[Freesurfer] center of pial surface in world coordinates

Dear Bruce,Thanks for your quick reply. I posted this question on the Neurolens-forum as well.  I too think it is just a problem of two different coordinate system. Rick (of the Neurolens forum) mentioned that the pial surface coordinate to world coordinate system is stated in a COR.info file. Howe

Re: [Freesurfer] GLM model

It depends on what you believe about how group membership affects the change of the thickness with age. If you believe that it does not affect it, then use doss. Otherwise use dods. You will lose a dof with dods. doug On Wed, 7 Jun 2006, Antao Du wrote: I want to test the difference of cor

[Freesurfer] GLM model

I want to test the difference of cortical thickness in two groups and age is accounted for as a covariate. Should I use "different offset, same slope" or "different offset, different slope" in GLM model? Thanks, Antao ___ Freesurfer mailing list Freesur

Re: [Freesurfer] func2sph-sess target brain setting

Oh, sorry, I forgot you were doing that. Setting -trgsubject to fsaverage actually simplifies things a lot as you do not need to run the paint command (or mri_surf2surf from the last email) as everything will be on fsaverage to begin with. doug [EMAIL PROTECTED] wrote: Thanks Doug, ju

Re: [Freesurfer] tksurfer hemodynamic waveforms for group analysis

It is definitely possible to display time courses in tksurfer, but I usually load them from the cmd line with -timecourse. I don't think I've ever done it from the gui. Kevin will have to look into that error. If you'd like to try loading from the cmd line then: cd fegroup/bold/ISI1TR_BERT_E

Re: [Freesurfer] func2sph-sess target brain setting

Thanks Doug, just a quick check that I understood correctly: > > There are two issues here: > > 1. Make sure that all of your subjects have been reconstructed with > the same version of freesurfer (it looks like you have done this). Correct > 2. If you've used an "older" version of freesurfe

[Freesurfer] tksurfer hemodynamic waveforms for group analysis

Dear Fellow Freesurfers, I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer. When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the dif

Re: [Freesurfer] func2sph-sess target brain setting

There are two issues here: 1. Make sure that all of your subjects have been reconstructed with the same version of freesurfer (it looks like you have done this). 2. If you've used an "older" version of freesurfer for the recon, then render (ie, paint) your results on average7 (the default

Re: [Freesurfer] functional group results on structural data

Do you mean that you have an average subject that you want to use or that you need to make one? The talairach brain is an average. doug On Wed, 7 Jun 2006, Paymon Hosseini wrote: hi i used the following commands to create a group subjects: func2tal-sess -res 4 -analysis rk_enc2_sm5 -sf s

RE: [Freesurfer] Segmentation optimization (fwd)

As far as the orientation goes, mri_convert will assume that the spm .mat file uses an RAS geometry. You should look at the volume in tkmedit and go through each orientation to make sure that each looks correct. ie, for sag the nose should be to the right, for ax the nose should be at the top. Fo

[Freesurfer] functional group results on structural data

hi i used the following commands to create a group subjects: func2tal-sess -res 4 -analysis rk_enc2_sm5 -sf sessid -df sesspar isxavg-fe-sess -analysis rk_enc2_sm5 -sf sessid -df sesspar -group Y15ENC2_sm5_grp -space tal stxgrinder-sess -analysis rk_enc2_sm5 -all -space tal -s Y15ENC2_sm5_

[Freesurfer] func2sph-sess target brain setting

Hi, Backround: I am running a fixed effects group analysis with fsaverage (mne305) as the target brain, and merging the activations across subjects on the spherical surface. The individual functional sessions have been co-registered to the individuals' structural brain reconstruction (i.e. the reg

Re: [Freesurfer] center of pial surface in world coordinates

I think it's probably just displaying them in different coordinate systems. tksurfer displays in an RAS coordinate system in which (0,0,0) is essentially the center of the volume, whereas Neurolens is probably displaying scanner coordinates. Does it matter to you? Not sure I understand - is it

[Freesurfer] FSL output overlay

Hi,   I'm a relatively new FS user. Ive a single subject functional dataset analyzed in FSL. I ran recon-all autorecon1 ,2 and 3 on the subject's SPGR. Everything worked fine.  i ran reg-feat2anat to register my functionals to the anatomical but when i hit compare button in tkregister2 , the

Re: [Freesurfer] make_average_subject memory issues

great! I couldn't get it to crash here either, but our machines all have a lot of RAM. Bruce On Wed, 7 Jun 2006, Lars M. Rimol wrote: Hi, I just ran make_average_subjects with increased swap (from 2G to 8G) on 178 subjects and now it worked, which would seem to indicate that it may have been

[Freesurfer] make_average_subject memory issues

Hi, I just ran make_average_subjects with increased swap (from 2G to 8G) on 178 subjects and now it worked, which would seem to indicate that it may have been a memory issue? I did not crash with 3, 10 and 113 subjects with 2G swap. yours, LMR >Hmmm, I've run it on >100 subjects without trouble.

[Freesurfer] center of pial surface in world coordinates

Dear freesurfer-users,I want to plot the freesurfer surface rendering (xxx.pial) in the program Neurolens. Loading the image gives no problem and Neurolens gives a beautiful rendering. However, when loading the pial surface in tksurfer I see a difference between the two renderings. The surface in t