Re: [Freesurfer] make_average_subject error?

Can you run make_average_surface and make_average_volume separately? Brian Schweinsburg, Ph.D. wrote: I ran it with make_average_subject --debug \ --subjects SC010 SC012 ... I also tried it with --echo. It provides no output. I checked the script and it is executable. I looked through th

Re: [Freesurfer] make_average_subject error?

Title: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. It exits to the prompt with no messages. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552-8

[Freesurfer] mri_convert doesn't recognize DICOM files

I installed Freesurfer on a G5 Tiger Mac, but mri_convert and mri_parse_sdcmdir don't recognize my Siemens DICOM files (from a Siemens Trio 3T) as DICOM files. Has anyone else encountered this? Other programs can read the DICOM files just fine. keith

[Freesurfer] (no subject)

Hi, I am trying to install and set-up freesurfer on a SuSE Linux system, I downloaded and installed the Redhat version, I'm not sure if this was the correct version to use, but when I try to fix the perl path with the command given on the wiki, it says that the command is not found, nor is nu_corre

Re: [Freesurfer] mri_convert doesn't recognize DICOM files

Keith, Can you tell me the command line use to attempt the conversion? It should be possible to convert DICOMS from a Siemens Trio 3T. Try this command-line, assuming the filename of the first slice of the structural run is called 958000-2-1.dcm: mri_convert -it dicom -ot mgz 958000-2-1.dcm 0

Re: [Freesurfer] (no subject)

Jeff, Can you tell me the error it is saying about MINC? Also, do you have a prior installation of the MINC tools? I am guessing you do, and that there is some prior setting of the MINC_BIN_DIR and MINC_LIB_DIR variables that is conflicting with the new installation. The MINC toolkit is inclu

Re: [Freesurfer] make_average_subject error?

Try editing those scripts so that the first line is: #!/bin/tcsh -efxv ie, adding "xv" This turns on all kinds of debugging Brian Schweinsburg, Ph.D. wrote: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. It exits to the

[Freesurfer] -autorecon1/-autorecon2

Hi, I'm using version "freesurfer-Linux-centos4.0_x86_64-dev20050921-full". After recon-all ... -autorecon1, the skull is stripped but a decent portion of the meninges remain. I tried using recon-all -skullstrip -wsthresh -subjid I ran that with h=20, h=10 and h=2. It didn't seem to help so I

Re: [Freesurfer] -autorecon1/-autorecon2

Hi Michele, it may not matter. Typically we don't use the cortical aseg, but the surface-based on instead. Bruce On Tue, 27 Sep 2005, Michele Perry wrote: Hi, I'm using version "freesurfer-Linux-centos4.0_x86_64-dev20050921-full". After recon-all ... -autorecon1, the skull is stripped but a d

[Freesurfer] Re: Freesurfer Digest, Vol 19, Issue 49

On Sep 27, 2005, at 3:06 PM, [EMAIL PROTECTED] wrote:Message: 2Date: Tue, 27 Sep 2005 13:42:02 -0400From: Keith Schneider <[EMAIL PROTECTED]>Subject: [Freesurfer] mri_convert doesn't recognize DICOM filesTo: freesurfer@nmr.mgh.harvard.eduMessage-ID: <[EMAIL PROTECTED]>Content-Type: text/plain; char

Re: [Freesurfer] Re: Freesurfer Digest, Vol 19, Issue 49

Blaise (and Keith), I was able to recreate the problem that Keith is seeing using a sample dicom file he sent, so I am working to resolve that issue. It seems to be a Mac-centric issue, as the same dicom will convert correctly on Linux. The odd thing is that the siemens_dicom files output from o

[Freesurfer] Mris_sample_parc

Hi, I'm trying to create an annotation file from a volume is mris_sample_parc. Is there any way to have it resample at 0.5 the distance between the white and pial surfaces? Thanks Satra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] Mris_sample_parc

Hi Satra, that's what it does by default. cheers, Bruce On Tue, 27 Sep 2005, Satrajit Ghosh wrote: Hi, I'm trying to create an annotation file from a volume is mris_sample_parc. Is there any way to have it resample at 0.5 the distance between the white and pial surfaces? Thanks Satra _

[Freesurfer] Pial surface errors

Hi, I've been having some problems with some of my images where the pial surface misses some parts of some gyri. Just wandering what the best way to fix this is. I've experimented changing the intensities using the configure volume brush tool in tkmedit with some success, but was wandering if t

Re: [Freesurfer] Pial surface errors

Hi Alex, it depends what the cause is. I think the most common is either bias field or intrinsic tissue variations. These can be fixed if the white matter at the base of the strand isn't intensity normalized, that is, if it has a value <110 in the T1 image. If that's the case, you can add some