Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota

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,


        

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