Freesurfer February 2007

freesurfer@nmr.mgh.harvard.edu

59 participants
80 discussions

reg-feat2anat problem
by Elaine Leung 20 Feb '07

20 Feb '07

Hello, I'm trying to display some FEAT statistics on a surface I created using Freesurfer using instructions from http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html. The automatic registration function reg-feat2anat seems to have failed and I'm not sure what I should do to re-orient the slices better. I've attached a picture, hopefully it will convey my problem. Also, looking at the log files, I noticed the line INFO: could not find /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file Where do I get the file avg152T1_brain.mat? Thanks for your help, Elaine

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Getting started with tutorial data.
by McLean John (NHS Greater Glasgow & Clyde) 20 Feb '07

20 Feb '07

Hi, I am new to Freesurfer and i'm hoping to learn how to use it by working through the tutorial data. I have installed FS correctly and ran recon-all -s bert -autorecon1 This completed without any errors. When i downloded the tutorial data: (buckner_data-tutorial_subjs.tar.gz) i noticed the file was only 2Gb (compressed), rather than the 6.5Gb reported in the FS documentation. After unzipping the files i am now concerned i do not have the full dataset that was intended. Within the folder .../buckner_data/tutorial_subjs i only seem to have the following folders and files bert fbert.feat group_analysis_tutorial fbert.design.fsf fbert.nii.gz I do not seem to have a folder called scrips, which i think i should have? Can anyone tell me where i am going wrong. I tried to start working through the FS tutorials and i failed at the first hurdle. Any help or comments are much appreciated. Best wishes John ********************************************************************** Information in this message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies; please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

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problem in running recon-all
by Shahabuddin Ansari 20 Feb '07

20 Feb '07

Hi, I ran "recon-all -subjid 2144 -all" and it just got frozen after a while. I have attached the log herewith. Appreciate your help. Thanks! Shahab --------------------------------- Need a quick answer? Get one in minutes from people who know. Ask your question on Yahoo! Answers.

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volumes of aseg, aparc
by Woo Suk, Tae 20 Feb '07

20 Feb '07

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear Freesurfer experts. Are the volumes of aseg, aparc files absolute volumes measured in native space or measured after spatial normalization? Woo Suk, Tae Seoul, Korea

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folding index on surface
by Sasha Wolosin 19 Feb '07

19 Feb '07

Dear all, Is it possible to display folding index on the cortical surface? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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coregistration of MRI and MEG
by Sameer Walawalkar 19 Feb '07

19 Feb '07

Hello, I am interested in coregistering mri images with MEG (elekta neuromag 306) data in order to do Dynamic Imaging of Coherent Sources (DICS analysis) using fieldtrip. I have installed freesurfer and have been able to open the mri files. How do I proceed next? Under what title will I be able to find the necessary info on Wiki? Thank you very much in advance for your help. best, sameer

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MNI 305 coordinates to average mesh vertex lookup
by Morgan G. Hough 19 Feb '07

19 Feb '07

Hi there, I was wondering what the best way would be to look up the vertex numbers that correspond to a set of MNI 152 locations we have from a parallel VBM analysis. Lets assume that I have transformed them to MNI 305 coordinates. Can I now do a lookup to get the vertex numbers on my freesurfer average mesh that would best correspond to that MNI 305 location? I see the MNI coordinate of a vertex when I am looking at results in tksurfer but not a way to get the vertex for a particular MNI coordinate. Thanks in advance. Cheers, -Morgan

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RE: [Freesurfer] Reconstruction problems
by Bruce Fischl 17 Feb '07

17 Feb '07

did you look at the surface? You'll probably need to either fix the watershed, or manually disconnect the cerebellum On Wed, 14 Feb 2007, Alex Fornito wrote: > Is there anything that can be done? (e.g., tweaking certain parameters) > > Alex Fornito > JN Peters Research Fellow > Melbourne Neuropsychiatry Centre > National Neuroscience Facility > The University of Melbourne > Levels 2 & 3, 161 Barry St > Carlton South 3053 Vic Australia > Ph: +61 3 8344 1861 > Fax: +61 3 9348 0469 > Email: fornitoa(a)unimelb.edu.au > > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Wednesday, 14 February 2007 2:01 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Reconstruction problems > > p.s. also the last defect it gets to is a really big one: > > retessellating defect 105 with 13082 vertices (convex hull=6596). > > which may cause it to run out of memory. In any case, my guess is something > is pretty seriousll wrong with this surface. > > > > On Wed, 14 Feb 2007, Fornito, > Alexander wrote: > >> Hi, >> I'm having problems reconstructing the surface for one individual on an > older version of recon-all (v. 1.104). It always seems to exit with no error > message during mris_fix_topology. I've tried to re-run this subject several > times, and even starting from scratch does not seem to help. I'm not sure > why this is happening, as I've used this version of recon-all on hundreds of > other images without any problem. There's no obvious difference between this > image and any of the others that I can see by looking at the T1 (e.g., no > apparent artifacts, etc.). I've attached recon-all.log. Any suggestions? >> Thanks, >> Alex >> >> Alex Fornito >> JN Peters Research Fellow >> Melbourne Neuropsychiatry Centre and Department of Psychology >> National Neuroscience Facility >> The University of Melbourne Levels 2 & 3, Alan Gilbert Building >> 161 Barry St Carlton South Vic 3053 Australia >> Ph: +61 3 8344 1861 >> Fax: +61 3 9348 0469 >> email: alexander.fornito(a)wh.org.au >> >> >> > > > WARNING: This message originated from outside the Northern/Melbourne/Western > Health e-mail network. The sender cannot be validated. Caution is advised. > Contact IT Services (+61 3) 9342 8888 for more information. > > >

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Re: [Freesurfer] Installation on sun grid]
by Inge K. Amlien 16 Feb '07

16 Feb '07

Bruce: Thank you. Uri: I believe all applications are installed on the compute-nodes via some rollout script at this datacenter. I try not to get into arguments with the IT people on how to configure the computers, but I am sure it is possible to do a central install. It sure would save some space. Have a nice day /Inge On Thu, February 15, 2007 20:04, Uri Hasson wrote: > Hello Inge, > I am curious to know if you are installing FreeSurfer on each > computing node seperately, or in one central location, that is > accessible to all the nodes. We managed to do a central install that > works pretty well at the University of Chicago. > > Best, > Uri > > > On 2/15/07, Inge K. Amlien <ingeam(a)student.sv.uio.no> wrote: >> Hello list, >> we are installing Freesurfer on a computer cluster (about 400 cpu's) >> running the >> Sun Grid Engine. As there are other applications installed on the >> compute >> nodes and space is limited, we would like to strip out any files from >> the >> Freesurfer installation not needed for processing. >> >> Is it safe to remove any files/folders other than the example subjects? >> Tkmedit/tksurfer? >> >> Kind regards >> Inge Kasbohm Amlien >> Department of Psychology >> University of Oslo >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >

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error in brainmask...
by Shahabuddin Ansari 15 Feb '07

15 Feb '07

Hi, Some the processed images have error in their brainmasks (e.g., partial stripping of skull, partial removing of neck and other parts etc.). Is there any way to correct them automatically? Appreciate it. Shahab --------------------------------- Need a quick answer? Get one in minutes from people who know. Ask your question on Yahoo! Answers.

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Freesurfer February 2007