Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

creation of special image...
by Gonzalo Rojas Costa 05 Aug '10

05 Aug '10

Hi: How can I create an image such as the "Be happy" one that appeared in the last slide of "Surface-based Analysis: Intersubject Registration and Smoothing" PPT?... Sincerely, Gonzalo Rojas Costa

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label 28 error
by Ilana Hairston 05 Aug '10

05 Aug '10

Hi there, We've been getting this label 28 error more often recently, and found that by adding '-no-ca-align' to the end of recon-all command, the error went away and visually the brain looks OK (at least first pass). Does this make sense? thanks ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Sentimental Insomnia and Nostalgia Disorders Sciences ********************

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qdec GLMDesign Problem
by Bruehl, Hannah 05 Aug '10

05 Aug '10

Hi there, I am having a problem with qdec when trying to rerun analyses (meaning this worked before), I get the following error message: Data table loading completed successfully. SUBJECTS_DIR is '/Users/bruehh01/Borderline_2' ERROR: QdecGlmDesign::Create: could not create directory /Users/bruehh01/Borderline_2/qdec/Untitled Since I haven't changed anything since I last ran analyses, I don't understand what the problem is. Any suggestions? Thanks and regards, Hannah ...................................................................................................................................... Dr. Hannah Brühl Freie Universität Berlin Institut für Psychologie Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft Habelschwerdter Allee 45 — Raum JK 25/222h 14195 Berlin Tel.: +49 (0)30 838 564 72 ......................................................................................................................................

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keyboard problem in freesurfer
by Katie Bettencourt 05 Aug '10

05 Aug '10

I am having a problem others have had before, but that I can't seem to see any resolution to in the archives. When I open tksurfer I can't use my keyboard to input anything. I don't get any errors, it just doesn't let me type or delete anything, making it next to impossible to use. I'm running Freesurfer4.5.0 on linux - Red Hat 4.1.2-48 (Centos 5.5) I checked my .cshrc file and couldn't find any issues there. Any other help please? Katie

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converting analyse roi to fs
by Prapti Gautam 05 Aug '10

05 Aug '10

Dear FreeSurfers, I am trying to convert an Analyze object map (saved as a set of .img /.hdr files) where I've traced ROIs so that I can load them as labels or overlays in FreeSurfer. Has anybody done this before? What would be the best way to proceed? Thanks, Prapti

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Re: [Freesurfer] Which version should I download?
by Matt Glasser 04 Aug '10

04 Aug '10

The CentOS 4 download works with Ubuntu. Just make sure to get the correct 32 or 64 bit version that matches your operating system. Use uname -m to tell. Peace, Matt. _____ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Glen Lee Sent: Wednesday, August 04, 2010 3:07 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Which version should I download? Hello, I just installed a recent version of Ubuntu to run the freesurfer and I know nothing about Linux yet. But I'm seeing that the download link only specifies CenOS 4. Does it mean that Ubuntu is not compatible with Freesurfer? Any help would be appreciated. Thanks,

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Calculating % Signal Change from roisummary-sess readout
by Adam Nitenson 04 Aug '10

04 Aug '10

Hi Freesurfers, I am trying to analyze functional activity in individual subjects. The structural constraint is a dACC label and the functional constraint is positive activation at a specific timepoint (6 sec after stimulus). I was just wondering what the numbers following the "# of estimates per condition" row actually represented, and how I could convert these to % signal change. I saw in an archived email http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00171.html that someone mentioned taking those values, dividing by the baseline offset value (row 4) and multiplying by 100 to get % signal change. Is this a valid method? Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital PS Here are the commands I used if that helps: func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -maskthresh 0.000000001 -masktail pos -maskframe 5 -maskmap sig -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects roisummary-sess -roidef lh_dACC -analysis RM_correct_error -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects -sumfile /autofs/space/ventzl_036/users/RespMon12C/ROI_Analysis/lh_dACC

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Which version should I download?
by Glen Lee 04 Aug '10

04 Aug '10

Hello, I just installed a recent version of Ubuntu to run the freesurfer and I know nothing about Linux yet. But I'm seeing that the download link only specifies CenOS 4. Does it mean that Ubuntu is not compatible with Freesurfer? Any help would be appreciated. Thanks,

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Group Analyses on Surface
by Pye, Brandon (NIH/NIMH) [F] 04 Aug '10

04 Aug '10

Hey guys and gals, I'm working with a post-doc (I'm a post-baccalaureate) on trying to view averages across subjects on the surface using freesurfer. I have read about creating an average subject and creating an average surface in freesurfer, but our functional data that we want to view on the surface is in AFNI format, and I don't know how to properly concatenate or average all of the values in the AFNI functional files to view on the freesurfer surface. Can anyone point me in the direction of some information that could help? Thanks a ton, Brandon --------------------------------------------------------------------- Brandon Pye Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 402-3893 Fax: (301) 402-0921 brandon.pye(a)nih.gov

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NiPyPe: Neuroimaging in Python Pipelines and Interfaces
by Chris Filo Gorgolewski 03 Aug '10

03 Aug '10

Dear members of the neuroimaging community, We are pleased to announce release 0.3.2 of NiPyPe [nai-pipe]: Neuroimaging in Python Pipelines and Interfaces (http://nipy.org/nipype) Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. Nipype allows you to: * easily interact with tools from different software packages * combine processing steps from different software packages * quickly develop new workflows by reusing common steps from existing workflows * process data faster by running it in parallel on many cores/machines * make your research easily reproducible * share your processing workflows with the community For example workflows see: http://nipy.sourceforge.net/nipype/users/pipeline_tutorial.html Nipype is a young community-based project and we welcome your inputs, contributions and criticisms. Release Notes Please see: http://nipy.org/nipype/changes.html Where to go for help * the user mailing list: nipy-user(a)googlegroups.com [subscribe]: http://groups.google.com/group/nipy-user * the developer mailing list: nipy-devel(a)neuroimaging.scipy.org [subscribe]: http://mail.scipy.org/mailman/listinfo/nipy-devel on both of these lists please prefix the subject heading with [nipype] to indicate a nipype relevant post. --- The NiPy Community

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Freesurfer