[Freesurfer] smoothing thickness

Hi! I'm trying to smooth thickness data using mri_surf2surf. The thickness vectors are mapped onto ico7, and I would like to smooth the thickness there (ico7). But when I add the --fwhm option to mri_surf2surf (equivalent to --fwhm-trg), mris_surf2surf looks for a real subject called "ico

Re: [Freesurfer] question about strange results after talairach transform

The problem is probably that the image is outside of the tkregister2 FOV -- I noticed that there is a large shift from magnet isocenter in your image (about 30 cm). tkregister2 centers the FOV at isocenter. I still have not found a work-around for this, but you can use mri_vol2vol --targ

Re: [Freesurfer] How to get masks on cerebral white matter and cortex?

I think you have an older version. Try the one in: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol Kai Li wrote: Yes, Doug did answered and thank you, Doug. I tried the command that Doug gave, but the command mri_vol2vol complained "Option --mov unknown". Then I tr

[Freesurfer] question about strange results after talairach transform

Hi! I use axial LAS system 3D nifti and analyze format images to perform autorecon1 process. Skull stripping results looked fine. However, when I checked talairachs transform results (tkregister2 --mgz --s C1 --fstal), a part of original image was just shown at left upper corner and talairac

Re: [Freesurfer] free surfer installation questions

Andrew, Answer to 1. - rename tksurfer_fc5 to tksurfer.bin. Beginning with v3.0.4 of freesurfer, 'tksurfer' became a wrapper script (which declares necessary tcl/tk environment vars and calls the binary tksurfer.bin, which was 'tksurfer' in older versions of freesurfer). Also, you may need to se

Re: [Freesurfer] recon-all -autorecon2-cp

Hi, All the steps of recon-all are set to save any manual edits you make unless you specify otherwise. autorecon2-cp will use any previous wm edits, as well as any previous edits you have made to the brainmask.mgz volume. In the event that you do NOT want your edits to be saved and used you

Re: [Freesurfer] recon-all -autorecon2-cp

It shouldn't. By default it should keep all edits (white matter or otherwise) On Wed, 3 Jan 2007, Shi, Bo wrote: Does recon-all -autorecon2-cp ... Remove all previous manual white-matter edits? Is there a way I can prevent this? ___ Freesurf

Re: [Freesurfer] mri_nu_correct: how to maintain original geometry?

Hi Stephen, you can just use nu_correct directly if you want (the MNI code, which we have a wrapper for) cheers, Bruce On Wed, 3 Jan 2007, Stephen Towler wrote: Hi all, Is there a way to get mri_nu_correct to output geometry identical to the input scan, with no interpolation? For example

Re: [Freesurfer] How to get masks on cerebral white matter and cortex?

Yes, Doug did answered and thank you, Doug. I tried the command that Doug gave, but the command mri_vol2vol complained "Option --mov unknown". Then I tried replace --mov with --in, it complained that --tar is unknown. I actually couldn't find the options --mov, --tar, --o, and --regheader in th

[Freesurfer] free surfer installation questions

Hi, We are trying to install Freesurfer on a Linux Fedora Core 6 platform. We downloaded the CentOS 4 platform and the FC 5 upgrade of tksurfer. We have two questions: 1. When we rename tksurfer_fc5 to tksurfer and move it into the Freesurfer directory, it is an executable file, whereas the

[Freesurfer] mri_nu_correct: how to maintain original geometry?

Hi all, Is there a way to get mri_nu_correct to output geometry identical to the input scan, with no interpolation? For example: if I run mri_nu_correct (only) on a T1 scan that is 124x256x256 (1.2mm x .9375 mm2), the output is 256x256x256 (.9375 mm3). Not desirable for my current applicatio

[Freesurfer] recon-all -autorecon2-cp

Does recon-all -autorecon2-cp ... Remove all previous manual white-matter edits? Is there a way I can prevent this? -- Bo Shi 300 Longwood Ave Pavilion 152 Boston, MA 02115 (617) 355-5167 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

WG: [Freesurfer] MRInormalize: could not find any valid peaks

Dear Freesurfer user I posted this question already on the mailing list and understood the answer. But this failure only occures when running on the grid. When I run the Freesurfer locally with the same brains, the error did not occur. Unfortunately, I have Fs version 3.0.4 on the grid and 3.0.3