Yes, it might be a normalization issue. You could try using the `-no-ants-n4`
recon-all flag to fallback to the v6 normalization method.
As for the wm edits, you don’t really need to load the surfaces, just the
norm.mgz and wm.mgz, but if you wanted to visualize the initial smooth
tessellation as well:
freeview -v mri/norm.mgz mri/wm.mgz:colormap=heat:opacity=0.5 -f
surf/?h.smoothwm.nofix
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yakupov, Renat /DZNE
<renat.yaku...@dzne.de>
Date: Friday, May 7, 2021 at 6:00 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology
External Email - Use Caution
Hi Andrew,
thank you for looking at the data!
I did check out that tutorial first, and the first thing it tells you to do is
load various surfaces into Freeview, which was what brought me here. In this
subject's `surf` directory there are no ?h.white and ?h.pial surface files.
Which files can I use instead in order to see the white matter surface and look
for those defects?
It is also interesting, that the processing didnt fail in Freesurfer 6. Looking
at the release notes, one of the changes was using N4 bias-field correction
instead of N3. Do you think this might mean that N4's inadequate bias-field
correction led to broken-up segmented white matter, which in turn caused larger
topological defects?
Best wishes,
Renat.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew
<ahoo...@mgh.harvard.edu>
Sent: Friday, May 7, 2021 5:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology
Hi Renat,
The third defect is too large and it’s causing a crash. When I run it, it hangs
forever at:
CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369)
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.
There are huge gaps missing in this subject’s white matter mask, resulting in a
bad surface tessellation (see attached pic). I would check out the info at
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview<https://secure-web.cisco.com/12gT4H7XBsnxMWWCG4F8T4qJBE2PnbITfcdxpaBTxDgzaZPjHt1Catp497o4oUcQVkGOLdV1H5oPZEhAnsBEWow0_4VGH6FsatlW_uUq3bBc-hRCpHluu5XhEuB-KQOMYmA6arEafPIf63cVVzOyZIn4hG1sVKMtcFUPlyUovEhCmOtR0jOZIyYiy7FQeC2_hSbRngcTvJKSaaE9nCnXO2Law1dP6lPrceor8a4XTA3T_mew60k5qF8QD5Vmg2YWpbOhlp1IWt2BeJQ0sfT1yQQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview>
and fill in the wm.mgz to manually edit.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yakupov, Renat /DZNE
<renat.yaku...@dzne.de>
Date: Thursday, May 6, 2021 at 4:21 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology
External Email - Use Caution
Hi Andrew,
thank you for your reply. I just uploaded the subject's directory under the
name "subject_from_RenatYakupov.tar.gz".
Regarding memory, I am running these jobs on our SGE cluster, which monitors
memory usage. Both of the subject's images had maximum memory usage of slightly
over 3GB, which is pretty typical from my experience. Interestingly, when
processed with Freesurfer 6, which didnt crash and finished successfully, the
maximum memory usage was around 11GB.
Thanks again and looking forward to your findings 😊
Best wishes,
Renat.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew
<ahoo...@mgh.harvard.edu>
Sent: Wednesday, May 5, 2021 7:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology
Hi Renat,
That 3rd defect is fairly large – normally it would hang but it’s possible
you’re running out of memory. If you can zip the subject and file drop it to
us, we can take a look:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange<https://secure-web.cisco.com/1u2I9K-ckbULcDN4h-_ZdylX5n2vBBOMX6EHfWnDs7-xWZI3mqQdWi7HFoMKz9tdNYKjuWfN_Nan4JpJGREsnwmGq3yxwMImknbbPMfasAVeeqV3mWyJDJQbZi7QtsM0L44JYsK6UYk_wuuwEf_p_Ed5vbQFvnR_qkoiA75YR3ueRivLu1VsrmbDCfIglg4xLUeLcU3w4JopYBtaAk1pJe5CQJ-Nwjy6wxShFB-45MwaCw2xP54Ka9a36Silz4XoVQFam74VwOrlnybPLjm3TGQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFtpFileExchange>
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yakupov, Renat /DZNE
<renat.yaku...@dzne.de>
Date: Friday, April 30, 2021 at 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology
External Email - Use Caution
Dear all,
I have a subject whose Freesurfer processing crashes during topology fixing
step. The last lines in `recon-all.log` are:
After retessellation of defect 2 (v0=22890), euler #=-15 (110444,329616,219157)
: difference with theory (-18) = -3
CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369)
Segmentation fault (core dumped)
Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29
UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 81489f2bb-M12_T1_01 exited with ERRORS at Tue Apr 27 21:23:59 CEST
2021
For the full `recon-all.log` and `recon-all.error` files please see the
attached files.
I tried to follow the manual topology fixing instructions from MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview<https://secure-web.cisco.com/1CVb3gwDr9GTwil5kr7FQYCZpGmZhLu9ovxhkC6nEa1QhFJIx6eypmT0rYaI6M3eFoajm5UGJThFtpEwrTovzNAg_qegvhWDxcy-m6gpWYAx55QHi7-eJxrS108DfdnILY9yauaca2pTGvSgA9CrUOR9Twoqnu5o6E2uJ_bMuvqjHfdZuxVU9dNQ0n1Pi4WCFH3_4H6PQilZLYZai-fJAGrNEqr7pFG9jzwrssq82FVnCamJT0vmbbW9I27W_DE1vKkW9T7lo9aEi6hbNTu3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview>,
but *.white and *.pial surface files are missing from `surf` directory. It
only contains these files:
lh.defect_borders lh.defect_labels lh.orig.nofix lh.smoothwm.nofix
rh.orig.nofix rh.smoothwm.nofix
lh.defect_chull lh.inflated.nofix lh.qsphere.nofix rh.inflated.nofix
rh.qsphere.nofix
Which files can I use in place of white and pial surface files in order to look
for WM segmentation defects?
Some additional information about the data:
- I am running Freesurfer 7.1
- overall, there are no gross errors in WM segmentation, although the subjects
does have significant temporal lobe atrophy
- there are two images acquired at different times, and processing fails for
both images
- interestingly, processing didnt crash with Freesurfer 6.
Thank you and have a great weekend,
Renat.
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