[Freesurfer] Rejoindre mon réseau sur LinkedIn

LinkedIn Nikolas Borrel-Jensen souhaite se connecter à vous sur LinkedIn : -- Freesurfer, Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Nikolas Borrel-J

Re: [Freesurfer] qdec and maximum p-value

Thanks for the reply! Is it then possible in Qdec to compute the average thickness of the gray matter in the significant areas, and can the data be exported? Right now, I'm copying the data (for a single vertex) from the shell and parsing it in Matlab, which is cumbersome. Kind regards, Nikola

[Freesurfer] qdec and maximum p-value

Hi all. I'm using Qdec to compare two groups of patients, and I'm wondering why the vertex with the highest p-value in the clusters changes when the threshold is changed? When lowering the threshold, the significant area should increase, but intuitively, the vertex corresponding to the area wit

[Freesurfer] mri_nu_correct.mni segmentation fault

Hi all. I have two subjects where the mri_nu_correct.mni in the autorecon1 step is aborting: $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16617/nu0.mnc -odt floa

Re: [Freesurfer] Bad orientation/registration in the motion correction step

Hello! I have found a solution for the problem causing the bad registration. In Freesurfer 5.0, the function mri_robust_template is used for registration creating the output volume rawavg.mgz when using the autorecon1 flag. It turns out, that in Freesurfer 4.0, this step is performed by the funct

Re: [Freesurfer] Bad orientation/registration in the motion correction step

Hi again. The orientation looks correct for both volumes (001.mgz and 002.mgz). Does anyone know what is then going wrong with the registration in Freesurfer? The average volume (orig.mgz) can be seen here: http://freesurfer.nikolasborrel.com/bad_registration.tif Kind regards Nikolas Borrel

[Freesurfer] Bad orientation/registration in the motion correction step

problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step? Kind regards Nikolas Borrel-Jensen ___ Freesurfer mailing list

Re: [Freesurfer] Spikes in the inflated surface

subj1dir.tar.gz <http://freesurfer.nikolasborrel.com/subj1dir.tar.gz> in the outermost directory. On Tue, Feb 1, 2011 at 5:28 PM, Bruce Fischl wrote: > what did you call it? > > On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote: > > Thanks for the fast reply. I have upload

Re: [Freesurfer] Spikes in the inflated surface

cal defect. If you > want to, you can tar and gzip the entire subject dir and ftp it for us and > I'll take a look. > > cheers > Bruce > > > On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote: > > Hi everybody. >> >> I have done all the auto-recon steps

[Freesurfer] Spikes in the inflated surface

Hi everybody. I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions. I have uploaded some images of the surfaces and segmentations of a su