Re: [Freesurfer] Difficulties with segmentation

Hi, sorry, I meant the cortical parcellation, the one that is used in aparc+aseg.mgz (I believe this uses the desikan killiany atlas?), thanks,JeffOn 6/20/06, Bruce Fischl [EMAIL PROTECTED] wrote: I'll leave 2 for Doug. In 1. by segmentation do you mean the wm.mgzvolume? Or the cortical

Re: [Freesurfer] Difficulties with segmentation

okay, Rahul is looking into it. On Wed, 21 Jun 2006, Jeffrey Spielberg wrote: Hi, sorry, I meant the cortical parcellation, the one that is used in aparc+aseg.mgz (I believe this uses the desikan killiany atlas?), thanks, Jeff On 6/20/06, Bruce Fischl [EMAIL PROTECTED] wrote: I'll leave 2

Re: [Freesurfer] Difficulties with segmentation

Hi, thanks, would the fix for this problem be released as something that I then would use to rerun mris_ca_label (and mris_anatomical_stats and mri_aprac2aseg) and get better results, or would I have to rerun a whole bunch of earlier steps (so I would want to hold off with processing for now)?

Re: [Freesurfer] Difficulties with segmentation

hopefully the former, but until we understand what's going on it's hard to say. On Wed, 21 Jun 2006, Jeffrey Spielberg wrote: Hi, thanks, would the fix for this problem be released as something that I then would use to rerun mris_ca_label (and mris_anatomical_stats and mri_aprac2aseg) and get

[Freesurfer] Basic questions

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

Re: [Freesurfer] Basic questions

1. Yes, we support minc. 2. There is a table of structures/volumes/thicknesses in each subjects stats directory. cheers, Bruce On Wed, 21 Jun 2006, Anil Roy wrote: Hello all, I have a few basic questions about FreeSurfer and would appreciate any help. 1) I have a number of brains in mnc

[Freesurfer] tksurfer rendering offscreen

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

Re: [Freesurfer] tksurfer rendering offscreen

Sorry, that isn't supported in tksurfer. Tksurfer has a lot of inefficient redrawing as it is a very old program and has a lot of old spaghetti code that isn't being updated. I'm working on moving all the tksurfer features into scuba. On Wed, Jun 21, 2006 at 12:13:51PM -0700, Don Hagler wrote:

[Freesurfer] recon-all without tcsh

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 KumarU

[Freesurfer] nu_correct problem

Hi Bruce: I installed the new version of freesurfer. I found that nu_correct does not work properly, the error message is spawn: exec of nu_estimate_np_and_em failed: No such file or directory nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) so I try to

Re: [Freesurfer] recon-all without tcsh

Aju, tcsh will need to be installed in order for recon-all to work. it should be possible to get tcsh for most any system, and can be built from source also. Nick Hi, Can recon-all run even if tcsh is not installed on the system. When I try running it, I get the message: -bash:

[Freesurfer] FS-FAST: mkcontrast-sess -setwdelay

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

Re: [Freesurfer] Basic questions

Anil, In freesurfer, the utility mri_convert will convert minc files to mgz. This would be the first step in the reconstruction process. You might want to have a look at the tutorial that is available: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Nick Hello all, I have a few

Re: [Freesurfer] Basic questions

Anil, In freesurfer, the utility mri_convert will convert minc files to mgz. This would be the first step in the reconstruction process. You might want to have a look at the tutorial that is available: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial Nick Hello all, I have a few

[Freesurfer] viewing group analysis results in tkmedit (3D) while using spherical space intersubject morphing

Hi FreeSurfers, A small group analysis question of fMRI data (fixed effects). The target brain is fsaverage. I have resampled and averaged the stat maps across subjects in _spherical_ space using func2sph-sess / sphsmooth-sess / isxavg-fe-sess / stxgrinder-sess. Viewing the results on a