Dear FreeSurfer experts,
I have some inquiries concerning the "make" option in recon-all:
1. It seems to me that the freeSurfer "make" option in recon-all (at least in 5.3.0 version) is not compatible with -FLAIRpial / -T2pial option.
I made some manual edits which required rerun of autorecon2 and autorecon3. The "recon-all -make all" did not rerun pial refinement, which means that the resulting surfaces were generated completely without any pial refinement. Therefore, as I noticed that, I had to rerun recon-all -autorecon3 -FLAIRpial in all affected subjects.
Are you aware of this bug/pitfall? I think that this is quite a problem since user need not notice this unexpected behavior which can seriously affect the final results. The user can believe he has surface refined, but instead they are not.
I think that modification of recon-all.makefile could solve this problem.
2. I also found that there is no "make" option for local gyrification index. Would you consider also to implement that?
3. My last question is concerning the touch files. It seems that most of the "make" directives do not examine touch files, but the original (volume or surface) files. Therefore, it seems that most of the touch files are never used. What is the significance of touch files?
4. I also noticed some inconsistency in documentation: reconAllTable for 5.3 version does not contain -FLAIRpial / T2 pial step at all.
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
They are documented only in dev version
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
but it does not correspond to 5.3.2 version - there seems to be difference in the position of -nuintensitycor step in the processing flow.
Is there an actual table of reconstruction steps for 5.3.2 version?
Regards,
Antonin Skoch Institute for Clinical and Experimental Medicine Prague, Czech Republic