[Freesurfer] Post-doctoral and data analyst positions (fMRI, MEG)

Applications are invited for two postdoctoral positions and one data analyst position funded by an ERC (European Research Council) Starting Grant. The research program examines the cognitive mechanisms and neural systems by which the human brain codes the recent past and predicts the immediate

Re: [Freesurfer] Binary masks and mri_vol2vol

It is better to use mri_label2vol using the registration matrix for the functional. You can set the "fill threshold" to control the percent of a segmentation that must be present in a voxel to declare that voxel to be in that segment. I would not set this to 1 (ie, 100%) as this can lead to som

Re: [Freesurfer] read data mri_vol2surf

yes, use the FreeSurfer MRIread matlab command Oya, Hiroyuki (UI Health Care) wrote: > > Hello > > > > Is it possible to load the outputs of mri_vol2surf with matlab? > > > > Thank you. > > > > Hiroyuki > > > > ___

Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess

The FIR does not assume a shape to the HRF but fits each point within the given time window. You might not be seeing activation for several reasons. FIRs are much less efficient than gamma functions. Also, by default, the FIR analysis gives you a sig map at each time point in the FIR, so you mi

Re: [Freesurfer] selxavg3-sess question

That version of fsfast is not version 5. The version ID for fast_selxavg3 is from april 2009. doug Eyal Dechter wrote: > Hi, I'm analyzing fMRI data using freesurfer 5.0.0. I run into the > following error when running selxavg3-sess. Any suggestions? > > Thanks, > Eyal > >

Re: [Freesurfer] label2label result is scatter line in tksurfer

You used the volume registration method and that won't work for surfaces. If the original label is from a surface, then use the surface-based registration method. doug Jin Li wrote: > Hello there, > I tried mri_label2label to convert label in a subject's space into > label into fsaverage's spa

Re: [Freesurfer] Total GM and WM volumes

Freesurfers, So you can ignore this last question. I double-checked my addition and got 1046270 for the sum of all structures which is indeed more than BrainSegNotVent. Oops. Chris On Nov 3 2010, bell0...@umn.edu wrote: > > >One other thing. I did the addition of all the structures in aseg a

Re: [Freesurfer] Total GM and WM volumes

One other thing. I did the addition of all the structures in aseg and am a bit confused. Here are the numbers for one subject. BrainSeg= 1035602 BrainSegNotVent= 1034954 These two are almost identical but that is most likely due to the lack of pv correction in BrainSeg, so I think that makes se

Re: [Freesurfer] Total GM and WM volumes

I had a question about gray matter and white matter volumes in FreeSurfer version 4.5. Sorry, we have too many subjects to rerun easily through 5.0. There is no gray matter listed in aseg.stats in 4.5. The two options I see are using mris_volume or summing the aparc gray matter structures, are

Re: [Freesurfer] Talairach failure detection error

did you check the accuracy of the talairach with tkregister2 or tkmedit? If it's really bad, then you can either fix it with tkregister2, or tell recon-all to not use it. If it is accurate but being incorrectly flagged, you can tell recon-all to skip the checking. cheers Bruce On Wed, 3 Nov 2

[Freesurfer] selxavg3-sess question

Hi, I'm analyzing fMRI data using freesurfer 5.0.0. I run into the following error when running selxavg3-sess. Any suggestions? Thanks, Eyal * edech...@

Re: [Freesurfer] Talairach failure detection error

Hi Kristina, You can find the answer to your question here: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F As a new user, you might find that FAQ helpful. Allison -- On Wed, 3 Nov 2010, Rapuano, Kristina (N

Re: [Freesurfer] Total GM and WM volumes

Ah, the "white matter" volume computed from the pial-white includes the subcortical structures. Once those are subtracted, you should get the #s in the aseg.stats file. doug Ed Gronenschild wrote: > Hi Doug, > > I checked the numbers again and found the difference: > > The last occurrence in th

[Freesurfer] Talairach failure detection error

Hello there, I am fairly new to freesurfer, and received an error message that I am not sure how to handle. I was running recon-all (-autorecon1 and -autorecon2) which then quit with this error: cp transforms/talairach.auto.xfm transforms/talairach.xfm #

[Freesurfer] Binary masks and mri_vol2vol

Hi Freesurfers, I have created a binary mask of the ventricles using mri_binarize using data from aparc+aseg.mgz. I want to resample this mask into native functional space, but I want to include only functional voxels that are 100% covered by by the structural mask. Because the anatomica

Re: [Freesurfer] Total GM and WM volumes

Hi Doug, I checked the numbers again and found the difference: The last occurrence in the recon-all.log reads: Getting Cerebral WM volumes from surface lh white matter volume 251139 rh white matter volume 254730 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTo

[Freesurfer] mri_normalize -noconform flag doesn't work in FS 5.0

Dear FreeSurfers, The –noconform flag of mri_normalize doesn’t seem to work properly in the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume with an isotropic resolution of 0.7mm using recon-all –cm –autorecon1 –s as the command line. The conformation is s