Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates

Hi Doug, Thank you for your reply. I computed the tkRAS coordinates using the formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS coordinates are normal since in label files obtained by saving ROI upon a certain threshol

Re: [Freesurfer] Extract coordinates from .mgh file

Hi I would like to extract cooridantes of "aparc.a2009s+aseg.mgz" file. This file is stored in the mri folder. Would you please help me in this regards? kind regards Mamun On Thu, Jul 27, 2017 at 9:36 AM, Redwan Maatoug wrote: > Hi Doug, > > Thank you for your reply, > I have used the tool *sur

Re: [Freesurfer] Pial surface missing GM

Hi Jake usually that means that there is a topology defect that is being incorrectly fixed. If you upload the subject and point us at the voxel coords we will take a look cheers Bruce On Wed, 26 Jul 2017, Jake Rieke wrote: > Hello surfers, > > I'm attempting to extend white and pial surfaces

Re: [Freesurfer] Extract coordinates from .mgh file

Hi Doug, Thank you for your reply, I have used the tool *surf_cluster* to have the MNI coordinates. Is it a good alternative to *mri_cor2label *? Thank you very much, Regards, Redwan On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve wrote: > mri_cor2label with extract the coordinates into a lab

Re: [Freesurfer] Extract coordinates from .mgh file

mri_cor2label with extract the coordinates into a label file. The coordinates will be in "tkregisterRAS". What coordinate system do you want? See See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 07/25/2017 07:32 PM, Redwan Maatoug wrote: > Hi experts, > > I just want to know

Re: [Freesurfer] error with fcseed-config & fcseed-sess

By default, you are using aparc+aseg.mgz as the ROI atlas, so use 1021 or 2021 for V1. 1021ctx-lh-pericalcarine120 100 60 0 On 07/26/2017 12:37 PM, Jessica Huang wrote: > > Hi freesurfer experts, > > > I’m using the fcseed-config and fcseed-sess commands to create a seed >

[Freesurfer] rh.white and rh.pial surface edit_Orbito-frontal Cort

Hello, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sharing Best, Farhad ___

Re: [Freesurfer] MNI coordinates

It is exactly what I want, Thank you for your responsiveness and for your help, Redwan On Wed, Jul 26, 2017 at 12:14 PM, Douglas N Greve wrote: > If you run it with --nofixmni, it will report MNI305 coords. Is that > what you want? > > > On 07/26/2017 03:11 PM, Redwan Maatoug wrote: > > Hi all

Re: [Freesurfer] MNI coordinates

If you run it with --nofixmni, it will report MNI305 coords. Is that what you want? On 07/26/2017 03:11 PM, Redwan Maatoug wrote: > Hi all, > > My goal is to extract the coordinates from a .mgh ROI surface file. > > I have used this tool : > mri_surfcluster with > > But the coordinates are in Ta

[Freesurfer] MNI coordinates

Hi all, My goal is to extract the coordinates from a .mgh ROI surface file. I have used this tool : mri_surfcluster with But the coordinates are in Tailarch and I would like the *MNI coordinates*. Someone has an idea ? Thank you, Redwan ___ Freesurfer

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

finding coordinates is the same problem as putting the results into the same space (except probably harder). There is not a simple formula for converting one to the other. Eg, fsaverage uses MNI305 space. What is SPM using? You have to figure out all these things to convert On 07/26/2017 04:10

[Freesurfer] error with fcseed-config & fcseed-sess

Hi freesurfer experts, I’m using the fcseed-config and fcseed-sess commands to create a seed at V1 in accordance with the FsFastFunctionalConnectivity Walkthrough Steps: *STEP 4: Use fcseed-config to configure the

Re: [Freesurfer] Clarification for aseg edits in longitudinal phase

Hi Tamara, this should finish the longitudinal recon-all. It picks it up from where you edited and completes the rest. It needs to know about the name of the time point and the name of the base to access files from there (e.g. to map initial surfaces from base ect). Best, Martin On 07/24

Re: [Freesurfer] help with finding exact and detailed coordinates of brain areas

Oh, sure you are right. But each analysis is done on different protocols, and also, for now I already have many of analysis results that has been run on the SPM and on Freesurfer, and has a difference in coordinates. So- for now, what is the right way to treat that? the link that you gave up here?