis.edu.

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Re: [Freesurfer] Folding Index question
by Graham Wideman 21 Nov '07

21 Nov '07

[Bruce wrote] >sounds reasonable to me, but we should call it something else (normalized >FI/CI?) Yes, dividing out area does look like a first step, justified by the way the per-vertex values are calculated. This gives the result units of mm^-2, which maybe has an interpretation something along the lines of "folds per square millimeter". But, as noted in off-list emails, I think it would be premature to release an "NewFI" revised only in this way, because it suggests that the other principles of FI are sound, which I'm currently not confident about. Rudolph and I are in the process of reconciling our understandings of how the FI calculations currently behave, and whether that was what was intended (and probably whether what was intended is even a useful idea). Anyhow, hopefully the outcome of this will be better calcs implementing something useful, (with documentation of intent and usefulness :-). Graham

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Re: [Freesurfer] Folding Index question
by Rudolph Pienaar 20 Nov '07

20 Nov '07

Hi Graham - First off, your observation that the FI seems correlated with area is completely correct. I'm not sure if you have the FS source code? Anyway, looking at the relevant code in 'mrisurf.c', the MRIScomputeCurvatureIndices(...) function pretty much computes the folding index (fi) as fi += area * Kmax * (Kmax - Kmin) ; and then, once having summed over the surface, simply divides by *pfi = fi / (4.0*M_PI) ; In essence, this is Van Essen's Folding index -- although I personally do have some issues with it. First of all, Van Essen normalizes his measure with 1/4/pi, indicating that the 1/4pi is the "integral for a cylinder the length of which equals its diameter). I seem to think this integral should be (1/2pi)^2, i.e. 1/4/pi^2. Either way, this is merely a fixed constant and doesn't change the behaviour. And irrespective of the 1/4pi or not, the measure is a strict function of "size", or more accurately, the radius of curvature. Since the curvatures run as the inverse of radius, the curvature values in small sulci/gyri can dominate the 'Folding Index', even if they are 'folded' exactly the same as larger sulci/gyri. In fact, there is nothing really related to 'folding' per se in the measure, so it is arguably something of a misnomer - but I fear I am digressing. I know Bruce originally wrote the FI into FS, but based on this quick re-analysis, I'm kind of thinking that we should normalize the fi (and ici for that matter) with the area overwhich each measure measure is computed... *pfi = fi / (4.0*M_PI) / areaCounted; This makes potentially more sense and removes the area dependency. What do you think, Bruce? -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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