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 mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd like to use another viewing package for the palm results (i.e., Surf Ice) because of its features and some quirks I've encountered while loading results in Freeview. Surf Ice accepts a number of formats ( https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_For...), including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among *many* others), but I have yet to successfully convert these .mgz maps to a readable format. Surf Ice can read .nii, but loading my mri_converted .nii files results in a uniform surface with 0 at all vertices. Thus, I have two questions:
1) Can you think of a means to convert these surface "volumes" (.mgh/.mgz) to a desired format that can be read by Surf Ice? I've attempted mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an appropriate format/get things to work. In case it's helpful, readable formats are:
2) My alternative idea would be to instead use mri_concat on subjects' lh.thickness files and later apply fwhm smoothing. Would this approach be feasible? I could test whether pre-palm smoothed and post-palm smoothed results are equivalent, but I'm afraid that the variable dimensions of subjects' native thickness files would cause problems either with palm or when later trying to view the group-level results.
Version information: Recon-all run with FreeSurfer 5.3.0 FSL 5.0.8 palm alpha112
Thank you in advance for any suggestions, and please let me know if any additional information would be helpful.
With gratitude, Dan
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 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 mri_convert in order to use fslmaths or fslstats. My dilemma is that I'd like to use another viewing package for the palm results (i.e., Surf Ice) because of its features and some quirks I've encountered while loading results in Freeview. Surf Ice accepts a number of formats (https://www.nitrc.org/plugins/mwiki/index.php/surfice:MainPage#Supported_For...), including Freesurfer's .asc, .srf, .curv, .gcs, .pial, and .w (among many others), but I have yet to successfully convert these .mgz maps to a readable format. Surf Ice can read .nii, but loading my mri_converted .nii files results in a uniform surface with 0 at all vertices. Thus, I have two questions:
- Can you think of a means to convert these surface "volumes" (.mgh/.mgz) to a desired format that can be read by
Surf Ice? I've attempted mri_vol2surf, mri_surf2surf, and mris_convert, but cannot find an appropriate format/get things to work. In case it's helpful, readable formats are:
- My alternative idea would be to instead use mri_concat on subjects' lh.thickness files and later apply fwhm
smoothing. Would this approach be feasible? I could test whether pre-palm smoothed and post-palm smoothed results are equivalent, but I'm afraid that the variable dimensions of subjects' native thickness files would cause problems either with palm or when later trying to view the group-level results.
Version information: Recon-all run with FreeSurfer 5.3.0 FSL 5.0.8 palm alpha112
Thank you in advance for any suggestions, and please let me know if any additional information would be helpful.
With gratitude, Dan
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Daniel Leopold