Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

mri_convert float to uchar
by Yang Liu 15 Dec '10

15 Dec '10

Hello all, I am converting one .mgz file to another like this: mri_convert -i a.mgz -o conformed_a.mgz --conform The data type of a.mgz is float. After the conversion, The conformed_a.mgz is uchar. However, I found that the places surrounding the brain which have 0 grayscale values in the a.mgz are having grayscale value 108 in the confored_a.mgz. This makes the conformed_a.mgz very whitish compared to the original one. Is there a way to make the float 0 to a uchar 0? Thanks. Yang

2 3

.xdebug_tkmedit
by Paola Valsasina 15 Dec '10

15 Dec '10

Dear List, I installed version 5.0 of freesurfer on my Linux machine, when I tried to run tkmedit I got the attached error. Do you have any suggestion? Kind regards, Paola ----------------------------------------------------------------------------------- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org

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CUDA on Mac
by Martin Kavec 15 Dec '10

15 Dec '10

Hi all, I wonder if there are any plans to support CUDA on Mac platform. I see there are libraries available for the platform. Thanks a lot for feedback, Martin

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Re: [Freesurfer] another recon-all error
by Thomas, Adam (NIH/NIMH) [E] 15 Dec '10

15 Dec '10

Bruce et al, Did you ever get to the bottom of Joakim's problem? I'm getting the same error. I checked the talairach and it looks fine. But for some reason mri_normalize can't find any peaks so T1.mgz comes out as all zeros. I just uploaded the subject to your anon FTP server.: ex03.2.tgz Thanks and let me know, -Adam On Thu, Nov 2010, Bruce Fischl wrote: Hi Joakim, you need to visualize the talairach.xfm applied to the orig.mgz in either tkregister2 or tkmedit to see if it is ok. mri_normalize clearly failed, and this is usually because of a failure in the talairach. It could also be that the nu intensity correction failed, so make sure to look at the nu.mgz as well. Or if you rather you can send us the nu.mgz and we can see what happened. cheers Bruce On Thu, 11 Nov 2010, Joakim Vinberg wrote: Bruce, I had quickly scanned the talairach.xfm, but I have to admit that I'm new to the process and wasn't sure what I was looking for. Here are the recon-all.log and talairach.xfm from this subject. Thank you for all the help! oakimJ -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, November 10, 2010 7:09 PM To: Joakim Vinberg Cc: <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] another recon-all error Did you check the talairach.xfm? Can you send us the recon-all.log file? On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" <jvinb...(a)omneuron.com> wrote: Sorry to add another! I ran recon-all on a subject of mine, and have recon-all exit with the error below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is in fact totally emptyÿÿdefinitely not enough values of 110. Is this due to a specific error that I might be able to bypass, or will adding in WM control points fix things? Thanks in advance! Joakim //******************************************************** mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010 i686 i686 i386 GNU/Linux recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010

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running in the background?
by Nathan Dankner 15 Dec '10

15 Dec '10

Hi All, I'm running freesurfer on a public station, so I need to sign out when I'm finished with sessions. Has anyone found a suitable way to run freesurfer in the background? I know that I can run matlab in the background here, so if there is a way to run the pipeline through matlab that may work... Thanks, Nathan

4 6

aparc+aseg
by Pedro Paulo de Magalhães Oliveira Junior 15 Dec '10

15 Dec '10

Hi, One quick question: In the aparc+aseg file I suppose we have two volumes (one for aparc and other for aseg). Are those volumes overlapped or one after another? thanks PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

2 1

flag for not stripping the image
by Navid Shiee 14 Dec '10

14 Dec '10

Hi, I have an image with very large ventricles, which makes the stripping step of the algorithm to fail. I have the stripped version of the image and was trying to use -noskullstrip flag to just input the stripped image. But I got an error of "could not open mask volume brainmask.mgz". Would you please guide me to hove to proceed for proceesing? Thanks, -- Navid

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Convert multiple analyze files to one nifti file
by Rita Loiotile 13 Dec '10

13 Dec '10

Hi, I have been given data that I need to put in a specific format so that it's useable to me. I know how to use mri_convert to convert between analyze and nifti. However, I need one file per run, whereas this data comes such that every frame is a separate analyze file. How do I combine them? Thanks!

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previous release compatibility and reliability set up
by Scott Sorg 13 Dec '10

13 Dec '10

Hi All, Can surface and volume values from a previous release (i.e., 4.X) be along side values from the current release? We have about 30 brains run through recon-all from a previous version and about 20 from the latest and want to know if we can combine those datasets or if we may need to rerun them all with the current version. Also, for an internal reliability analysis, is it permissible to simply copy a subject folder from subjectdir that was run through -autorecon2 (e.g., P012 > P012-SS), then have different users complete the pial and wm checks on those separate directories, or should we reimport the duplicate volumes and start from scratch? Thank you all for your help, -Scott

2 1

Новое сообщение
by Vovan 12 Dec '10

12 Dec '10

http://samec.org.ua/

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