Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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

1 0

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!

2 4

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/

1 0

TurboVNC and tkmedit, white matter voxel edit
by c.micheli＠fcdonders.ru.nl 12 Dec '10

12 Dec '10

Hi all i am using tkmedit in linux 64bit CentOS and i have problems in editing the voxels. My aim is to edit/correct the segmentation of the white matter. I load anatomy and segmented volume with the command: vglrun tkmedit -f brain.mgz -aux wm.mgz vglrun is a prefix command that allows my TurboVNC remote session to view the GUI. The problem is that i can add voxels with the middle mouse button but i cannot erase them with right one (it does nothing) Is that a problem occurring to anyone else? Could it be depending from the use of the VNC session? Best regards Cristiano

1 0

--fsl flag in bbregister
by Nasim Maleki 11 Dec '10

11 Dec '10

Hello Doug, I get an error message when using --fsl flag with bbregister: "ERROR: Flag --fsl unrecognized." I'm using: bbregister,v 1.14.2.12 2009/08/07 22:21:00 greve Is this version of the bbregister that I'm using the latest? Thank you, Nasim

3 2

source code for freesurfer
by Alexander Taghva 11 Dec '10

11 Dec '10

Is it possible to get the source code for freesurfer for research purposes? There are mentions of open source distributions but I can't find them. Thanks! -- Alexander Taghva, MD Department of Neurological Surgery Ohio State University

1 0

inaccuracy in surface reconstruction
by Sasa Kivisaari 10 Dec '10

10 Dec '10

Hi all, I have a question about what to me looks like an inaccurate surface reconstruction. I attach here 3 consecutive coronnal slices: in the first and second, the pial surface doesn't seem to follow the whole extent of the collateral sulcus on the right hemisphere (the location of the crosshair). Just eye balling it, it looks like there is a relatively deep sulcus there, but the pial surface doesn't go all the way in. In the third screen shot, 2mm posterior to the first, the sulcus is reconstructed the way I would expect it to. Could you please give me some insights into the reason behind this? Is there a way of fixing it without touching the gray matter voxels? Please let me know if you need any additional information! Thank you in advance, Sasa

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