Hi Matthieu

yes, you will want to run all of your subjects with it

cheers
Bruce
On Tue, 18 Sep 2018, Matthieu Vanhoutte wrote:

        External Email - Use Caution        

Dear Bram,

It looks like the -bigventricles flag fixed my problem with my specific subject. Not only, this took
into account large ventricles but also corrected grey matter segmentation from extra Dura tissue
that was erroneously segmented in GM.

I understand the first point of amelioration allowed by the flag but don't understand where the
second point come from ?

If I used the -bigventricles flag for all my atrophied and large ventricles patients and not for my
healthy patients, wouldn't it introduce a bias when further statistically comparing groups between
them ?

Best,
Matthieu

2018-09-14 15:35 GMT+00:00 Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>:
      If you haven't already, you may want to run the subject through recon-all with the
      -bigventricles flag since it looks like the lateral ventricle was significantly
      mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you
      can edit the aseg.mgz manually by following the directions in this tutorial. Then run
      the following command (again, substituting <subj_id> for your subject's id):
recon-all -autorecon2-noaseg -autorecon3 -subjid <subj_id>

I would try this before doing the wm.mgz edits I suggested in my previous email.

Best,
Bram

____________________________________________________________________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on
behalf of Diamond, Bram Ryder <BRDIAMOND@mgh.harvard.edu>
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhoutte@gmail.com
Cc: freesurfer@nmr.mgh.harvard.edu; astevens@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubles to determine the type of recon editing needed  

Hi Matthieu,


I've taken a look through the files you shared with us and I see the poor surfaces in the
posterior right hemisphere you were referring to in your message. It looks like your subject
has a combination of abnormally large ventricles and significant wm abnormalities, so I'm
surprised FreeSurfer did as well as it did.


As for the recon editing - I would recommend editing the wm.mgz to more accurately represent
the wm from slice 84 to 39. You can take a look at the white matter edits tutorial for details
on how to do that. Then run the following command (substituting <subj_id> for your
subject's id):


recon-all -autorecon2-wm -autorecon3 -subjid <subj_id>


The surface reconstruction may also benefit from labeling the right lateral ventricle in the
wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces
for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and
tell us how that goes.


All the best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street 
Charlestown, MA 02129
(p): 617-726-6598

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