Re: [Freesurfer] loading label in tksurfer

Hi Sharmili, this is not an error message. It is sampling the volume label coords onto the surface. What happens next? Does tksurfer display the label? cheers, Bruce On Wed, 29 Jul 2009, Sharmili 57 wrote: Hi ! Thats all it says. The window with the inflated brain shuts down, as soon as

[Freesurfer] Adding .mnc

Hello Everyone, I am attempting to add .mnc data but get the following error when trying to convert using: mri_convert subject.mnc subject/mri/orig/001.mgz I am following the tutorial reconstruction slides online. Here is the error: mri_convert EF0114.mnc EF0114/orig/001.mgz $Id:

Re: [Freesurfer] Adding .mnc

That worked, thank you. I used -force at the end instead of -all and it looks good. Jesse On Wed, Jul 29, 2009 at 10:20 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jesse, does that directory exist? Are you going to run recon-all afterwards? If so, you might just do: recon-all -i

Re: [Freesurfer] Adding .mnc

you should probably use -force and -all On Wed, 29 Jul 2009, Jesse Bledsoe wrote: That worked, thank you. I used -force at the end instead of -all and it looks good. Jesse On Wed, Jul 29, 2009 at 10:20 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jesse, does that directory

Re: [Freesurfer] Adding .mnc

Right. I wondered why it went so fast - thanks again for the help. It is processing everything now. Jesse On Wed, Jul 29, 2009 at 11:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: you should probably use -force and -all On Wed, 29 Jul 2009, Jesse Bledsoe wrote: That worked, thank

Re: [Freesurfer] Surface Analysis of the Anterior Cingulate

Rahul, thanks for the ref to the atlas definitions. Is there a similar definition for the cortex mask (?h.cortex.label)? Bruce, yes we are using the latest version. Some of our surfaces seem to exhibit a lot of noise between the anterior cingulate and the corpus callosum, sometimes encroaching

Re: [Freesurfer] Surface Analysis of the Anterior Cingulate

do you mean noise in the surface placement or in the parcellation labels? On Wed, 29 Jul 2009, Stephen Tyree wrote: Rahul, thanks for the ref to the atlas definitions. Is there a similar definition for the cortex mask (?h.cortex.label)? Bruce, yes we are using the latest version. Some of

Re: [Freesurfer] Surface Analysis of the Anterior Cingulate

Surface shape is the way I would characterize it. We would at times segment the white/gray/other differently than Freesurfer along that boundary. But at the same time it is hard to tell exactly how it should be segmented, but could possibly be improved by manual edits. -- Stephen Tyree

[Freesurfer] mri_convert with old GE-LX data

Hello, I'm trying to use mri_convert to convert old (~1999) functional data that was acquired on a GE LX scanner. However, nothing seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's my command line: (results are similar if I omit the -in_type flag) [matl...@occipital functional]$

Re: [Freesurfer] mri_convert with old GE-LX data

I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge option, it is still looking for the old filename, it seems) [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm image mri_convert I.1 -it lx -ot spm image $Id:

Re: [Freesurfer] mri_convert with old GE-LX data

sorry, it's a little finicky, I think it is looking for a %03d format, meaning I.001 for slices numbers less than 1000, and I.1001 for greater Chris Watson wrote: I renamed them all to I.1, I.2, ..., I.8000 (there are 8000 images total), and I got the same error messages. (With the -it ge

Re: [Freesurfer] mri_convert with old GE-LX data

It got a little further (with -it ge and without any --in_type flag), but I get this error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm image mri_convert I.001 -it ge -ot spm image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from I.001...

Re: [Freesurfer] mri_convert with old GE-LX data

You can try specifying the input geometry with something like -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 this is undoubtedly wrong, but should allow the command to finish Chris Watson wrote: It got a little further (with -it ge and without any --in_type flag), but I get this

Re: [Freesurfer] mri_convert with old GE-LX data

Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks

Re: [Freesurfer] mri_convert with old GE-LX data

sorry, also add -ic 0 0 0 Chris Watson wrote: Still get an error: [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 image $Id:

Re: [Freesurfer] mri_convert with old GE-LX data

It completed but it's only giving me 1 .img file, and when I loaded it into mricro, it thinks the z dimension is 8000 (the number of slices total). It should give me 400 volumes (20 slices each). So I want image001.img, 002.img, and so on. How can I do this? Do I have to rename the files

Re: [Freesurfer] mri_convert with old GE-LX data

Sorry, I don't know how to make our tools do this. It's a one-off on an old data set on a file format that we don't really support anymore, so I'm afraid that you're on your own on this one. doug Chris Watson wrote: It completed but it's only giving me 1 .img file, and when I loaded it