Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 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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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 >

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Intersection of labels with other labels or volumes
by James Porter 09 Sep '09

09 Sep '09

Hello- Is there a simple way to obtain the intersection of two labels, output into a third label? Or the intersection of a label and an .mgh file output by mri_surfcluster? For instance, I have a cluster defined by mri_glmfit/mri_surfcluster that spans multiple anatomical regions, and I want to investigate the values from subsections of the cluster. That is to say, I want to run mris_anatomical_stats on only the section of my cluster that covers, say, precentral cortex but not caudal middle frontal or pars opercularis. I've tried several strategies without success. The most promising seemed to be just having mri_surfcluster output an aparc file, and then pass that aparc file into mris_anatomical_stats. However, that aparc just puts the very first region definition to every vertex. The same happens if I run mri_label2aparc on the labels output by mri_surfcluster. This happens no matter which LUT or ctab I use, i.e., with aparc.annot.ctab the whole volume gets labeled "bankssts" and with FreeSurferColorLUT.txt every vertex in the cluster volume gets labeled "Left-Cerebral-Exterior." I guess there are a few issues in this email, but the most important one to me is being able to run mris_anatomical_stats on the union of a cluster file and the individual regions from the standard aparc atlas. Any suggestions? Thanks in advance, --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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Input/Output to specific atlas space/dimensions?
by Alexander Li Cohen 01 Sep '09

01 Sep '09

Hi all, Just starting using Freesurfer, and while I did search the mailing list archive, I didn't see a ready answer for this question: I would like to use Freesurfer to generate surfaces for my subjects (currently using Caret's SureFit routine), however I need to maintain a specific atlas space for my subjects (in this case, the WU 711-2B, T88-derived space). I can imagine two possibilities, but not how to do them, nor which is more accurate/appropriate: 1. Input the raw T1 for my subject in scanner space (1x1x1 isovolumetric) and then convert the Freesurfer surface and volume outputs to my atlas space using a previously defined linear affine transform (using local scripts written by Avi). This requires Freesurfer to back-convert all results to the original supplied space, then for me to additionally learn how to transform the surfaces. 2. Input the T1 for my subject already in my atlas space, and have Freesurfer output all results in the original supplied space. This, however, will be providing Freesurfer with data that has undergone an additional transform, but is obviously simpler.... in either case, the methodological question becomes simply: how can I tell recon-all to output all files in the original space provided. Given that it must perform the necessary transforms to get into the internal MNI305 space (I'm assuming), I'm simply wanting to undo all of the applied transforms. For obvious reasons, I want to use the same affine transform and transform routine consistently across this and my other datatypes. As a side note, there appears to be a switch for recon-all: -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol yet there is no documentation as to what this determines, nor whether the raw, or locally atlas-aligned data should be provided. (Avi didn't know either...) Many Thanks! -Alex Li Cohen ~)----------------- ---------------------------------------------------------------------- Alexander Li Cohen alexc(a)npg.wustl.edu (WORK Email) alexcohen(a)gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ---------------------------------------------------------------------- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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isxconcat-sess error
by Garth Coombs 31 Aug '09

31 Aug '09

Hi, I've been running into a problem when trying to run a group analysis. When I go to run isxconcat-sess, I use this command: isxconcat-sess -sf hc.txt -df sesspar -analysis Ext -c CS+lvsCS-l - percent -o ./HC-Ext-083109 -hemis -trgsubject fsaverage It runs through the whole isxconcat without stopping, and there appears to be the normal outputs. However, when I scroll through the text in the terminal window, the following error appears repeatedly (I think once for every subject, possibly for each hemi of each subject): Reading source surface registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/ ext005_anat/surf/lh.sphere.reg Done loading source registration surface Reading target registration /autofs/space/dinah_001/users/balaji/SUBJECTS_DIR/subjects/ fsaverage/surf/lh.sphere.reg ERROR: could not find volume /autofs/space/dinah_001/users/balaji/ SUBJECTS_DIR/subjects/fsaverage/surf/../mri/orig. Does it exist? Done loading target registration surface Mapping Surfaces (ext005_anat -> fsaverage) When I go to fsaverage's folder, the orig.mgz file does exist, but for some reason, it looks like it's trying to direct it into the surf folder and then back out and into the mri folder and having trouble for some reason. When I try to type in the cd command as it appears (with the /../), it does take me to the mri folder where orig.mgz is stored, so I'm not sure why I get the error. I run into trouble after I run mri_glmfit, when I go to run surf- sess. I get the error: grep: /autofs/space/ricki_001/users/brittany/ext_fmri/HC-Ext-083109/ session.info: No such file or directory ERROR: cannot find /autofs/space/ricki_001/users/brittany/ext_fmri/HC- Ext-083109/ext/register.dat and then it exits. So for some reason, it looks like, even though isxconcat and mri_glmfit run and give outputs, they aren't registering to fsaverage somewhere along the way and are therefore not giving all of the outputs I need. Any idea of what I need to do? Thanks! Garth

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Freesurfer August 2009