[Freesurfer] Cortical thickness in average space

Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each su

[Freesurfer] Fwd: Cortical thickness in average space

ta to get the cortical thickness values at each vertex of every subject? Rafa & Gabi 2013/3/26 Bruce Fischl : > Hi Rafa and Gabi > > yes, that's pretty much what the -qcache flag does in recon-all. Or you can > use mri_surf2surf to do it. > > cheers > Bruce > > O

[Freesurfer] CT as covariate

Dear Freesurfers I will introduce the mean cortial thickness as covariate into my statistical model, but I'm wonderind which way will be the best. To get the cortical thickness in individual space, or in AVG space? Thank you all in advanced, Rafa. __

[Freesurfer] recon-all error

Dear freesurfer experts, I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1 #@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g mri_segstats --seg mri/aseg.mgz --sum

Re: [Freesurfer] recon-all error

some files from it > (e.g. no mri/transforms/talairach.xfm). Don't email it to me - use our ftp > site > > > cheers > Bruce > On Tue, 4 Jun 2013, Rafa X wrote: > > Hi Bruce,Thanks for your reply. I have attached the zipped subject dir >> (please, note that I had

[Freesurfer] Vermis of cerebellum segmentation

Hi Freesurfers, There is avaliable a cerebelum mask in "http://surfer.nmr.mgh.harvard.edu/fswiki/CerebellumParcellation_Buckner2011"; however the corregistration from MNI152 space to subject space produces a few deformation that introduce an error in the fit of the mask into the real vermis of the

[Freesurfer] Work with MRI and PET simultaneously

Hello FS team, I would like to know if it's possible to load a PET image in tkmedit and tksurfer, and overall I need to know if I can coregistrer a PET image with a MRI (of the same patient). I have the tags of the cortical segmentation generated by recon2 based on the MRI and I want to work with t

[Freesurfer] bbregister: PET and MRI

Dear FS Team, I have a problem with the bbregister command. I used it for coregister a MRI with a PET. My first step is set the same origin and orientation for both images (approximately) (I use SPM or tkregister2). After, I write in the terminal "bbregister --mov s24PET.img --t1 --s sr24 --init-f

[Freesurfer] Scale factor

Dear FS team, I'm writing matlab code to obtain smaller parcellated regions of equal size starting from the freesurfer parcellation performed on the average subject. Should I apply a scale factor If I wanted to use the areas stored in ?h.white.avg.area.mgh for the new parcellation? My Freesurfer r

Re: [Freesurfer] Scale factor

bem dir to try, to give you different > number of faces. > > Nick > > > On Thu, 2009-02-26 at 11:39 +0100, Rafa x wrote: >> Dear FS team, >> >> I'm writing matlab code to obtain smaller parcellated regions of equal >> size starting from the freesurfer

[Freesurfer] ¿write_annotation?

Dear FS team, I used read_annotation(lh.aparca.annot) for obtaining [vertexs, label, colortable]. After that, I have modified these variables and would like to write a new annotation file. Is there the function "write_annotation" (or something similar)? Thanks in advance. Best, Rafa

[Freesurfer] mris_anatomical_stats with an average subject

Dear FS team I would like to execute the command mris_anatomical_stats with one average subject, the problem is that the file wm.mgz is required. Is there some way to obtain the stats of one average subject?(I need the area of all the parcellations) Thank you in advance Rafa. _

[Freesurfer] Talairach coordinates

Dear Freesurfer team, I used the lh.inflated file in an average subject to obtain its vertex’s coordinates. My question is: What anatomical space or reference system was use in this file? or instead, How I could obtain the Talairach coordinates of each vertex? Thank you in advance, Rafa. _

[Freesurfer] reading PET in Matlab

Dear Freesurfers, I’m trying to obtain in matlab the PET value of each vertex of the cortex from one freesurfer subject. To calculate it, first I do the coregister with: bbregister -–mov PETimage.nii –-t2 –-s subjectName –-init-fsl –-reg register.dat I have checked the result and it is provides p

[Freesurfer] mri_glmfit error

Dear Freesurfers, In Freesurfer v5.0 when I try to run the command: mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1 --sim-sign pos --seed 6555731749 I always get the

Re: [Freesurfer] mri_glmfit error

I would strongly recommend it as that will make sure that > all the arguments are correct. > > doug > > Rafa x wrote: >> >> Dear Freesurfers, >> In Freesurfer v5.0 when I try to run the command: >> >> mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast