[Freesurfer] request for guide (fwd)

I am forwarding Hengameh's questions to the list since I am not sure about the answers and somehow she couldn't send emails to the list (do people need to subscribe to the list first?). Please help if you know the answers to her questions. Thanks, -Xiao

Re: [Freesurfer] labels

It's not normal. It's very likely that you load a rh annotation to a lh surface or the other way around. Pls double check. -Xiao On Mon, 14 Nov 2005, Sasha Wolosin wrote: Dear all, When I load the ?h.aparc.annot with the ?h.white surface in tksurfer, the labels look very scattered, is

Re: [Freesurfer] automated parcellation

Hi Goulven, There should be a recon-all.log file under the $SUBJECTS_DIR/subject/script/ directory, if you processed the data using the recon-all script. The log files you attached were produced by the tools to visuallize the results, not by the programs that create the label result. Thus we

Re: [Freesurfer] mri_watershed

Hi Sasha, If you use tkmedit to visualize the results, then the contrast change you saw may be just due to the display problem (not exactly a problem) of tkmedit. You can move the mouse around the image to actually see whether the image intensity values were changed or not. I used

Re: [Freesurfer] coregistration

You may try FLIRT from FSL. http://www.fmrib.ox.ac.uk/fsl/flirt/ -Xiao On Fri, 19 Aug 2005 [EMAIL PROTECTED] wrote: I always have a problem to coregistrate T1 images to Talairach, Is there any way to improve the accuracy of coregistration besides tkregister2? Thanks, Antao

Re: [Freesurfer] skull strip

Yes, skull-stripping is pretty robust. You can definitely try that on your data. -Xiao On Wed, 10 Aug 2005, Sasha Wolosin wrote: Is it possible to do skull stripping without motion correction or intensity normalization? Disclaimer: The materials in this e-mail are private and may

Re: [Freesurfer] tkregister2 help

The final objective function seems too high, which indicates that mritotal wasn't able to find a good registration. One approach worth trying is to do the skull-stripping first, then register the skull-stripped brain to the talairach space. From my experience, it can correct the talairach

Re: [Freesurfer] Failed segmentation

. Then, save the edited WM to replace the old one. After the editing of WM, rerun mri_fill (or -stage2 of recon-all). Hope that helps. Xiao Han On Tue, 12 Jul 2005, Bakkour, Akram wrote: Dear all, I am working on a recent MPRAGE image obtained at MGH. First, we had trouble converting the files

Re: [Freesurfer] recon-all-nmr -disable-autoseg

I think you need to put -disable-autoseg in front of -stage1. -Xiao On Tue, 7 Jun 2005, Elizabeth Fenstermacher wrote: Hello All, I have a number of jobs that I will be running through recon-all-nmr -stage1 in the next few days. I tried using the -disable-autoseg flag, but it seems not

Re: [Freesurfer] wm fill won't work with partial brain

Hi Akram, One possible way is to manually set the Seed points for corpus callosum etc using the -C, -P, -lh, and -rh options of mri_fill. Note that these coordinates must be in the Talairach space. -Xiao On Mon, 23 May 2005, Bakkour, Akram wrote: Hello, I have a high resolution image

Re: [Freesurfer] average curvature on individual subjects

It is possible. You can try mri_surf2surf. -Xiao On Wed, 18 May 2005, Frida Polli wrote: Hi I just learned that it is possible to make an average curvature file from a bunch of subjects, but specify the output subject as an individual brain. given that, is it possible to put average7's curvature