[Freesurfer] annotations & functional activation

Hi Freesurfers, I have functional activation files (.mgh) which I can overlay onto a subject's surface. Now I am trying to do a functional ROI analysis based on the annotation files, e.g. to get information about the mean activation in a specific area based on FS segmentations. Does anybody h

Re: [Freesurfer] annotations & functional activation

. Does anyone have a suggestion what the problem may be? Thanks a lot. Sandy Doug Greve <[EMAIL PROTECTED]> wrote: You can map the segmentations (aseg or aparc+aseg) to the functional space with mri_label2vol, then run mri_segstats passing it the func space aseg and your inp

[Freesurfer] aseg2feat

Hi Doug & others, It seems that aseg2feat takes lower level .feat directories to get stats on annotations. It does not seem to work for higher level g.feat directories. Is there a way around it? cheers, Sandy - Don't be flakey. Get Yahoo! Mail for Mobile and

[Freesurfer] fMRI stats on the surface

Hi Doug & Ohers, I see that there are nice interfaces between Feat and Freesurfer for rendering Feat output onto the surface. Now for group fMRI stats it would obviously be advantageous to do all the stats directly on the surface, avoiding volume space altogether. Especially clsuter thresholdin

Re: [Freesurfer] fMRI stats on the surface

Thank you very much! I assume that when doing the first-level analysis with Feat and then project onto the surface, one shouldn't smooth so much in 3D volume space, right? How much smoothing should be used? Thanks a lot, Christine Bruce Fischl <[EMAIL PROTECTED]> wrote: Hi Chr

[Freesurfer] reg-feat2anat regsitration problems

Hi Doug & others, I am trying to use reg-feat2anat as it is described on the FSL web page: http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html However, I always seem t get a very bad registration. I tried using different values for --maxangle --cost mutualinfo --bins, but maintained

[Freesurfer] FS & group feat

Hi, I have a 3 level feat analysis with 2 runs in each subject on the first level. At the second level these two get combined with a fixed effect analysis to produce a mean for each subject. At the third level, the second level results are combined with FLAME to produce group maps. I was able

[Freesurfer] nu_correct error

Hi, I am trying to run an MPRRAGE scan through the first step of autorecon-all, but get the following error message: Iteration 1 Thu Feb 21 14:57:06 PST 2008 nu_correct -clobber ./tmp.mri_nu_correct.mni.28541/nu0.mnc ./tmp.mri_nu_correct.mni.28541/nu1.mnc spawn: exec of nu_estim

[Freesurfer] Workstation Spec

I am about to purchase a workstation which will be used to run Freesurfer. Can you tell me the recommended specification for suitable hardware and OS. Many thanks Mary Fitzsimons Epilepsy Programme Beaumont Hospital Dublin

[Freesurfer] tklib8.3.so

hi-- i've recently installed the February 18th 2004 (561M) snapshot on my linux. when trying to run any process requiring graphical display of surfaces/volumes, i get the following error: "/usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libtk8.3.so: cannot open s

[Freesurfer] inflated and pial node mismatch

I wasn't able to run the afni programs 3dVol2Surf or MapIcosahedron on the Freesurfer surfaces since the number of nodes in the smoothwm vs pial surfaces differed: ** invalid surfaces, different # nodes (166167,166157) How can we best resolve this difference in the node numbers? thanks, -Ron

[Freesurfer] flattening

Hi We are trying to create flattened surfaces for doing surface based statistical analysis of ventral temporal cortex, but the flattening method described in the freesurfer manual creates cuts right through this region. It would be better for us if we had a contiguous region of VT cortex to ana