what does the aseg look like? Why isn't the cerebllum being removed? Dura
is harder (unless you have a T2 or FLAIR)
On Sun, 10 May 2020, Billah,
Tashrif wrote:
Running the commands separately, I see the following log for some of the
defects. Is the weblink my cue?
CORRECTING DEFECT 0 (vertices=4912, convex hull=886, v0=0)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from
wm.mgz.
This may cause recon-all to run very slowly or crash.
if so,
seehttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free
view
-Tashrif
.
____________________________________________________________________________
From: Billah, Tashrif
Sent: Sunday, May 10, 2020 2:11 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Bouix, Sylvain,Ph.D. <sylv...@bwh.harvard.edu>; Knyazhanskaya, Evdokiya
<eknyazhansk...@bwh.harvard.edu>
Subject: mris_fix_topology command does not finish
Hi there,
The following commands part of `recon-alll -i some_T1w.nii.gz -autorecon2`
does not finish for some of our data:
#@# Fix Topology lh Sat May 9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
lh
#@# Fix Topology rh Sat May 9 14:17:52 EDT 2020
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig
orig.nofix -out orig.premesh -ga -seed 1234 sub-7049_ses-01_desc-XcMaN4_T1w
rh
Waiting for PID 57296 of (57296 57299) to complete...
Waiting for PID 57299 of (57296 57299) to complete...
We kept them running for about 48 hours in multiple attempts, yet no luck.
Moreover, mris_fix_topology is a binary file so I am unable to debug
through.
Any suggestion on where to look at?
Best,
Tashrif
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