Re: [Freesurfer] tksurfer

Hi Emalie tksurfer and tkmedit have been deprecated for a long time. Can you try using freeview instead? cheers Bruce On Fri, 21 Feb 2020, Emalie McMahon wrote: External Email - Use Caution Hello,  I get an error (see below) when opening tksurfer and tkmedit. Is there

[Freesurfer] tksurfer

External Email - Use Caution Hello, I get an error (see below) when opening tksurfer and tkmedit. Is there anyway to resolve this? tksurfer s001 lh inflated /Applications/freesurfer/tktools/tksurfer.bin: Bad CPU type in executable. Freesurfer Details:

[Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary

External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the cerebellum of the marmoset, based on ultra-high (80um) resolution ex-vivo images. I manually segment the cerebellum into the white matter and the gray

[Freesurfer] Optseq2 help needed

External Email - Use Caution Dear Developers, I am planning to run PVT (psychomotor vigilance task) in fMRI using event related design. This is an extremely simple reaction time task: participant has to respond to the appeared geometric shape as quickly as possible. The key

[Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] surfreg function

External Email - Use Caution Hi Doug, Thank you for your replay. I understood that if I did not specify "--surfreg my_avg_subject.sphere.reg" mri_preproc was going to use the original file ( sphere.reg), because in the help of mri_preproc it mentions this: --surfreg SurfReg :

Re: [Freesurfer] Question regarding Qdec vs mri_glmfit

External Email - Use Caution Hi,Douglas, Thanks for your reply! I have changed the classes and the contrast as your suggestion. But I still met some problem when viewed the results. I still met the problem when I loaded the sig.mgh file into freeview or qdec. I

Re: [Freesurfer] Question regarding Qdec vs mri_glmfit

External Email - Use Caution Hi,Douglas, Thanks for your reply! I have changed the classes and the contrast as your suggestion. But I still met some problem when viewed the results. I still met the problem when I loaded the sig.mgh file into freeview or qdec. I still

Re: [Freesurfer] Error in long_mris_slopes

Hi Guillaume, not sure what is going on. It could be missing permissions or it could be that the disk is full? You could also try to drop the --do-label and see if that works. Best, Martin On Fri, 2020-02-14 at 10:12 +0100, Guillaume Carey wrote: > > Hello everyone, > I’m currently

Re: [Freesurfer] questions about batch running longitudinal data using long_submit_jobs on cluste

Hi, looks like someone changed the default python to version 3, and you are still using a script written for python 2. I think Andrew updated this recently, so obtaining a newer version of the long_submit_jobs script from dev may fix this. Best, Martin On Tue, 2020-02-11 at 18:03 +,

Re: [Freesurfer] some basic questions regarding longitudinal analyses in Freesurfer

Hi Lara, no, you should not use time point 1 as base. You need to distinguish between the image processing part and the statistics post processing analysis (LME). These are two separate things. For the image processing in the longitudinal pipeline, we create the base (=subject template). The

[Freesurfer] GLM DOSS questions

External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients,