Re: [Freesurfer] mri_ca_register

Hi Aaron that is for longitudinal analysis. We have been trying to document this kind of thing, but there are still gaps cheers Bruce On Fri, 27 Apr 2018, Aaron Tanenbaum wrote: External Email - Use Caution Hello FreeSurfers, I am trying to find what the -l flag does for

[Freesurfer] mri_ca_register

External Email - Use Caution Hello FreeSurfers, I am trying to find what the -l flag does for the program mri_ca_register program. Does not seem to be documented anywhere but i could be mistaken. Aaron Tanenbaum ___ Freesurfer mailing lis

Re: [Freesurfer] Problems Extending the Pial Surface

Hi Saum it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be

[Freesurfer] Problems Extending the Pial Surface

External Email - Use Caution Hi guys, I'm having some trouble extending the pial surface of my bm volume. I am aware that the general procedure for extending the pial is to extend the wm first and the pial will follow. However, is it possible to extend the pial surface without aff

Re: [Freesurfer] vertex wise cortical thickness within ROIs

oh sorry, I misunderstood. Hmm, that's a bit trickier. I think if you create the label with the thickness overlaid, then the label file will contain the thickness at each vertex, but that might only work in dev in freeview. Perhaps Ruopeng can comment? cheers Bruce On Fri, 27 Apr 2018, Fujiwa

Re: [Freesurfer] vertex wise cortical thickness within ROIs

External Email - Use Caution Thank you, Bruce for your prompt reply. I used mris_anatomical_stats first but this only gave me an averaged thickness and std etc. I'd like to get absolute cortical thickness for each vertex within ROIs. I do not interested to compute vertex-wise vo

Re: [Freesurfer] vertex wise cortical thickness within ROIs

Hi Hisako you can use mris_anatomical_stats for this purpose. cheers Bruce On Fri, 27 Apr 2018, Fujiwara, Hisako wrote: External Email - Use Caution Hello FreeSurfer Developers,   I'm attempting to compute absolute cortical thickness for each vertices within anatomical R

[Freesurfer] vertex wise cortical thickness within ROIs

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute absolute cortical thickness for each vertices within anatomical ROIs using apac.annot. I have successfully output the whole brain vertex wise cortical thickness using: mris_convert -c /surf/?h.t

Re: [Freesurfer] mri_watershed error/global region of the brain empty

I think so. Or apply it with mri_convert -at On Fri, 27 Apr 2018, miracle ozzoude wrote: External Email - Use Caution Hello Bruce,  Thanks. Can I use tkregisterfv to visualize it? Best,  Paul On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl wrote: Hi Paul that

Re: [Freesurfer] mri_watershed error/global region of the brain empty

External Email - Use Caution Hello Bruce, Thanks. Can I use tkregisterfv to visualize it? Best, Paul On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl wrote: > Hi Paul > > that usually means something went wrong before the watershed. Check the > input image to make sure that it

Re: [Freesurfer] mri_watershed error/global region of the brain empty

Hi Paul that usually means something went wrong before the watershed. Check the input image to make sure that it and the talairach_with_skull.lta are ok cheers Bruce On Fri, 27 Apr 2018, miracle ozzoude wrote: External Email - Use Caution Hello FreeSurfer,  While runnin

Re: [Freesurfer] ?h.area

Yes, Anderson's truncted pyramid is used to compute the ?h.volume files as well as the volume in the aparc stats files On 4/27/18 11:25 AM, Joost Janssen wrote: Hi, what is the Winkler method to compute area? Anderson has a method to compute volume using an obliquely truncated pyra

Re: [Freesurfer] mri_compute_volume_fractions

If you want to run in 5.3, you will need a registration file, which you can generate with tkregister --mov subject/mri/norm.mgz --s subject --regheader --reg regheader.subject.dat then something like  mri_compute_volume_fractions regheader.subject.dat subject/mri/pvf On 4/26/18 5:22 PM, Sri

Re: [Freesurfer] ?h.area

External Email - Use Caution Hi, what is the Winkler method to compute area? Anderson has a method to > compute volume using an obliquely truncated pyramid > > Indeed. My bad. -joost > On 4/27/18 10:52 AM, Bruce Fischl wrote: > > Hi Joost > > I think you can do it with mris_m

[Freesurfer] mri_watershed error/global region of the brain empty

External Email - Use Caution Hello FreeSurfer, While running recon-all on a subject, i got encountered an error during the watershed step (mri_watershed). How do i fix this problem? I have attached the recon-all.log and recon-all-status.log files. Thank you Best, Paul recon-all

Re: [Freesurfer] ?h.area

what is the Winkler method to compute area? Anderson has a method to compute volume using an obliquely truncated pyramid On 4/27/18 10:52 AM, Bruce Fischl wrote: Hi Joost I think you can do it with mris_make_surfaces by setting the number of iterations to 0 (-n 0) so it doesn't do any deform

Re: [Freesurfer] ?h.area

Hi Joost I think you can do it with mris_make_surfaces by setting the number of iterations to 0 (-n 0) so it doesn't do any deformation, and starting with the surface you want to end with (e.g. -orig_white white) cheers Bruce On Fri, 27 Apr 2018, Joost Janssen wrote: External Em

[Freesurfer] ?h.area

External Email - Use Caution Hi, Short: Is it possible to generate v6.-style ?h.area based on v5.1-recon output? If so, how? Long: I have 5.1 processed data and would like to re-generate ?h.area v6-style (Winkler et al. 2018). I would like to avoid complete rerunning through v6.