Hi Antonin
Sorry for the trouble. We can add a -mask option to it going forward
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Antonín Škoch
Sent: Friday, December 11, 2020 1:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Computing thickness from woT2.pial surfaces {Disarmed}
External Email - Use Caution
Hi, Bruce,
I did not find any mris_thickness command line option for masking medial wall
during thickness computation.
The masking of ?h.thickness file ex post would not probably help, since it is
not equivalent.
I tested this by running mris_anatomical_stats (which I suppose by principle
takes medial wall into account) and obtained still slightly different results.
So I finally retreated to rerunning recon-all -pial and recon-all -T2pial and
stored ?h.thickness of both processes.
Regards,
Antonin
You probably want to mask the medial wall
Bruce
On Dec 9, 2020, at 11:31 PM, Antonín Škoch <a...@ikem.cz<mailto:a...@ikem.cz>>
wrote:
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Hi, Bruce,
in the meantime, I found the old thread
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05989.html<https://secure-web.cisco.com/1aNvaY2F2Wzk88I3TCWDZ8sNnAxHgbRgs7ryiKYBIUsjQEMXKVjOhDjjv-tTq_A_mcp9_w3p_xfMYU4K3oN8ts9WChKgWsA9AtPmq5FF3Y6zzmD5t03nbQ2-r7t_sAfYx_dpfAZlYbPGy4CPfDSu5ieNyHQqLkZi45uWSi8DuXWenZA7BmM-pWlZxZ4Q1fqJJL4CMsQNSCkWdl9AWJSU5eX_iFpea_HkxRXx2lJwGl1ZMPlZDvcLsHctgVn_kEM4I-mofA4DczPVAZ5QS9mCTPw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg05989.html>
which suggests to set -N 20 parameter to mris_thickness to make thickness
computation consistent to mris_make_surfaces. Indeed, the values are now
consistent,
with exception of several thousands of vertices mainly around medial wall. Is
here any other option missing, which makes mris_thickness computed values of
thickness fully consistent to mris_make_surfaces?
Thank you in advance,
Antonin
Hi, Bruce,
thank you for the instructions!
I ran mris_thickness on one example subject to test the procedure. However,
inspecting the values of created thickness file, I encountered problem.
In many locations, the values of thickness file differ from the values of
thickness file created in recon-all -T2pial.
Even when the input files used for thickness measurement are (should) be the
same. (I double-checked my input surfaces,
when I use woT2.pial surface, the thickness values are different everywhere).
Attached see the binarized difference of these thickness files with the cursor,
where difference is zero (red spots)
and where is non-zero (transparent).
Could you please clarify, where could be the problem? Does not the thickness
computation in mris_make_surfaces use different options?
Could it be the reason, that I am operating with data processed by longitudinal
stream? (I don't think so...).
This inconsistence makes me puzzled.
Regards,
Antonin
Hi Antonín
You can specify what surfaces to use in mris_thickness:
mris_thickness -pial <path to pial surface> -white <path to white surface> …
cheers
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Antonín Škoch
Sent: Wednesday, December 9, 2020 6:16 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Computing thickness from woT2.pial surfaces
External Email - Use Caution
Dear experts,
I have processed my data with -T2pial option. I would like now to also compute
thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a
comannd which does the trick, without running recon-all -pial (which rewrites
current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer
version 6.0.
Thank you in advance,
Antonin Skoch
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