[Freesurfer] anatomical stats

HI, I'm finishing a study I completed using an older version of freesurfer (20040218), and have noticed that I get different values for surface area and grey matter volume when using mris_anatomical_stats for my labels depending on whether I use the mris_anatomical_stats that it is part of this

Re: [Freesurfer] anatomical stats

Hi Alex, we've fixed a couple of small discrepancies in mris_anatomical_stats. I would use the new version - it should be fine on old surfaces. Bruce On Tue, 27 Sep 2005, Fornito, Alexander wrote: HI, I'm finishing a study I completed using an older version of freesurfer (20040218), and

Re: [Freesurfer] make_average_subject error?

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 the code and everything seems reasonable given my system except the part that says: "if person = brian; exit 0"

Re: [Freesurfer] make_average_subject error?

try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh wit

[Freesurfer] make_average_subject error?

Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 S

Re: [Freesurfer] Scuba/recon-all

yes, ignore it. We will remove it. Bruce On Mon, 26 Sep 2005, Satrajit Ghosh wrote: I see the following statement printed several times through the recon-all processing and when I try to manipulate images in scuba. Is this something I can safely ignore? INFO: Volume /tmp/mritotal_5799/nu_8_d

[Freesurfer] Scuba/recon-all

I see the following statement printed several times through the recon-all processing and when I try to manipulate images in scuba. Is this something I can safely ignore? INFO: Volume /tmp/mritotal_5799/nu_8_dxyz.mnc cannot be found. Thanks, Satra ___

Re: [Freesurfer] Freesurfer output question

1. Of whatever surface you specify (white by default I think). 2. Yes. 3. Easy enough to do in matlab I guess. Bruce On Mon, 26 Sep 2005, Michele Perry wrote: Hi, I have some questions (sent to me by someone else, actually) about freesurfer output from make_cortex_table.csh. 1. Do integrate

Re: [Freesurfer] mgz format

nothing unless you specify -conform. On Mon, 26 Sep 2005, Fornito, Alexander wrote: Hi, Just wandering if someone could tell me what converting to mgh or mgz actually does to the image. COR changed it to 256x256x256, 1mm3, what happens with mgz/mgh? Thanks, Alex ___

[Freesurfer] Freesurfer output question

Hi, I have some questions (sent to me by someone else, actually) about freesurfer output from make_cortex_table.csh. 1. Do integrated_rectified_mean_curvature & integrated_rectified_Gaussian_curvature refer to the shape/arc of the surface of the cortex either before or after inflation? Or are t

Re: [Freesurfer] Freesurfer staff,

Tony, See also the on-line tutorial for converting DICOMs to mgz: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion On Mon, 2005-09-26 at 12:17 -0400, Doug Greve wrote: > > You should have a file called 1801_4/mri/orig/001.mgz. This is what it > uses as input data. If you have

Re: [Freesurfer] Freesurfer staff,

You should have a file called 1801_4/mri/orig/001.mgz. This is what it uses as input data. If you have more than one run, then label the 2nd run as 002.mgz, etc. doug Anthony Cacace wrote: Freesurfer staff, We're relatively new at running freesurfer, everything works fine until we run

[Freesurfer] Freesurfer staff,

Freesurfer staff, We're relatively new at running freesurfer, everything works fine until we run: recon-all -subjid 1801-4 -autorecon1 -mgz then we get the message: no run data found in: /home/amc/freesurfer_new/freesurfer/subjects/1801-4/mri Is there something simple here that we're missing?

Re: [Freesurfer] old version

Alex, The 2004-02-18 version of freesurfer is now posted here: https://surfer.nmr.mgh.harvard.edu/pub/dist/ called this: freesurfer-20040218-Linux.tar.gz un-gzipped by: tar zxvf freesurfer-20040218-Linux.tar.gz which uncompresses a number of files, including an INSTALL file to

Re: [Freesurfer] mgz format

It has no effect on the pixel data, resolution, or geometry. Fornito, Alexander wrote: Hi, Just wandering if someone could tell me what converting to mgh or mgz actually does to the image. COR changed it to 256x256x256, 1mm3, what happens with mgz/mgh? Thanks, Alex

[Freesurfer] old version

HI, I need to re-install an older version of freesurfer in order to finish a study I have been working on, but it seems that particular distribution is no longer on the website. I think it was the 20040218 distribution (or maybe that was that update for it, I'm not sure). The recon-all -version