[Freesurfer] mri_surf2surf (and mri_preproc) clarification

External Email - Use Caution Dear Freesurfer experts, The mri_surf2surf example 1 specifies that lh thickness is resampled onto the 7th order icosahedron. Does it place the lh.thickness curv into freesurfer space, or is it still in the subject's native space (i.e., pre-transformat

[Freesurfer] Accessing posted files

External Email - Use Caution Dear FS experts, Can you please direct me as to how I can access/download a file suggested in the listserv? I've tried ftp (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange), scp, ssh, Googling, clicking on the hyperlink, etc. using comb

Re: [Freesurfer] Extracting stats from palm results (.mgz)

External Email - Use Caution Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to take advantage of NPC and exchangeability blocks because I've got twins and singletons in the sample. Does --pargs allow for all palm functionality, including things like TFCE, eb's,

[Freesurfer] Extracting stats from palm results (.mgz)

External Email - Use Caution Hi all, Do you have any suggestions on how I could extract stats (e.g., thickness, area, LGI, etc.) from a cluster(s) identified via palm? I've tried mri_label2label in order to turn the palm output .mgz into a paint .label file, but mri_label2label ca

[Freesurfer] Advice re: cluster thresholding, smoothing, and best practices?

External Email - Use Caution Hi all, I'm hoping to get some input on clustering, multiple correction, smoothing preferences, and (if available) best practices. Please correct me if I'm wrong, but it seems that the amount of attention given to multiple correction and spatial depend

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

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., data-per-vertex)

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

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_conver

[Freesurfer] Error saving NPC results

External Email - Use Caution Dear Freesurfer Community, Drs. Winkler, Greve, Fischl, et al. *My apologies if this reposts, but this is my first time emailing the listserv, and I'm not sure if my earlier email went through* Could anyone help me understand which palm options are ne

[Freesurfer] Error while saving NPC results

External Email - Use Caution Dear Drs. Winkler, Greve, Fischl, et al. Could you help me understand which palm options are needed in order to produce tfce and clustere NPC results that are fwe-corrected across contrasts (i.e., _cfwep_)? I'm analyzing area and thickness and have fo