Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Vinny K
External Email - Use Caution Actually, I was able to match the boundaries with the referenced publication. So it's all good, thanks again for your help! Vinny On Mon, Sep 10, 2018 at 6:55 PM Vinny K wrote: > Hi Eugenio, > > Thank you for your reply. Somehow the display from m

Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Vinny K
External Email - Use Caution Hi Eugenio, Thank you for your reply. Somehow the display from my thalamic segmentation does not capture the colors in your publication and furthermore, the nuclei are not clearly delineated from each other visually since one color may encompass two o

Re: [Freesurfer] Head circumference of fsaverage?

2018-09-10 Thread Bruce Fischl
Hi Gladia fsaverage isn't a single subject - it is an average of 40 (and we don't have heard circumference information on them) cheers Bruce On Mon, 10 Sep 2018, Gladia Hotan wrote: External Email - Use Caution Hi, What is the head circumference of the fsaverage subject?

Re: [Freesurfer] Head circumference of fsaverage?

2018-09-10 Thread Douglas N. Greve
fsaverage is an average of 40 subjects, so it does not have a circumference per se. Why do you need it? On 09/10/2018 04:31 PM, Gladia Hotan wrote: > > External Email - Use Caution > > Hi, > > What is the head circumference of the fsaverage subject? > > Thanks and Best, > Gladia > > > ___

[Freesurfer] Head circumference of fsaverage?

2018-09-10 Thread Gladia Hotan
External Email - Use Caution Hi, What is the head circumference of the fsaverage subject? Thanks and Best, Gladia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Hi Vinny, The anatomical definitions can be found in the paper, which is open access (see Table 2): https://www.sciencedirect.com/science/article/pii/S1053811918307109 Kind regards Eugenio Sent from my phone, please excuse brevity and typos Fr

Re: [Freesurfer] amygdala segmentation using additional scan error

2018-09-10 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Hi Jinyoung Sorry for the slow response but I'm traveling these days I believe this is a bug that was fixed in the dev version 2-3 weeks ago. Would you mind trying the latest dev, and checking whether that solves the problem? Cheers Eugenio Sent from

Re: [Freesurfer] Using the new Thalamus tool

2018-09-10 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Dear Erik, Installing only the thalamic tool is technically possible but requires a level of hacking that i don't want to encourage or support ;-) Please install the new dev on a separate directory, and make FREESURFER_HOME point to that the directory

Re: [Freesurfer] Seeing the Results in the Original Space

2018-09-10 Thread Douglas Greve
check out this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 9/9/18 11:18 AM, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer Experts, How can i have the results of FreeSurfer in its original space? The results have rotation and also the a

Re: [Freesurfer] thalamic segmentation

2018-09-10 Thread Vinny K
External Email - Use Caution Hi, I ran recon-all to generate the required files for the thalamic segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the latest development version of Freesurfer (06/09/2018) linux-cent06. The segmented thalamic nuclei were visual