Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

2019-01-30 Thread Glasser, Matthew
External Email - Use Caution IsnĀ¹t this what GIFTI is for? PALM and FreeSurfer can use GIFTI. Matt. On 1/30/19, 9:17 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: >Hi Dan > >sorry, I'm not really sure what you are asking. Doug implemented a

Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

2019-01-30 Thread Bruce Fischl
Hi Dan sorry, I'm not really sure what you are asking. Doug implemented a work-around for nifti in which it breaks up the number of vertices into multiple dimensions (to get around the 16-bit dimensions in nifti, which was a crazy design decision). freeview detects this and displays them

Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

2019-01-30 Thread Daniel Leopold
External Email - Use Caution Hi Bruce, Chris Rorden informed me that Surfice previously assumed that MGZ/MGH files were voxelwise images used to surface-paint a mesh. Anderson's palm, however, uses the format as a one-to-one correspondence with the vertices (i.e.,

Re: [Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

2019-01-24 Thread Bruce Fischl
Hi Daniel I don't think we can help you with why Surf Ice is failing (at least I can't). What are the features that freeview doesn't have? I'll leave question 2 for Doug cheers Bruce On Wed, 23 Jan 2019, Daniel Leopold wrote: External Email - Use Caution Hello FS experts

[Freesurfer] Smoothing before or after PALM (and results conversion for Surf Ice)

2019-01-23 Thread Daniel Leopold
External Email - Use Caution Hello FS experts and enthusiasts, Thus far, I have used mri_concat to make 4D files of subjects' lh.thickness.fwhm15.fsaverage.mgh files to be used as input for palm. The results maps are of the .mgz format. I can convert these to .nii using