Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 discussions

Question about "Getting started with your own data
by 卯野賢太 19 Aug '09

19 Aug '09

Hi freesurfer gurus, We are trying to do reconstruction in tksurfer section according to the text. We have a question in "Getting started with your own data" section. In the text, the following commands are written, recon-all -s <subjid> \ -i <path_to_dicoms>/95555-2-1.dcm -i <path_to_dicoms>/95555-3-1.dcm In the above commands, 95555-2-1.dcm and 95555-3-1.dcm represent the data within the same session? Because the directories, path_to_dicoms, were the same, I thought so. However, 2 or 3 in each 95555-2-1.dcm and 95555-3-1 might represent the session number. We can't understand which is right. Please give me your suggestion. Thank you, Kenta

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a "redraw failed: no gl window open" problem
by Guang Zeng 18 Aug '09

18 Aug '09

Hi, there, I am still facing the problem of "redraw failed: no gl window open", I got another linux machine with Nvidia graphic card, I ran the tksurfer command "tksurfer bert lh inflated", it still gave me the "redraw failed: no gl window open" error. surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599 surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: double buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I read a previously posted thread by Nick, it looks like we can download a new tksurfer.bin file to solve this problem at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/cento… I clicked the link, the file has been removed. Does any one can help me get the new link of this file? Thanks a lot! Guang _________________________________________________________________ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

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WM intensity normalization problem
by Garth Coombs 18 Aug '09

18 Aug '09

Hi, I am running a patient of ours with some cortical degeneration through the recon process and have run across an interesting problem. It appears as if the intensity normalization process is missing a large portion of the cortex, resulting in an almost straight line through the middle of his head, with the center portion looking like the intensity normalization worked, but the cortex portion is very dark. The white matter in the cortex hasn't been normalized, and some of the gray matter looks as if it has been washed out or stripped away (that may just be due to the degeneration though). I have been going through and attempting to pick out control points to run -autorecon2-cp, but we wanted to check in and see if that was the best course of action for this particular subject before I got too far into it. The data can be found in /autofs/space/dinah_001/users/balaji/ SUBJECTS_DIR/subjects/ and the subject ID is amcg_anat Any advice would be greatly appreciated. Thanks! -Garth

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ROI reliability
by jentis＠nmr.mgh.harvard.edu 18 Aug '09

18 Aug '09

Hi Freesurfer team, I am trying to get intra-rater reliability statistics on an ROI manually traced twice (blindly). The scans are anisotropic (.38 x .38 x .8 mm) and so I have not run them automatically through the Freesurfer segmentation because they fail after autorecon1. I tried to use the following command but have had problems: mris_anatomical_stats -a ${s}/label/${h}.aparc.annot -f cortical_thickness_stats/${h}_${s}.txt $s $h It seems this command requires certain data from the autorecon process such as wm.mgz and other surface information that I cannot get because autorecon fails on these types of scans. I have only traced one hemisphere (the Left) and the ROIs are saved as label files; an example is: /autofs/space/phrenic_007/users/jon/hires_amy/Round_2/HRDEV126/ whole_amygdala.label Is there another way to get reliability (pixel overlap, total number of pixels, etc.) for two ROIs? Would you suggest another command or is there a way to bypass those requirements for the mri_anatomical_stats command? Thanks!

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Re: [Freesurfer] installing FS - permission denied
by Pedro Paulo de Magalhães Oliveira Junior 18 Aug '09

18 Aug '09

You don't have permission to write in /usr/local Try using sudo before the mv Enviado do meu celular Nokia -----Msg original----- De: Ahmed, F, Me <fahmed(a)sun.ac.za> Enviada: 18/08/2009 05:37:54 Para: Freesurfer Mailing List Assunto: [Freesurfer] installing FS - permission denied Hello. I am trying to install FS and tried the following command: [fsl@localhost Desktop]$ mv freesurfer-Linux-centos4-stable-pub-v4.3.1-= full.tar.gz /usr/local mv: cannot move `freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz= ' to `/usr/local/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz= ': Permission denied [fsl@localhost Desktop]$ Can someone please explain to me why it says permission denied? Thank you, Fatima ----- End of message -----

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installing FS - permission denied
by Ahmed, F, Me <fahmed＠sun.ac.za> 18 Aug '09

18 Aug '09

Hello. I am trying to install FS and tried the following command: [fsl@localhost Desktop]$ mv freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz /usr/local mv: cannot move `freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz' to `/usr/local/freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz': Permission denied [fsl@localhost Desktop]$ Can someone please explain to me why it says permission denied? Thank you, Fatima

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generative group averages
by Dana W. Moore 17 Aug '09

17 Aug '09

Hi everyone, I am using aparcstatstable2 and asegstatstable2 to generate group information so I can get mean values for a group for certain regions. Is there a way to generate group results for right and left total thickness from mris_anatomical_stats? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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patch flattening and back
by oxro0＠yahoo.com 17 Aug '09

17 Aug '09

Hi, Does anyone know of a script that takes a surface patch, flattens it and then gives you the transformation matrix for each verrtex that allows you to put it back into the initial form? The purpose is to do 2D plane geometric operations on the flattened surface and then re-transform the output back onto the original surf configuration. I am working on it in Matlab, so Matlab code would be best. But it could also use FS surf files as input and output. Any suggestions are greatly appreciated! Best, Thomas

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white/pial surface in lateral ventricle
by Mira Michelle Raman 17 Aug '09

17 Aug '09

Hi, I was looking at some of my data and noticed that the white and pial surfaces occasionally invade the lateral ventricle (see attached picture). I went over to the bert sample dataset and noticed the same thing (coronal slice 87). Is this something I should be correcting or is it something that is ignored during the registration and labeling process? If I don't care about the choroid plexus volume, should I fill the white matter mask throughout the ventricle? Thank you in advance, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 940305 http://cibsr.stanford.edu

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(no subject)
by caoaize 17 Aug '09

17 Aug '09

Hi, there, I have some problem for the hippocampus segmentation results. 1. My structural data are originally in par-rec file. I used r2agui to convert them into .nii format, then use recon-all -i to convert the .nii data into freesurfer .mgz format. Based on these operations, I run recon-all -all on all my data, the statistical report show that the mean left hippocampus volume is bigger than the right one, while literature shows that the right one should be bigger. This problem continuously appeared in our different studies. I am not sure whether it is r2agui's problem, which changed the oritation of the structural data. Do you have any idea? 2. After autosegmentation, we did a statistical comparison analysis between automatic segmentation and manual segmentation, and the correlation is quite low, less than 80%, which is not acceptable for us. 3. Can I edit the auto segmentation results in Freesurfer if we think the auto segmentation is not good enough in some area? I will be really appreciated for your help. Aize _________________________________________________________________ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/

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Freesurfer August 2009