Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 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]$

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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

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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

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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

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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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Re: [Freesurfer] transverse gyrus and translucent brain renderings
by Nick Schmansky 15 Oct '09

15 Oct '09

forwarding to the list.... On Thu, 2009-08-06 at 20:57 +0200, Christophe Destrieux wrote: > Hi Narly > > below are a few explanations on the transverse temporal gyrus in the > a2005 parcellation > > At the superior aspect of the superior temporal gyrus: > > * the transverse temporal *sulcus* limits the planum temporale > (posteriorly) from the transverse temporal gyrus (anteriorly); it > originates at the posterior segment of the lateral sulcus, runs > anterior and lateral and joins the lateral aspect of the temporal > lobe. > > * The transverse temporal gyrus (or Heschl's gyrus) is just anterior > and parallel to the transverse temporal sulcus. Instead of a > single transverse temporal gyrus, several “transverse” temporal > gyri bordered by intermediate sulci may be present. Only the more > anterior transverse temporal gyrus is labeled in Freesurfer, the > posterior ones being included in the planum temporale since they > where shown not to correspond to primary, but to secondary > auditory cortex > > I hope that it helped > > cheers > > -- > Christophe Destrieux > Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > Narly, > > > > I'm forwarding this to Christophe Destrieux, cc'd, who I think can > > answer your question about how that region is labelled. > > > > It is not possible to do translucent viewing in tksurfer. However, it > > is possible in qdec. Just use the load surface and load annotation menu > > options. > > > > Nick > > > > > > On Thu, 2009-08-06 at 16:26 +0100, Narly A Golestani wrote: > > > >> Hello, > >> > >> I would like to know more about the automatic labelling of the transverse > >> temporal gyrus is done. I looked at the below article but don't see any > >> details about this structure. > >> > >> https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf > >> > >> I would for example like to know how the boundaries of this structure are > >> defined/determined. > >> > >> Also, when using tksurfer to view labels ('import annotation'), is it > >> possible to make the 3D brain surface (and labels) translucent so that one > >> can more carefully view where this (medial-spanning) gyrus was identified? > >> > >> thanks in advance, > >> Narly. > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > > > > > >

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map .xls or .txt file to fsaverage
by Feng-Xian Yan 13 Oct '09

13 Oct '09

Hi, I have a problem want to solve. I want to map the data file (.xls or .txt) to fsaverage. What command do I type? Thank you in advance! Feng-Xian

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optseq2 help: DPSD and jitter
by Asaf Kaftory 06 Oct '09

06 Oct '09

Hello list, I'm new to optseq, and would like your help with the following issues: 1. What exactly does DPSD mean? and why does the TR has to be an integer of it? 2. My experiment design uses jitter - both ITI (i.e., between trials) and ISI (i.e., between stimulus within a compound event). As i understood, optseq can only supply me with the ITI jitter but no the ISI jitter. is that right? do you happen to know a computerized method to introduce a jitter within a compound event? 3. Is it true that jitter in optseq is made by inserting "NULLS", and that the DPSD determines the "steps" of the jitter (for e.g., if DPSD equals 1, Nullmin equals 2 and Nullmax equals 4, the NULL events will be 2 3 or 4). Did i understand it right? hope to hear from you soon, Asaf.

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How to calculate differences using the longitudinal data
by Weisinger, Brian (NIH/OD) [E] 01 Oct '09

01 Oct '09

I have run the longitudinal stream on the scans I need, but now I am not sure what to use to compare the differences. If someone could clarify this for me I would really appreciate it. Thanks

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tksurfer
by Ahmed, F, Me <fahmed＠sun.ac.za> 01 Oct '09

01 Oct '09

Hello, I'm trying to view and check the smoothing and inflation surfaces, the white and pial surfaces for "bert" using tksurfer as I'm trying to get used to using Freesurfer, but I'm a little confused to what I'm seeing. When I type in: "tksurfer bert lh inflated" for example, I only see a very small section at the very end of the image...is this correct? When I view the curv files, I do see a green pattern overlaid on the inflated surface, however it's still so small. When I view the pial and white surfaces, again, the section displayed is very small, I don't know if this is correct or if this is what I am supposed to be seeing? Also, when I type in: "tksurfer bert lh sphere", I see nothing at all. If someone could shed some light on the matter I'd be extremely grateful. Thank you

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Freesurfer September 2009