[Freesurfer] mri_label2label holes

Dear Doug et al I was doing some cross-subject label morphing over a bunch of subjects (a big continuous patch of vertices) and was having problems with quite a number of 'missing' vertices in the morphed label. I saw Doug's previous response to this  on the message board that there was a dev

Re: [Freesurfer] Labels to MNI152, SPM compatible

Hi, I was using Mango and MriCron to view the results. But you are right that in freeview it looks just fine :) I saved the yeo atlas image as nifti and it is now looking well also on mango and MRIcroN. So I suppose that the problem was with analyze format. Thank you all for the help :) Mat

Re: [Freesurfer] mri_label2label holes

Hi Fred, I think there are problems with trying to use v6 binaries without the v6 distribution. Zeke may have more of an idea. doug On 8/4/16 4:32 AM, Fred Dick wrote: Dear Doug et al I was doing some cross-subject label morphing over a bunch of subjects (a big continuous patch of vertices)

Re: [Freesurfer] mri_label2label holes

Note that this is a development version and should not be used to run recon-all On 8/4/16 9:02 AM, zkauf...@nmr.mgh.harvard.edu wrote: > Hello Fred, > > Yes, newer development binaries on Mac are not compatible with previous > releases of freesurfer. If you wish the use a newer binary you will n

Re: [Freesurfer] mri_label2label holes

Hello Fred, Yes, newer development binaries on Mac are not compatible with previous releases of freesurfer. If you wish the use a newer binary you will need to use the latest developmemnt version of freesurfer. This can be downloaded from the following page (see "Development Version"): https://

Re: [Freesurfer] mri_label2label holes

Hi Fred what version are you running? I think we fixed this bug a long time ago. cheers Bruce On Thu, 4 Aug 2016, Fred Dick wrote: Dear Doug et al I was doing some cross-subject label morphing over a bunch of subjects (a big continuous patch of vertices) and was having problems with quite a

Re: [Freesurfer] mri_label2label holes

it might be fixed in 5.3, no? What version are you using Fred? On Thu, 4 Aug 2016, Douglas Greve wrote: Hi Fred, I think there are problems with trying to use v6 binaries without the v6 distribution. Zeke may have more of an idea. doug On 8/4/16 4:32 AM, Fred Dick wrote: Dear Doug et

Re: [Freesurfer] Labels to MNI152, SPM compatible

One possibility is the header information. I looked at the header information and they are not exactly the same between the template and atlas. Perhaps you can try the following: >> mri_convert --targ Template_T1_IXI555_MNI152.nii --mov >> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalM

Re: [Freesurfer] Poor automatic segmentation of the cerebellum

Hi Sam usually this means that the cerebellum is too far from isocenter and hence has low SNR/more distortion. If you can place your subjects higher in the scanner that might help. For existing data try putting some control points in cerebellar wm or brainstem. That might help cheers Bruce

Re: [Freesurfer] Flattening the surface

Hi Bruce, Thanks to your advice, I was able to generate a mgh file using mri_vol2surf, and thus map the texture onto both the inflated and the flattened surfaces. I wonder whether it is possible to reversely map the vertices on the vectorized surface (such as, ‘lh.orig’ or ‘lh.inflate') back to t

[Freesurfer] Problems with QDEC

Dear Freesurfers, Sorry if the question sounds too basic. 1. I am running an analysis on qdec with paired groups - normal and patients, To control for IntraCranialVolume(ICV),I am adding it as an 'nuisance factor',Is it correct? The suggested mode to add ICV to the tabled was to *demean* the ICV.