[Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-14 Thread Anil Roy
Also, I ran it on a Red Hat system and I'm still getting the error so I don't think it is a machine specific problem. Any suggestions. Thanks. Anil. On 2/14/07, Anil Roy <[EMAIL PROTECTED]> wrote: Here are the details of the acquisitions: Images acquired on a 3T Signa scanner with a standard

[Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-14 Thread Anil Roy
Here are the details of the acquisitions: Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix) The machine has 4 gigs of RAM. Also, AFNI is able to t

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-14 Thread Nick Schmansky
Anil, I was able to successfully run -autorecon1 (after performing my own tal alignment). This included the skullstrip. How much memory does your machine have? It needs to have at least 2GB. Nick On Wed, 2007-02-14 at 15:49 -0600, Anil Roy wrote: > Nick, > > The files were acquired axially(

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-14 Thread Nick Schmansky
Anil, On this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide there is a TIFF image of some example scans having decent contrast. Nick On Wed, 2007-02-14 at 17:03 -0500, Bruce Fischl wrote: > can you tell us the details of the acquisition? The contrast is > intrinsic

[Freesurfer] longitudinal analysis - error

2007-02-14 Thread Chacko Cherian
Hello all, This is an error I got while running the longitudinal analysis on one of our subjects.It didnt create the filled.mgz volume and so the surfaces weren't created. [EMAIL PROTECTED] Fill Tue Feb 13 20:59:04 MST 2007 /ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri mri_fill -a ../script

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-14 Thread Bruce Fischl
can you tell us the details of the acquisition? The contrast is intrinsic, and it has to be sufficient for g/w segmentation. On Wed, 14 Feb 2007, Anil Roy wrote: Nick, The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform yo

[Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-14 Thread Anil Roy
Nick, The files were acquired axially(120 slices) on a GE scanner. These scans are a couple of years old. I should also inform you that I converted the orginal 120 slices into afni brik format (afni was able to read them) and then used mri_convert to convert the BRIK to cor. Freesurfer then used

Re: [Freesurfer] recon-all error

2007-02-14 Thread Nick Schmansky
Anil, Can you send me the orig.mgz file? You can upload it to my email address via: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Wed, 2007-02-14 at 14:54 -0600, Anil Roy wrote: > Hi All, > > I followed the steps in the tutorial on tkregister2 to align the two > vo

Re: [Freesurfer] 64bit centos utilities: mris_wm_volume & mris_volume

2007-02-14 Thread Nick Schmansky
Jenifer, The 32bit version of the tools will also work on 64bit systems. But I've just uploaded the 64bit centos versions for you if you want those. Goto: ftp://surfer.nmr.mgh.harvard.edu/pub/dist and get: mris_volume_x86_64.tar.gz and copy to your $FREESURFER_HOME/bin and type: tar zx

[Freesurfer] pial editing

2007-02-14 Thread Derin Cobia
I have a question regarding editing the pial surface. Many times it includes bright spots, such as fat or vessels. Should I be editing this out? I'm pretty clear on getting rid of included dura, but if I spent the time to edit out every little bright spot, it would be pretty time intensive. Wou

[Freesurfer] WM vol

2007-02-14 Thread Nurunisa Neyzi
Hi, when I use mri_anatomical stats - I get a total WM value 503450 for left and right hemispheres that's the same number in the stats file in the stats folder. but when I use mris_wm_volume - I get 174896 and 178464 which one is the accurate one? also, is the GM volume I get from mris_anatomica

Re: [Freesurfer] average thickness overlay per group

2007-02-14 Thread Doug Greve
Marie Schaer wrote: Dear Doug Greve, Many thanks for your reply, however when I overlay group1.mgh and group2.mgh on my average subject, they look pretty similar. So I read it in matlab, using load_mgh(group*.mgh), which gave me files having exactly the same structure as beta.mgh (size

[Freesurfer] 64bit centos utilities: mris_wm_volume & mris_volume

2007-02-14 Thread Juranek, Jenifer
Recently (7 Feb 2007) mris_wm_volume for 32bit centos was posted in /pub/dist. Is there any possibility of posting 64bit centos versions of mris_wm_volume & mris_volume? I'm running Freesurfer 3.0.4 Many Thanks, Jenifer ___ Freesurfer mailin

Re: [Freesurfer] smoothing question

2007-02-14 Thread Doug Greve
something like: mri_surf2surf --s subject --hemi lh --sval input --tval output --fwhm 5 doug Goldman, Aaron (NIH/NIMH) [C] wrote: Hi, I'm attempting to do thickness analysis based on the guide at: http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf For the smoothing part usin

[Freesurfer] smoothing question

2007-02-14 Thread Goldman, Aaron (NIH/NIMH) [C]
Hi, I'm attempting to do thickness analysis based on the guide at: http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsgroupana.pdf For the smoothing part using mri_surf2surf (page 14), I was wondering what a typical command line should look like. Thanks, -Aaron-

RE: [Freesurfer] Reconstruction problems

2007-02-14 Thread Bruce Fischl
did you look at the surface? You'll probably need to either fix the watershed, or manually disconnect the cerebellum On Wed, 14 Feb 2007, Alex Fornito wrote: Is there anything that can be done? (e.g., tweaking certain parameters) Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatr

Re: [Freesurfer] average thickness overlay per group

2007-02-14 Thread Marie Schaer
Dear Doug Greve, Many thanks for your reply, however when I overlay group1.mgh and group2.mgh on my average subject, they look pretty similar. So I read it in matlab, using load_mgh(group*.mgh), which gave me files having exactly the same structure as beta.mgh (size of 23406 x 1 x 7 x 6)