Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 I think the info was at the end of the original email, as per instructions. I'm guessing it was just hidden, but let me kno

Re: [Freesurfer] Freesurfer Digest, Vol 137, Issue 13

Hi Sandro yes, you will find some dependence. Much as we would like it to be otherwise when you change resolution you change a bunch of other things typically (min TE, bandwidth, big SNR changes) that will cause changes in our measured volumes cheers Bruce On Sat, 11 Jul 2015, Sandro Marin

Re: [Freesurfer] Freesurfer Digest, Vol 137, Issue 13

Hi Bruce, Thanks for your help. Yes, I would like to run recon-all on each one separately and then use all the output data irrespective of the original MRI voxel size. In other words, do the output values (i.e white matter volume) depend on the voxel size of the original MRI? Best, Sandro Message

Re: [Freesurfer] Regarding: Brainstem substructures

​Thanks so much Bruce for ​your reply. when I open the link for brain stem structures (https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures), it says "*This functionality is present in FreeSurfer 6.0 and later*" . And, when I go to

Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

I think the info was at the end of the email, as per instructions. Is there any other info you need? Thanks! Ione FREESURFER_HOME: /usr/local/freesurfer/stable5_3 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: 7.6 Kernel info: Linux 3.2.0-4-amd64 x86_64 -O

Re: [Freesurfer] voxel of different size

Hi Sandro can you clarify what you mean? Do you want to run recon-all on each one separately? That would be fine. Or do you mean somehow average all the different res volumes into a single recon? cheers Bruce On Sat, 11 Jul 2015, Sandro Marini wrote: Dear FreeSurfer experts, we have col

Re: [Freesurfer] Load a .label as a mask in tksurfer

Hi Kai try the mask_label command from the tcl prompt. cheers Bruce On Sat, 11 Jul 2015, LiuKai wrote: Dear experts, Is there a way in tksurfer which could enable us to load a surface mask (e.g., lh.cortex.label) to confine the visualization of annotation files within certain cortical regio

Re: [Freesurfer] mri_tessellate: max vertices 1000000 exceeded

Hi Iona if you tell us what your hardware/software environment is we'll get you a newer version. cheers Bruce On Sat, 11 Jul 2015, Ione Fine wrote: Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentat

Re: [Freesurfer] Regarding: Brainstem substructures

Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: > Dear freesurfer experts, > > I am trying to do the brainstem volumetric analy

[Freesurfer] voxel of different size

Dear FreeSurfer experts, we have collected some data with different voxel size (from 0.78 to 0.94 mm iso). I would like to do an analysis of all these scans. Is it possible ? Should I use -cw256 option to make the sample uniform? Many thanks Best, Sandro __

[Freesurfer] mri_tessellate: max vertices 1000000 exceeded

Lovely experts, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following command: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There's apparen

[Freesurfer] Load a .label as a mask in tksurfer

Dear experts,Is there a way in tksurfer which could enable us to load a surface mask (e.g., lh.cortex.label) to confine the visualization of annotation files within certain cortical region? For example, now I want to confine the visualization of brain surface values within cortex (with corpus ca

[Freesurfer] mri_tessellate: max vertices 1000000 exceeded

Hi, I am running to an error analyzing a 0.5 mm resolution T1 structural with the following with the following: recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT the issue seems to be: mri_tessellate: max vertices 100 exceeded There's apparently a version of mri_tessela