Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

aseg error?
by Inge K. Amlien 22 Jun '06

22 Jun '06

As seen in the attached image, voxels outside the pial surface has been labelled as cortex. Will these voxels be included in aseg.stats, or is it normal? mri_ca_register segfaulted during an earlier run, and I restarted it without touching any files, could this have caused it? Regards Inge Amlien University of Oslo (Norway) ----- Freesurfer 3.03 x86_64

2 1

Basic questions
by Anil Roy 21 Jun '06

21 Jun '06

Hello all, I have a few basic questions about FreeSurfer and would appreciate any help. 1) I have a number of brains in mnc format. I was wondering if these could be used in FreeSurfer because the tutorials only mention usage of the mgz format. Also, how do we convert from mnc to mgz. 2) What is the exact method of extracting the volume and cortical thickness of a particular region once the brain has been loaded into freesurfer. I can't seem to find any docs that outline how this is to be done with freesufer. If someone could point me in the right direction it would be really helpful. Thanks a lot, Anil Roy.

3 3

FS-FAST: mkcontrast-sess -setwdelay
by raij＠nmr.mgh.harvard.edu 21 Jun '06

21 Jun '06

Hi, I have a large (~100) number of FIR analyses where I need to set the weights for each post-stimulus delay (and then collapse them with -sumdelays). The weights are the same for all analyses. However the -setwdelay weights can only be entered manually upon prompt. This means that I would have to sit by the computer for a few days just to copy-paste a short series of numbers every 25 min. This makes no sense of course. Is there a way to make feeding the -setwdelay numbers part of the analysis script so I could just let it run without human intervention? I would be very happy if I could just set in the analysis script, for example, mkcontrast-sess -analysis XXX -setwdelay 0 0 0 0 1 1 1 0 0 0 0 0 -sumdelays -contrast A-REST -a 1 -c 0 Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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recon-all without tcsh
by Ajith Kumar U 21 Jun '06

21 Jun '06

Hi, Can recon-all run even if tcsh is not installed on the system. When I try running it, I get the message: -bash: /home/aju/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory Thanks, Aju. ************************************************** Mr.Ajith Kumar U Junior Research Fellow, Department of Audiology, All India Institute of Speech and Hearing, Naimisham Camppus, Manasagangothri, Mysore,570006 INDIA. Ph: +91 821 2514449 Ext 186 (O) +91 821 2514449 Ext 224 (R) Fax: +91 821 2510515 Email: ajithajitkumar18(a)rediffmail.com **************************************************

2 1

tksurfer rendering offscreen
by Don Hagler 21 Jun '06

21 Jun '06

In older versions of tksurfer, it was possible to set a renderoffscreen flag (in a tcl script) that would make it possible to render images in the background. I find this very valuable for rendering large batches of stats. I would like to store surface-painted timeseries data in mgh format and render each frame in order to make a movie. Since the old version of tksurfer will not read mgh files, I need to use the new one for this. But rendering onscreen is very annoying because it means you can't use your computer for hours (if rendering lots of images). The problem seems to be that tksurfer is opening a window and drawing it twice before the tcl script even begins to be interpreted. Is this something that can be fixed? Just in general, why should time be wasted drawing the surface twice upon opening? And can the tcl script be interpreted *before* any open_window or redraw commands are given?

2 1

tksurfer:troubleshooting surface problems
by Chacko Cherian 20 Jun '06

20 Jun '06

Hello everyone, I have used an Analyze format data(.img) on Freesurfer and was running the Morphometry and REconstruction tutorial on the wiki.THey were running fine till i reached the automatic topology defect correction step. I used :recon-all -fix -s <subject_name> and it started fxing all the defects.There were 66 defects which took me 5 hours on my machine.After this I'm not able to view the output files at ../surf/ clearly.I can only see a small piece of the surface. Could you also please tell me how to create the final surfaces because the make_final_surfaces command is also not running through. Thanks in advance, Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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display surface tessellation
by R. Chen 20 Jun '06

20 Jun '06

Hi, I have a suface file such as lh.white. Now I try to view the surface tessellation. I use tksurfer. However, I cannot display the edge between vertices. I try Matlab and use patch function and set edge as a constant color. But it is very hard to see these edges. Could anyone recommand a tool for this task? Thank you, Ron --------------------------------- Do you Yahoo!? Next-gen email? Have it all with the all-new Yahoo! Mail Beta.

2 1

Finding ROI and average
by Joongnam Yang 19 Jun '06

19 Jun '06

Hi All, Is there a method of isolating an area of the overlay image (functional onto anatomical) on Freesurfer as ROI and get the average of the amplitude of the ROI? Any suggestions would be appreciated. Nam.

3 2

basic questions about cortical thickness
by Chunchun Ni 19 Jun '06

19 Jun '06

Hi, I have some basic questions about cortical thickness. 1) What's the image requirement for calculating cortical thickness? slice thickness, resolution? 2) If analyzing one brain image on basic system requirement linux machine ( 2G ram, 2G processor ). How long does it take? Thanks Chunchun

2 1

Cortical classifier
by Satrajit Ghosh 18 Jun '06

18 Jun '06

Hi Bruce, I'm finding that sometimes the cortical autoparcellation has disjoint areas with the same label and finger like projections that don't appear anatomically accurate. 1. Is there any way I can enforce continuity of labels so that I don't get these islands? 2. Is there any way to enforce a certain level of coarse curvature control, to avoid getting the finger like projections? Thanks, Satra

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Freesurfer June 2006