Re: [Freesurfer] Using a2009s.annot as seed masks for tractography

Hi Lee, Thanks for your reply. I have repeated this step in /Applications/freesurfer/subjects/HC001/mri using the following command: mri_label2vol --seg left_thalamus.nii.gz --temp b0_brain.nii.gz --reg registration2b0.dat --o left_thalamus_dwi_seed.nii.gz And got this output: Number of

[Freesurfer] labelling

Dear freesurfer experts, I intend to create ROIs from the aparc+seg.mgz file and would like to ask whether the following assignments are correct (sorry for the long list): 10: left_thalamus 11: left_caudate 12: left_putamen 13: left_pallidum 17: left_hippocampus 18: left_amygdala 26:

Re: [Freesurfer] crossing medial surfaces

Dear Bruce, thanks for the reply. I often have the case that the aseg.mgz is already correct, however the surfaces cross because the aparc+aseg.mgz incorrectly classified the hemispheres. If running autorecon2-cp uses the aseg.mgz, which is already correct, would that make any changes to the

Re: [Freesurfer] labelling

Hi Andre they look right, but check the FreeSurferColorLUT.txt file - that is the definitive location cheers Bruce On Fri, 24 Apr 2015, André Schmidt wrote: Dear freesurfer experts, I intend to create ROIs from the aparc+seg.mgz file and would like to ask whether the following assignments

Re: [Freesurfer] crossing medial surfaces

no, I don't think it would. If you upload a case with crossing surfaces I'll take a look cheers Bruce On Fri, 24 Apr 2015, Clara Kuehn wrote: Dear Bruce, thanks for the reply. I often have the case that the aseg.mgz is already correct, however the surfaces cross because the aparc+aseg.mgz

Re: [Freesurfer] Fwd: Problem with Freesurfer 5.3

Hi Cecilio this means that the automatic checking determined that the Talairach transform to be very unlikely and probably a failure. What was your input data? If you bring it up in tkmedit or freeview do the directions on the screen correspond to true anatomical ones (e.g. is A really

Re: [Freesurfer] Viewing gfeat results on inflated brain

If you're just doing a one-sample group mean, then use --osgm instead of --X and --C doug On 4/23/15 7:47 PM, ghazal.ki...@alumni.ubc.ca wrote: Hi, We are working on the analysis step of a project, in which we are interested in the brain activation pattern in response to five different body

[Freesurfer] Fwd: Problem with Freesurfer 5.3

Hi! My name is Cecilio! I'm using the freesurfer 5.3 and I'm having some issues that I hope you could help me with. When I perform: recon-all -s patienttesta -all I get this error: recon-all -s patienttesta exited with ERRORS ERROR: talairach_afd: Talairach Transform:

Re: [Freesurfer] Visualising surfaces at different fractional depths

Thank you - right as you sent your reply I was writing an apology because I'd just seen that flag. It's Friday evening here in the UK and it might be time to stop sending emails for a little while! So sorry! And thank you! Kx On 24 April 2015 at 18:33, Bruce Fischl fis...@nmr.mgh.harvard.edu

Re: [Freesurfer] Visualising surfaces at different fractional depths

no worries. I hope it works for you Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you - right as you sent your reply I was writing an apology because I'd just seen that flag. It's Friday evening here in the UK and it might be time to stop sending emails for a little while! So

Re: [Freesurfer] advice/question regarding your LME toolbox for freesurfer

Dear Jorge, Just wondering if you had any thoughts on the below? Particularly point 1 - that is, how to assess whether linear or quadratic time effects fit the data better? Thanks, Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Visualising surfaces at different fractional depths

Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which the vertex lands that is assigned to the vertex or is there any interpolation across multiple voxels before assigning the vertex a value? Thanks

Re: [Freesurfer] Visualising surfaces at different fractional depths

Hi Kirstie I think you get to decide how you want the sampling done in mri_vol2surf. cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: Thank you Bruce - that's excellent and works perfectly. Can I ask - when I sample from the new surface from a volume is it the voxel value in which

Re: [Freesurfer] Visualising surfaces at different fractional depths

I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and I've read the --help output and this page: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf The help is very clear about which surface the volume is being sampled to etc, but I can't see

Re: [Freesurfer] Visualising surfaces at different fractional depths

Hi Kirstie you can pick the interpolation method with --interp string where string is one of: nearest trilinear sinc cubic cheers Bruce On Fri, 24 Apr 2015, Kirstie Whitaker wrote: I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send. I'm using mri_vol2surf and

[Freesurfer] TRACULA: distance between tract sections in pathstats.byvoxel.txt

Hi Anastasia and Tracula experts I did analyses with Tracula using the very nice feature that allows to perform the statistics along the tracts. I reported the result as function of location along the tracts expressed as voxel index, meaning that the first section was voxel index 1, the 2nd tract

Re: [Freesurfer] Reconall not properly parcellating brain

Yes, attached is a screenshot of talairach.xfm. It does look brighter in the same region that was excluded in the white/pial matter. Could this be the problem, and what do you suggest I do? Thanks!! ___ Freesurfer mailing list