Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Downloading v4.5.0
by Chester Kang 20 Dec '10

20 Dec '10

Hi, When I try to download v4.5.0 (Mac version) from the Archive, it seems like the file is missing/unavailable? http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.5.0/freesurfer-Darwi n-leopard-i686-stable-pub-v4.5.0-full.dmg Have also tried the mirrors link but that is down also. Could someone point me to an alternate location or correct URL? Thanks very much! Regards, Chester

2 1

black screen when using tksurfer
by Amir Tahmasebi 20 Dec '10

20 Dec '10

Hi there, When I am using the "tksurfer" command for visualization, I only get a black screen: tksurfer $subject rh inflated There is no error reported at the command prompt except for a warning: No colortable found! Here is the version of the freesurfer I am using: freesurfer-Linux-centos4-stable-pub-v4.5.0 Any help is appreciated. Thank you, Amir -- ________________________________ Amir M. Tahmasebi, Ph.D. postdoctoral researcher Rotman Research Institute, University of Toronto, Toronto, Ontario CANADA ________________________________ Tel: (416) 785-2500, ext. 3130 Web: www.cs.queensu.ca/~tahmaseb

1 0

Sulci segmentation
by FIDEL ALFARO ALMAGRO 20 Dec '10

20 Dec '10

Hi, I am pretty new in freesurfer and I do not know if this question has been answered before (It is difficult to search for 1 basic question), so I will post it anyways: - Is there any segmentation/labeling in freesurfer that allows the user to identify all the sulci of an MR image? I have done the recon-all, correctly, but I am not able to see any sulcus using tkmedit with the generated segmentations. Thanks in advance.

2 4

ICV differs systematically in repeated measurements
by Diederick Stoffers 20 Dec '10

20 Dec '10

Hi all, I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks! Cheers, Diederick

5 6

tkmedit white matter editing
by Micheli, C. 20 Dec '10

20 Dec '10

Dear all I am using the tkmedit GUI to add/erase pixel in a slice-wise fashion in order to subsequently apply a tessellation on the white matter. I launch the command cd subject/mri tkmedit -f brain.mgz -aux wm.mgz from linux shell (64bit CentOS), where brain.mgz is the anatomical MRI and wm is the segmented white matter, both in the subject/mri folder Editing the voxels of the aux image works only when i want to insert pixels but not when i want to erase them (menu->EditVoxelsTool->right mouse click). I wonder if anybody uses this feature of tkmedit GUI and had the same problem. Appreciate any input Best, Cristiano

1 0

[New release] - iSurf Brainview 2.0.0
by Pedro Paulo de Magalhães Oliveira Junior 19 Dec '10

19 Dec '10

Today it was released a major upgrade of iSurf Brainview. Major improvements could be noticed on the IPad. Now you can click the name of the brain structure and have a popup control with the definition and references for the area. As usual suggestions are welcome. Upcoming features include the use of Destrieux atlas and 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Cheers Pedro Paulo Jr. -- iOS 4.2

1 0

tksurfer wrong .annot
by Lemkaddem Alia 19 Dec '10

19 Dec '10

Hello, I'm working on the latest release of freesurfer 5 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz). Everything has been working fine until recently. When I open tksurfer to view the parcelation of my subjects, the region of unknown and CC is not recognized (it's named None). However, for "fsaverage" (see attachment) it's right but for "bert" and all my subjects it's wrong. I'm working on Ubuntu 10 and suspect that one of the package updates could have effected the tksurfer viewer. I have checked the segmentation of my subjects and it seems like all the regions are correct, so it's just a matter of tksurfer (I think). Have you faced this issue before? I'm thankful for all the help I could get. Thank you in advance, Alia

2 1

Cortical Classifier for PALS
by Lena Palaniyappan 18 Dec '10

18 Dec '10

I want to use the annot file for lobar areas in fsaverage to be mapped onto all of my subjects. As I don't want to disassemble the annot to single labels but generate lobar.annot for all subjects, I intend to use mris_ca_label -l fsaverage/label/lh.PALS_B12_Lobes.annot <subjid> lh lh.sphere.reg <classifier> subjid/label/lh.PALS_Lobes.annot For this purpose. What cortical classifier file should I use to map the different PALS atlases (at least - the two of them : Brodmann and Lobes) Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 4

(no subject)
by Giovanni Rodriguez 17 Dec '10

17 Dec '10

To Whom It May Concern: My name is Giovanni Rodriguez, I am a high school student working at the University of Miami in a research lab. My lab professor told me to work through the basics on my own and to download the tutorial and dataset. Is there anyway that I could find a dumb proof, step by step manual on how to download and work through Freesurfer? Thank you in advance, Gio

2 1

Re: [Freesurfer] Difficulty running FreeSurfer
by Nisser ali umar 17 Dec '10

17 Dec '10

2 1

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