Re: [Freesurfer] new GPU binaries

Hi Nick, Richard, Freesurfanados and GPU fans, I've downloaded the latest _cuda binaries from the tarball you have posted, but when I try to run the recon-all on the mri_ca_register_cuda it appears: * #...@# CA Reg Mon Oct 25 10:33:15 CEST 2010 /home/neuro/proc/OutPBS_GPU/AAG_106/mri mri_ca_regi

Re: [Freesurfer] new GPU binaries

what does the freesurfer utility 'cudadetect' return when you run it? can you try rebooting your machine, then try running 'mri_em_register_cuda' (with no args) to see if it gives the same message or returns help text? if it returns help text, then that means it found a device. n. On Mon, 2010-

[Freesurfer] average p-value from an ROI

Dear all, I have a follow-up question to the previous discussion ("correction for behavioral varialbles in qdec" Tue, 04 Aug 2009. Is there an option to extract the average p-value from a ROI? After a group analysis I specified ROIs at p < 0.001 and extracted the mean cortical thickness, the peak

Re: [Freesurfer] data not Surving FDR

FDR adjusts the threshold on a case-by-case basis, so it's not surprising that you see different thresholds for different data sets. The actual threshold is set based on the search space and the amount of activation. If you have a large search space, and not very much activation, then it is goi

Re: [Freesurfer] average p-value from an ROI

You can load in the sig.mgh file instead of the ces.mgh file. Convert the sig to p with p = 10.^(-abs(sig)). It is fairly unusual to report the average p-value in an ROI, you might want to double check that this is really what you want to do. doug Agnieszka Burzynska wrote: > Dear all, > I hav

Re: [Freesurfer] mni coordinates to volume index

Yes, but you'll need to create the matrix to do it. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.ppt for more info. doug Yigal Agam wrote: > Hi, > > Is it possible in matlab to get the volume index coordinates > corresponding to

Re: [Freesurfer] average p-value from an ROI

Hi Aga, maybe you want to compute the average thickness in the roi and then the (single) p value for that? Best, Martin On Mon, 2010-10-25 at 16:21 +0200, Agnieszka Burzynska wrote: > Dear all, > I have a follow-up question to the previous discussion ("correction for > behavioral varialbles in q

[Freesurfer] Error with mri_segstats

Hi, I'm trying to use mri_segstats and get the following error: ERROR: could not open stats/aseg1.stats for writing The full command I gave was: mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- subcortgray --in mri/

Re: [Freesurfer] Error with mri_segstats

Are you in the C001 directory when you run the command? Can you send the terminal output? Ed Gronenschild wrote: > Hi, > > I'm trying to use mri_segstats and get the following error: > > ERROR: could not open stats/aseg1.stats for writing > > The full command I gave was: > > mri_segstats --seg mr

[Freesurfer] Total GM and WM volumes

Hi, In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can

[Freesurfer] How to transform the thickness per vertex to another space?

Dear FS experts, I 've question concerning the thickness per vertex. Here is what I want to do: I have a data series which entered the FS pipeline. Afterwards, I transformed the aparc+aseg file to another space. Is it somehow possible to transform the thickness per vertex to this space using t

Re: [Freesurfer] How to transform the thickness per vertex to another space?

Hi Mo, You can sample them into the volume with mri_surf2vol, then transform that volume. cheers Bruce On Tue, 26 Oct 2010, Mohammed el Morabit wrote: > > Dear FS experts, > > I 've question concerning the thickness per vertex. Here is what I want to do: > > I have a data series which entered