Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Re: [Freesurfer] Freesurfer auto verse manual segmentation for hippocampus
by Bruce Fischl 06 Oct '09

06 Oct '09

Hi Aize, what is your definition of hippocampus? Does it coincide with our's? Is fimbria included? Alveus? Bruce On Tue, 6 Oct 2009, caoaize wrote: > > Hello Bruce, > > > > We did manual and freesurfer auto segmentation on hippocampus for 39 subjects. I attached the comparison plot here. As seen in this figure, the left hemisphere sysmatically larger from auto segmentation than from manual segmentation, except one brain, with manual slightly bigger than the auto. While is not the same for the right hemisphere. We just wonder what is behind it, is it because our image contrast, or something inside freesurfer? Do you have any comments? I will be appreciated for your reply. > > > > Aize > > _________________________________________________________________ > ÉÏWindows Live ÖÐ¹úÊ×Ò³£¬ÏÂÔØ×îÐÂ°æMessenger£¡ > http://www.windowslive.cn

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skull strip...
by Gonzalo Rojas 06 Oct '09

06 Oct '09

Hi: The command: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s <subj> only runs the skullstrip procedure ?... Which is the "clone" tool ?... Sincerely, -- Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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QDEC
by Jose Soares 06 Oct '09

06 Oct '09

Hi all, I am working with QDEC and I would like to know if it is possible to do subcortical structures (e.g. hippocampus, amygdala, putamen) analyses in qdec?? I only have cortical structures mapped in my analyses. Thanks for the help, Miguel. ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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mri_glm-sim
by Martin Kavec 06 Oct '09

06 Oct '09

I wonder how log does it ususally take to complete cluster-wise correction for multiple comparisons using mri_glm-sim. I have a group analysis of 19 subjects with 1 continuous and 1 discrete factor (two levels) and the mri_glm-sim is running now for about 4 days. Is there any way to track the progress and estimate when it may finish? Thanks in advance. Martin

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[FreeSurfer] Is source code available?
by Youngsang Cho 06 Oct '09

06 Oct '09

Dear all, It seems that freesurfer's source code is open. But I couldn't find any link for source code or cvs id and password. Could anybody tell me whether the source code is available to external people for academic purpose? If it's available, where can I download the source code? Please tell me the information. Thanks, Youngsang Cho Dept. of CS KAIST

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mri_nu_correct.mni intensity correction problem
by Jeff Sadino 06 Oct '09

06 Oct '09

Hello, I am running FS 3 and am having problems with auto-recon1, in particular the mri_nu_correct.mni step. My orig volume has intensities around 150-250, but my nu.mgz image has intensities all below 20. I am having errors further down the line, but I think they are all due to this step. Can anyone help me get my intensity values to work out right? Thank you! Jeff Sadino _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/

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freeview and annotation file
by tulu＠ms36.hinet.net 05 Oct '09

05 Oct '09

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volume difference in aparc.stats and wmparc.stats
by Guang Zeng 05 Oct '09

05 Oct '09

Hi, there, I am looking at the volume size of front pole . In lh.aparc.stats, this volume is 590, while in wmparc.stats (it is called ctx-lh-frontalpole), this value is 610, which one is accurate? Thanks a lot! BTW: In FreeSurfer Tutorial : Process Flow (http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) The follwing command is called at the end of recon-all -autorecon2 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 006_S_0547_20070924 --surf-wm-vol --ctab /home/m047599/freesurfer-install/freesurfer/ASegStatsLUT.txt However, when I looked at the recon-all.log file, it is called at the very end of autorecon3, am I right? Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/177141664/direct/01/

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images with poor resolution
by Dana W. Moore 05 Oct '09

05 Oct '09

Hi everyone, I am trying to salvage some images that were done with poor gray/white boundary contrasts. First, FreeSurfer includes an area of dura in the skull strip. I tried adjusting the watershed but it made no differences. FreeSurfer is subsequently unable to detect the gray/white boundary and labels the dura as cortex: [] Looking at the raw images, the gray/white boundaries are faint but visible. Is there anything I can adjust to try to make this work with FreeSurfer? 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: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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WM surface errors
by Alex Fornito 05 Oct '09

05 Oct '09

Hi, I am trying to reconstruct the surfaces of some 1.5T images that I have. For a subset of images, portions of the white matter surface in the occipital cortex are missed, even though the wm.mgz volume seems to have segmented the area correctly. The aseg also seems to have labelled this region correctly (e.g., it is not labelled erroneously as ventricle). I have tried using control points, but this had little impact on the final solution. I've attached pics of the surfaces on the anatomical and wm volumes, along with the locations of the control points so you can see for yourself (note that I placed control points on consecutive slices through the areas). Any advice on how I can fix this problem? Thanks, Alex

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