Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

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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tumor volume segmentation...
by Gonzalo Rojas Costa 03 Aug '10

03 Aug '10

Hi: I segmented a T1 volume of a patient with a tumor... in the aparc+aseg and aparc.2009s segmentation,that tumor appears as "none"... How can I got the volume of the tumor ?... Sincerely, Gonzalo Rojas Costa

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Vertex-wise thickness and mean thickness of clusters
by Joana Braga Pereira 03 Aug '10

03 Aug '10

Dear all, I would like to ask you whether there should be an exact correspondence between vertex-wise thickness and mean thickness of clusters. I'll explain you my problem. I did an analysis with 2 groups and 2 covariates. Then i run the mri_glmfit script and found clusters of greater thickness in controls compared to patients. When i extracted the mean thickness of these clusters and did a two sample t test i observed that the controls had greater thickness than patients, however not statistically significant, even after including in this analysis the 2 covariates. Is this normal? How does freesurfer uses the covariates when performing an analysis? Many thanks

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ROI-questions
by liyari5018 03 Aug '10

03 Aug '10

Hi All, I use QDEC to compare two groups differences, find some regions with significant differences. Considering this regions as ROI, i want to extract the mean thickness of ROIs for every subject, then compute the correlation between mean thickness and some scales . My questions is : should I extract mean thickness from the individual space or the common space? Any advice would be most appreciated LJ

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intracranial volume in qdec
by York, Philip 02 Aug '10

02 Aug '10

Hi experts, I was wondering it is possible to account for total intracranial volume in qdec statistical calculations, and if so, where do I find that under the 'general stats data tables' Thanks, Philip York UCDenver Radiology

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Re: [Freesurfer] .license file on Mac (Krish Subramaniam)
by sere f 02 Aug '10

02 Aug '10

Hi Krish, > thank you for your advice....now it works!!! Serena. > > > > > > > > ------------------------------ > > Message: 7 > Date: Mon, 2 Aug 2010 03:16:09 -0400 > From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] .license file on Mac > To: sere f <serenaf33(a)gmail.com> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <2B627F31-D101-430F-B236-0EE5AACD59BE(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Serena > > It means you don't have write permissions in the directory. You should > invoke pico like > > sudo pico /Applications/freesurfer/.license > > ..it'll ask for your password and save successfully, provided you have > permissions. > > -Krish > > On Aug 1, 2010, at 8:32 AM, sere f wrote: > > > > > > > Hi All, > > > > I am new user of Freesurfer and i am getting trouble to install it. > > I want to install it on MacBook Pro and I have problem with the > > license file. > > I have tried to create it with: > > > > pico /Applications/freesurfer/.license > > > > and when I save it, I get this message: > > Error writing /Applications/freesurfer/.license: Permission denied > > and it is not saved. > > > > How can i do? any idea? > > Thanks. > > > > Serena. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 78, Issue 1 > ***************************************** > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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Undefined Variable
by Carl Dambkowski 02 Aug '10

02 Aug '10

Hi! I may be missing something basic but when I enter: recon-all -s bert -autorecon1 I get: FREESURFER_HOME: Undefined variable. But I have already ran: setenv FREESURFER_HOME /Applications/freesurfer so that FREESURFER_HOME should be defined, right? I'm not sure if I'm missing something basic or something is completely wrong. I can access the already created files but it doesn't let me run a recon-all for some reason. Thanks for your help! Carl -- Carl Dambkowski, MS Research Assistant Cerebral Localization Laboratory Columbia University Medical Center (212) 342-3668

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Freesurfer August 2010