Most likely to Nick S, unless anyone else would like to chime in...
I'm gearing up for some extensive use of FS... it's downloaded, installed, and initial tests run OK... so far with minimum of pain (yay team!).
Now... I need to discover how to feed in data other than raw scanned files, because we want to try several alternatives to the initial processing, which we have in AFNI format, ac-pc aligned with iso-sided voxels but not 1 mm.
I suspect I'll end up scouring the recon-all script, but a few hints would be helpful, mainly aimed at (a) taking advantage of processing that we have done by other methods, (b) minimizing resampling and (c) winding up with surfaces and segmentations that are most readily overlayed with our other processed data, tracings etc.
1. If we want to feed in already ac-pc aligned, brain-extracted input, at what stage of recon-all should we be looking to supply it? (I can figure out where in the directories to put the data, but not sure on the stage of processing to start at).
2. It used to be that FS's surface pipeline didn't insist on Talairaching the voxel data, and skipping that resulted in output that is true to original space. Is that still the case?
3. Does current FS proper require 256x256x256 1mm data, or can it take any shape "brick" and voxel size (ie: without resampling) these days?
4. If FS *does* want to work with 1mm voxels only: It used to be that though FS wanted 1mm input voxels, you could feed in some other sizes by do-it-yourself creation of the COR images, and FS was fine... is that still the case (but now with mgz format)?
4. Is it the case that the subcortical voxel-based parcellation *does* require the Talairaching step for correspondence with the probability atlas?
5. The surface and voxel-based pipelines are separate, not even sharing the white segmentation step, right?
Thanks in advance, Graham _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
