Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

4 4

Using peak activation voxels to determine structural areas of interest
by Nathan Dankner 01 Jun '10

01 Jun '10

Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks, Nathan

5 4

masking out ROIs on the surface
by Mishkin Derakhshan 07 Nov '09

07 Nov '09

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin

3 5

building from source
by Michael Scheel 29 Oct '09

29 Oct '09

Hi everybody, I have the opportunity to run my analysis with freesurfer on a big computer-cluster that is running on AIX. However to install freesurfer there I need to build it from source. Is the source code available? I found some older entries in the archives and the issue seemed at that time rather complicated. Are there any news regarding building from source? Thanks, Michael

4 4

problem starting qdec
by Dana W. Moore 29 Oct '09

29 Oct '09

Hi everyone, I am trying to use qdec for the first time, and I get the following error message: X Error of failed request: GLXBadRenderRequest Major opcode of failed request: 132 (GLX) Minor opcode of failed request: 1 (X_GLXRender) Serial number of failed request: 1705 Current serial number in output stream: 1709 Locking assertion failure. Backtrace: #0 /usr/lib/libxcb-xlib.so.0 [0x4455a767] #1 /usr/lib/libxcb-xlib.so.0(xcb_xlib_lock+0x2e) [0x4455a81e] #2 /usr/lib/libX11.so.6 [0x4033d518] #3 /usr/lib/libX11.so.6(XESetCloseDisplay+0x31) [0x403208d1] #4 /usr/lib/libGL.so.1 [0x40291b69] I am accessing our linux computer remotely using ssh from a windows machine--I don't know if this is related to the problem. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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Longitudinal analysis with old version
by l.gutierrez＠ion.ucl.ac.uk 11 Sep '09

11 Sep '09

Hi, We have installed the 4.0.1 version and we are starting the longitudinal analysis. I have some problems with -base flag( recon-all -base <baseid> -base-insubj <tp1subjid> -base-insubj <tp2subjid> ... -all). Should 4.0.1 version be one problem in order to do that? Many thanks Leticia >

6 10

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

2 1

-randomness flag for recon-all
by Pernille Iversen 21 Aug '09

21 Aug '09

Hi, In the release notes for version 4.4.0 it says that "The -randomness flag can be used to allow usage of a random seed", however, running the following command: recon-all -all -nowmsa -randomness -subjid f4168_1r gives the following error: ERROR: Flag -randomness unrecognized. Is there another way to reintroduce the randomness? I am using the following version: v 1.133.2.51 2009/06/11 Thanks, Pernille

2 3

cerebral white matter volume
by saulg＠ualberta.ca 31 Jul '09

31 Jul '09

Hi there, In the aseg.stats file, there are two reports of cerebral white matter volume. The first report is near the top of the file, as such: # Title Segmentation Statistics # ... # surface-based-volume mm3 lh-cerebral-white-matter 172917.046875 # surface-based-volume mm3 rh-cerebral-white-matter 173269.906250 # surface-based-volume mm3 tot-cerebral-white-matter 346186.953125 ... The second report is lower in the file, contained in the section that would be turned into a spreadsheet by the 'asegstats2table' function: # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 2 167965 167965.0 Left-Cerebral-White-Matter 104.1714 8.0979 41.0000 131.0000 90.0000 ... 21 41 179570 179570.0 Right-Cerebral-White-Matter 102.5936 8.2544 50.0000 133.0000 83.0000 ... I noticed these numbers are consistently different, so I have two questions: 1) Why are they different? Is it because the first is surface based? 2) Which numbers should I use when reporting total cerebral white matter volume? Thanks so much!

2 1

Freeview on Mac
by jentis＠nmr.mgh.harvard.edu 31 Jul '09

31 Jul '09

Hi Guys, Is it possible to get Freeview compiled for a Mac? Last time I check, it wasn't supported, but it would be of great help to me and at least a couple other members of my lab. Thanks. Best, Jon

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Freesurfer July 2009