Jim, There is a way to insert special flags into the recon-all command stream for a particular binary. See the section 'EXPERT OPTIONS FILE' in recon-all --help. So you would create a file called expert.opts containing:
mris_make_surfaces -fix_mtl and then add the string '-expert expert.opts' to recon-all. You could add -dontrun to recon-all to confirm that it is grabbing that change. Nick On Mon, 2007-12-10 at 13:32 -0600, James N. Porter wrote: > Hello Bruce- > > From the wiki, I gather that I would rerun recon-all from -finalsurfs > onward, as that is the step that calls make_final_surfaces. In order to > insert the fix_mtl flag I'll have to run that section via a separate > command line outside of recon-all. Are there any other subsequent steps > that require manual intervention or nonstandard parameters, or would > something like the code below do the work? > > for S in $SUBJ; do > for H in $HEMI; do > mris_make_surfaces --noaparc --mgz -T1 --fix_mtl brain.finalsurfs $S $H > done > recon-all -s $S -cortribbon -autorecon3 > done > > Thanks, > > Jim Porter > Graduate Student > Clinical Science & Psychopathology Research > University of Minnesota > > > > > > Bruce Fischl wrote: > > Hi Jim, > > > > you can actually run mris_make_surfaces with -fix_mtl and it will > > inhibit all deformations in these regions. I didn't enable that by > > default as I was afraid it would mean missing a bit of entorhinal. In > > general it doesn't really matter as the gray and white volumes > > computed from the surfaces will exclude amygdala and hippocampal > > voxels that are interior to the surface. > > > > For your second question: we use the gray matter volume estimated from > > the surfaces instead of the aseg, as we find it to be more accurate > > than the voxel-based techniques. > > > > cheers, > > Bruce > > > > > > On Tue, 27 Nov 2007, James N. Porter wrote: > > > >> Hello FreeSurfer Folks- > >> > >> I've seen several threads in the archives discussing the expected > >> inaccuracies in the pial, white, and orig surfaces running through > >> subcortical structures. However, I've been unable to ascertain > >> exactly how much and what kind of inaccuracy is acceptable. It makes > >> sense to me that if the entirety of a structure, say the amygdala, > >> were included or excluded in the pial surface, then it would be easy > >> to adjust later measurements. However, what we see in all of our > >> subjects is a random pattern of half in/half out, with weird shapes, > >> when it comes to the surfaces running in and around subcortical > >> structures. For example, take a look the image at this link. > >> > >> http://www.tc.umn.edu/~norb0062/Amygdala.tiff > >> > >> There you will see the how the hippocampus and amygdala are both half > >> included in the pial surface. Item 1 has a strange guitar-shaped > >> chunk taken out of the amygdala, and item 2 has a triangle and a > >> peanut-shaped area removed. Are these the types of expected and > >> accepted inaccuracies, or is there something afoul here that needs to > >> be corrected? > >> > >> I have one other question regarding the interactions of aseg and > >> surface information. Item 3 in the image points out a section of > >> apparent subdural matter that has been classified as grey matter in > >> the aseg but has been excluded from the pial surface. When the final > >> statistics are spit out of recon-all, is there a section of > >> processing that says something like, "Based on the aseg values my > >> grey matter volume is X, but since Y of that is outside of the pial > >> surface I'll call my total volume X-Y"? Or, is this another item to > >> that requires correction and re-running of recon-all? > >> > >> Many thanks in advance, > >> > >> > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
