Freesurfer March 2009

freesurfer@nmr.mgh.harvard.edu

73 participants
100 discussions

Aseg
by Kelly Silva 09 Mar '09

09 Mar '09

Hello, I did the conversion of aseg.mgz to analyze format, but when I open it, it appears only with the coordinates and not with the "seg ids". How can I do that? By the way, is there any posibility to open the "asegstatsLUT.txt" together with the aseg.hdr/aseg.img? Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

2 1

Label display
by Jesse Friedman 09 Mar '09

09 Mar '09

In tksurfer, is it possible to display some labels as outlines and other labels as opaque? If not, I would find this a very useful feature (namely, for masking out subcortical regions while showing activation within cortical labels). -- Jesse Friedman, B.A. Massachusetts General Hospital Martinos Center, Manoach Lab Psychiatric Neuroimaging 149 13th Street #2613 Charlestown, MA 02129 Phone: (617) 726-1908 Fax: (617) 726-4078 jessef(a)nmr.mgh.harvard.edu

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gray-white matter density
by Jose Luis Cantero Lorente 09 Mar '09

09 Mar '09

Dear Freesurfers, I would like to obtain values of gray and white matter density for the left and right hemisphere separately. I am a little bit confused since I have seen this info in different stat files, but not sure which is the correct one. I am using the release 4.2 Any help would be very welcome. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Freesurfer segmentation to analyze
by Jose Luis Cantero Lorente 09 Mar '09

09 Mar '09

Dear Freesurfers, I would need to export the regions segmented with Freesurfer to an analyze file (all regions within the same analyze file) keeping the label codes (Seg Ids) appearing in the aseg.stats. Is that possible? Thanks in advance. Best regards, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Confusing error from 'noaseg' option.
by Zhen Zonglei 08 Mar '09

08 Mar '09

Dear all: While reconstructing monkey brain with FreeSurfer, in the stage of autorecon2, I used 'noaseg' option to avoid the segmentation. The command is as follows: recon-all -s monkey_040409632 -autorecon2 -noaseg -cc-crs 128 117 123 -pons-crs 128 154 108 However, FreeSurfer finally reported me a confusing 'ERROR: cannot find aseg.mgz' and exited. In my mind, FS should know that aseg.mgz does not exist. What's this error mean? Thanks. The details of the error are as follows: #@# Cortical ribbon mask Sun Mar 8 14:22:24 CST 2009 /nfs/h1/r3/Subjects/monkey_040409632/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance monkey_040409632 SUBJECTS_DIR is /nfs/h1/r3/Subjects Exception caught while processing input files 7IoError loading input data... ERROR: cannot find /nfs/h1/r3/Subjects/monkey_040409632/mri/aseg.mgz Linux annex.cnl 2.6.9-42.ELsmp #1 SMP Tue Aug 15 10:35:26 BST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sun Mar 8 14:22:36 CST 2009 -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

1 0

zooming
by Sam Torrisi 08 Mar '09

08 Mar '09

hi FS peeps this seems like such a dumb question but in tkmedit can you zoom in floats? ie not just integers? thanks -Sam

1 0

drawing ROIs in surface space
by Jeff Phillips 07 Mar '09

07 Mar '09

Hello all, I am trying to hand draw ROIs from a functional overlay. The wiki mentions a Cut Area tool in tksurfer, which sounds ideal for getting rid of the area outside my ROI, but it's nowhere to be found in the tksurfer GUI for our installation, Centos 4 x86 64 bit. Has this tool been renamed or subsumed under some other tool? If there is an easier way for me to draw ROIs? Thanks, Jeff Phillips University of Pittsburgh

2 3

New Neuroscience Forum
by Anatoly 07 Mar '09

07 Mar '09

Hello World, Announcing a new Neuroscience Forum http://www.neuroscienceforums.com Forum Topics: . Neuroscience News . Neuroscience Podcasts . Molecular and Cellular Neuroscience . Behavioral Neuroscience . Systems Neuroscience . Developmental neuroscience . Cognitive Neuroscience . Theoretical and Computational Neuroscience . Diseases and Aging . Neural Engineering . Neurolinguistics . Neuroscience Schools & Programs . Neuroscience Jobs . Neuroscience Books . Clinical Trials in Neuroscience Please check it out at: http://www.neuroscienceforums.com Thanks for your attention and hope to see you on the forum !

1 0

Editing results from recon-all -long.
by gmszh 06 Mar '09

06 Mar '09

Hi all, We used the longitudinal processing for our phase 2 data. For some subjects, I found very bad segmentation and surface reconstructions. Suspecting it's a registration problem, I loaded brainmask.mgz from tp1 and tp2 in tkmedit. I could see they are not aligned to each other (attached image). My questions are: 1. Is the problem due to registration? If yes, how can I fix it? 2. If we are to edit the segmentation results from "-long" processing, do we follow the same steps as what we did for tp1? Thanks, Zheng Hui

2 1

mris_anatomical_stats with an average subject
by Rafa x 06 Mar '09

06 Mar '09

Dear FS team I would like to execute the command mris_anatomical_stats with one average subject, the problem is that the file wm.mgz is required. Is there some way to obtain the stats of one average subject?(I need the area of all the parcellations) Thank you in advance Rafa.

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Freesurfer March 2009