Freesurfer

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30131 discussions

mri_divide_parcellation
by Diana Wotruba 30 Jan '09

30 Jan '09

Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) into about 1000 smaller parcellations, using mri_divide_parcellation. What would be the easiest way to get the cortical thickness in these areas for each subject? Is it reasonable to copy the new .annot file from fsaverage into each subjects label folder ensuing mris_anatomical_stats? Any help would be appreciated Regards Diana

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research assistant position in intracranial EEG
by Thomas Thesen 29 Jan '09

29 Jan '09

Research Assistant Position in Cognitive Neuroscience Department of Neurology, School of Medicine, New York University We are seeking a full-time Research Assistant to assist with cognitive neuroscience experiments involving human intracranial EEG. Main topics of investigation are language, memory, multisensory, brain-computer interface, seizures and others. Responsibilities include, but are not limited to, recruiting and scheduling of control subjects and patients, testing and recording from intracranial patients, maintenance of equipment, databases and files, as well as data analysis and manuscript preparation. Candidates who have experience with neuroimaging data collection and analysis are especially encouraged to apply. Other neuroimaging methods employed by the lab include fMRI and MEG. The laboratory provides a unique exposure to both basic research and clinical neuroscience. The position requires interaction with patients and hospital staff and therefore excellent verbal and interpersonal skills are required. Must be well-organized and detail oriented; extensive computer experience strongly preferred, with programming highly desirable. B.A. or B.S. required, such as in neuroscience, psychology, biology, computer science or biomedical engineering. The position is ideal for exceptional candidates seeking to pursue an advanced research degree in neuroscience or a related field. Likely start date is June 2009. Please visit our web lab page for more information: http://mmil.ucsd.edu/thomas/group Please send resume and cover letter to: Thomas Thesen, Ph.D.Assistant Professor of Neurology New York University School of Medicine thomas.thesen(a)med.nyu.edu

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Measuring regional cortical thickness
by Jeff Sadino 29 Jan '09

29 Jan '09

Hello, I would like to measure the cortical thickness for each region. All I can find is how to do it for user-defined ROI's, but not for each auto-segmented region. Can anyone point me in the right direction? Also, can you manually add and subtract pixels from region labels from the surface in tksurfer in a similar way that you can in tkmedit? Thank you very much. Jeff Sadino _________________________________________________________________ Windows Live™ Hotmail®…more than just e-mail. http://windowslive.com/howitworks?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_how…

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sulc & curv
by Juranek, Jenifer 29 Jan '09

29 Jan '09

Rudolph, many thanks for the additional details. Just a follow-up question (or two): 1. Short stubby gyri might have the following morphometric properties? a) Short feature: shallow sulcal depths would be expected to have sulc values hovering around the mean surface (e.g. around 0) in negative curvature areas b) Stubby feature: increased GM volume, increased surface area, and perhaps increased cortical thickness depending on how the WM behaved Thanks so much, Jenifer

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Graphical problems or more
by Jürgen Hänggi 29 Jan '09

29 Jan '09

Dear FS experts We parcellated the aparc.a2005s of fsaverage into parcellations of 300 mm^2 (attached file FinerParcells_fsaverage). When I overlaid this new parcellations on a single subject, there seems to be something wrong (attached file FinerParcells_individual). Because I use this new finer parcellations with the command mris_anatomical_stats to get cortical thickness of these finer parcellations across subjects, I am wondering whether there is only a graphical problem. When I have a look at the resulted thickness values and the reported number and names of parcellations, everything seems to be OK. Any ideas? I use FS 4.2.0 Mac Intel. Thanks in advance Regards Jürgen ---------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division 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[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------------------

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Re: [Freesurfer] --fsgd file
by Siddharth Srivastava 29 Jan '09

