[Freesurfer] funcroi-table-sess: average baseline activity?

Hi all, I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I've posted two questions (Q1 Q2 below) in my previous email regarding ROI analysis, and I'd like to add one more (Q3). Q1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with

[Freesurfer] fsaverage triangle mesh data

Dear all I am interested doing some visualization of my cortical FreeSurfer results in other software. In order to do so I need to some information about how the cortical surface is defined. Usually these surfaces consists of a set of 3D coordinates which gives the position of the vertices

Re: [Freesurfer] fsaverage triangle mesh data

Hi Ørjan, yes, you can either use our matlab functions for reading surfaces, or use mris_convert with an output surface with an extension .asc to create an ascii file. cheers Bruce On Mon, 6 Dec 2010, [UTF-8] Ørjan Bergmann wrote: Dear all I am interested doing some visualization of

Re: [Freesurfer] fsaverage triangle mesh data

take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile:

Re: [Freesurfer] fsaverage triangle mesh data

Dear Ørjan, With SUMA you can convert freesurfer's anatomically correct images to .ply format. Uri 2010/12/6 Ørjan Bergmann orjan.bergm...@medisin.uio.no: Dear all I am interested doing some visualization of my cortical FreeSurfer results in other software. In order to do so I need to

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Hi Yuko, answers below Yuko Yotsumoto wrote: Hi all, I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 I've posted two questions (Q1 Q2 below) in my previous email regarding ROI analysis, and I'd like to add one more (Q3). Q1) If I don't want to use any thresholding for ROI

Re: [Freesurfer] mri_convert batch conversion of ima files

There's no easy way to do it. You can convert to a volume and then use the --slice-crop option in mri_convert to extract out individual slices. doug Lisa F. Akiyama wrote: Hello, I have a large number of slice files in ima format. I would like to convert each of these ima files into either

Re: [Freesurfer] recon-all

Have you looked at the filled.mgz volume to make sure that cerebellum is not attached? doug Yang Liu wrote: Hi, I am processing the anatomical monkey brain now. When recon-all runs, it stops at the step of mris_fix_topology I inserted the last part of my recon-all.log below: It stops at

[Freesurfer] Using mri_segstats

Hi, I have two questions about using mri_segstats. First, I notice that on the individual dti tutorial, you don't use the --pvol option to correct for partial voluming. Is there a reason for this? Second, would there be any disadvantage to using mri_segstats with aparc+aseg.mgz to get volume/

Re: [Freesurfer] Using mri_segstats

Hi Tyler, by mapping the DTI to the anatomical space, you will automatically account for partial voluming in the DTI space. The partial volume correction in mri_segstats is for correcting within the 1mm3 anatomical voxel, which seemed excessive given the large DTI voxel sizes (but maybe it's

Re: [Freesurfer] recon-all

Hi Doug, Thanks for replying! I checked the filled.mgz. The cerebellum is still attached. How can I fix the problem? I am a new user of Freesurfer. My guess is to select the correct pons cutting plane. But I found that the instruction on

Re: [Freesurfer] recon-all

Yes, fix the pons cutting plane. I've modified the text in that link to be clearer. Let me know if you still have trouble. doug Yang Liu wrote: Hi Doug, Thanks for replying! I checked the filled.mgz. The cerebellum is still attached. How can I fix the problem? I am a new user of

Re: [Freesurfer] mri_convert batch conversion of ima files

Hi Doug, Alright. I'll try doing that. Thanks for the information. Best, Lisa __ Lisa F. Akiyama Research Study Assistant Institute for Learning Brain Sciences (I-LABS) University of Washington Portage Bay Building, BOX 357988 Seattle, WA 98195-7988 U.S.A. E-mail:

[Freesurfer] RAW files

Hi FSL and FreeSurfer folk: Does anyone know how to convert *.raw files to analyze, nifti or mgz format? thanks much, Alan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] RAW files

I've never seen a .raw format. Where does it come from? I don't think mri_convert will handle it, but you can just try something like mri_convert your.raw your.nii (or your.mgz). doug Alan Francis wrote: Hi FSL and FreeSurfer folk: Does anyone know how to convert *.raw files to analyze,

[Freesurfer] recon-all -make all error?

Hello, I am reprocessing a number of subjects from fs 4.5.0 to fs 5.0.0. I am doing this by issuing the recon-all -make all -s subject command. It stops right away with the message: make: Nothing to be done for `all'. There exists the wmparc.stats file from the fs450 recon, but there is no

Re: [Freesurfer] funcroi-table-sess: average baseline activity?

Thanks Doug, On Dec 7, 2010, at 12:02 AM, Douglas N Greve wrote: I'm using: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Q1) If I don't want to use any thresholding for ROI analysis, can I use -sign abs -thresh 0 with funcroi-config? Even easier: just don't specify a contrast.

[Freesurfer] vertex wise ICC

Hello freesurfer experts, I am keen on generating vertexwise intra-class correlation maps for a group of subjects with paired measurements - similar to that in Wonderlick et al in Neuroimage 2009. Reliability of MRI-derived cortical and subcortical morphometric measures: Effects of pulse