29 Jan '09

Hi Jurgen, Thanks for the response. Seems like a feasible idea. I can do it for my "Normals", but the atypicals have a large variability in the measure. And only the atypicals have missing data. Thanks for the idea though... sid. On Thu, Jan 29, 2009 at 11:02 AM, Jürgen Hänggi < j.haenggi(a)psychologie.uzh.ch> wrote: > Hi Siddharth > > If there are not too many missing values, you can fill the missing values > by the mean of the values you have and hope that the subjects who completed > all tasks did not systematically deviate from the subjects who did not > complete the tasks. > > Regards > Jürgen > > > > On 28.1.2009 20:46 Uhr, "Siddharth Srivastava" <siddys(a)gmail.com> wrote: > > Hi everyone, > I was wondering if it is possible to flag missing > entries in > the covariates corresponding to subjects, in the construction of the file > passed > through --fsgd to mri_glmfit ? Not all my subjects completed all the > tasks, > and i need to code them in the file, somehow. > thanks, > sid. > > ------------------------------ > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > ---------------------------------------------------------- > Juergen Haenggi > Ph.D. (Dr. des.) > Division 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[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > ---------------------------------------------------------- > >

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--fsgd file
by Siddharth Srivastava 29 Jan '09

29 Jan '09

Hi everyone, I was wondering if it is possible to flag missing entries in the covariates corresponding to subjects, in the construction of the file passed through --fsgd to mri_glmfit ? Not all my subjects completed all the tasks, and i need to code them in the file, somehow. thanks, sid.

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using old GE data to run FSFAST
by Krishna Srihasam 29 Jan '09

29 Jan '09

Hi, I have some fMRI data which i collect from GE signa 3T machine. I have the data in two formats : (1) IMA format ( where each run is a directory like "000001.SER" and each such directory has separate files for each acquisition i.e. if I had 150 acquisitions, I have 150 .IMA files (2) I also have the above-mentioned data in nifti format exactly like before..Separate directories for each runs and separate files for each acquisition. Is there any command or way to convert these files into a format that I can use to do analysis with FSFAST. regards, Krishna

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Calculate Corticol Thickness
by Jeff Sadino 28 Jan '09

28 Jan '09

Nevermind, I figured out my mistake. Thanks for your help! _________________________________________________________________ Windows Live™: E-mail. Chat. Share. Get more ways to connect. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_allup_explore_012009

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Calculate corticol thickness
by Jeff Sadino 28 Jan '09

28 Jan '09

Hello all, Real basic question: How do I calculate the thickness of the cortex, preferably at each vertex/face? I have tried read_curv.m, but get this error: [thickness, f] = read_curv('lh.thickness') ??? Undefined function or method 'fread3' for input arguments of type 'double'. Error in ==> read_curv at 21 vnum = fread3(fid) ; This should be simple, but the discussion board starts one step after me I think :) Any help would be appreciate! Second, when I try to load it in freesurfer, I get an error: [FSuser@cluster ~]$ tksurfer 050080_S01 lh thickness surfer: current subjects dir: /share/apps/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /export/home/FSuser Talairach transform /home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm surfer: Reading header info from /share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz I tried loading the inflated first, then loading the thickness, which works, but the surface just turns all red. Are the minimum thicknesses maxing out my color map? This seems unlikely. Can anybody help me? [FSuser@cluster ~]$ tksurfer 050080_S01 lh inflated surfer: current subjects dir: /share/apps/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /export/home/FSuser Talairach transform /home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm surfer: Reading header info from /share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz surfer: vertices=144686, faces=289368 Talairach transform /home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /share/apps/freesurfer/subjects/050080_S01/surf/../mri/transforms/talairach.xfm surfer: single buffered window libGL error: open DRM failed (Operation not permitted) libGL error: reverting to (slow) indirect rendering surfer: using interface /share/apps/freesurfer/lib/tcl/tksurfer.tcl Reading /share/apps/freesurfer/lib/tcl/tkm_common.tcl Reading /share/apps/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /share/apps/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /share/apps/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl (And then File -> Load Curvature -> lh.thickness) % surfer: curvature read: min=0.226951 max=5.000000 Thanks you very much, Jeff Sadino _________________________________________________________________ Windows Live™: E-mail. Chat. Share. Get more ways to connect. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_allup_explore_012009

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