Dear David,
I did not see your data, but maybe couple of relevant remarks could be useful:
1.
By default the wm.mgz edits are not propagated from cross to the base, but from
the cross to long. And surfaces in long are initialized from the base.
Therefore the wm.mgz has to be OK both in the cross and in the base. My view
and current experience is, that this means that in many cases it is probably
necessary to edit wm.mgz both in cross and base. This would explain your
observation that the wm.mgz edits in cross are not propagated to the base and
the edits in base (but not in cross) are not seen in the long.
I implemented a custom script which transfers INTERSECTION of the wm.mgz edits
from all cross points to the base. I think that to transfer the intersection of
edits is safe approach to prevent to introduce errors in wm.mgz in base due to
the false propagation of wm.mgz edits from cross to base in case of significant
changes in the anatomy between cross and base. My preliminary testing shows
that this approach works well and saves time in wm.mgz editing of large errors
which are consistently present in all timepoints. But in case of significant
errors, the wm.mgz in the base still needs some additional editing. Therefore I
think that there is not any single intervention point in wm.mgz edits.
I was discussing the approach of transferring wm.mgz edits with Martin Reuter
in the following thread:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51092.html
2.
When there are spots in the cross, where wm.mgz edits do not take an effect, I
would suggest to inspect the brain.finalsurfs.mgz to see if there is sufficient
contrast of the white/gray matter. In many such cases where I observe my wm.mgz
edits do not take an effect, there is local issue with insufficient white/gray
matter contrast. The white surface placement is primarily driven by the local
gradient of intensity in brain.finalsurfs.mgz, the boundaries/edits of wm.mgz
play only supplementary role (as an starting point for gradient search, via
?h.orig, at least in default invocation of mris_make_surfaces, AFAIK).
If I have enough clues where the white surface should lie (i.e. from FLAIR) and
there is insufficient white/gray matter contrast (typically there are spots in
gray matter with spuriously high signal intensity, similar to white matter), I
am currently experimenting with workaround, by directly editing gray matter
voxels of 001.mgz in problematic spots by setting their values to typical gray
matter values to enforce better white surface placement.
I decided to place my edits just in the beginning to the recon-all stream
(001.mgz) to ensure the edits are not overwritten in case of new recon-all
rerun.
Maybe other experts could comment on my workaround approach, it would also help
me out.
Regards,
Antonin Skoch
I believe what I am seeing in the long stream is the edits not properly taking
effect.I uploaded a subject with two timepoints, and only baseline edits to the
wm as
dsemanek2.zip about a week and a half ago. There doesn’t seem to be any
significant changes to the surfaces in the base or either of the long runs. I
will redo this subject on my end with some more extreme edits for testing to
see if I can “force” something.
Thanks again for looking,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
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From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Date: Wednesday, April 5, 2017 at 2:19 AM
To: David Semanek <seman...@nyspi.columbia.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "Hoopes,
Andrew" <ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Hi David,
so edits are affecting the surfaces in cross, just not as much as you would
like. We need to check if there is a problem there.
For the longitudinal stream, edits in the base should affect surfaces in the
base, which in turn will affect surfaces in the long. In long, surfaces would
start from a better starting position. Furthermore, wm edits from cross should
be propagated to long, to make sure that surfaces don’t move back to the wrong
position. So far the theory.
If you don’t see any effect of WM edits (in the base) on surfaces (in the base)
then there is a problem. This step should be basically identical to how we
treat edits in cross.
Best, Martin
On 04 Apr 2017, at 23:13, David Semanek
<seman...@nyspi.columbia.edu<mailto:seman...@nyspi.columbia.edu>> wrote:
Thanks for looking into this. I have uploaded another two subject folders as
dsemanek3.zip, this time from a single time point for the same subject having
been run through the cross stream of recon-all, the one with “test” appended at
the end has had white matter edits on sagittal slices 126-142.
So, I have been able to get the surfaces to change in a single cross run as
demonstrated in this upload. For this test, I did some edits that are typical
on this dataset. Although the surfaces did change to reflect the edits, in a
couple of places the surfaces did not change enough, and still encompassed
space in the wm volume which had the white matter voxels removed.
For the first pass through these data before I realized there was a potential
problem, I had initially edited the cross folders for the subjects and then ran
the base, expecting the edits to be transferred over, but they did not seem to
be. So I am still left with two issues: 1) incomplete incorporation of cross
edits on the cross folders, 2) so far being unable to find an intervention
point which will change the surfaces in the long stream, I have edited the base
and then ran the long folders and these were not carried over as demonstrated
in my previous uploads.
Thanks again,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
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From: Martin Reuter
<mreu...@nmr.mgh.harvard.edu<mailto:mreu...@nmr.mgh.harvard.edu>>
Date: Tuesday, April 4, 2017 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
So the way to debug this is to test if we can replicate the problem of WM edits
not taking effect in a regular cross sectional stream.
If true this means that there is a bug to the way WM edits are considered in
FS6.0. It is unlikely that we missed that, but can happen. Probably something
else is going on here.
For that it would be good to have a single time point (cross sectional step)
with WM edits send over, so that Andrew can take a look at that.
Best, Martin
On 04/04/2017 05:03 PM, David Semanek wrote:
I used –uselongbasewmedits only as a test to see if I could get some condition
under which the wm edits would be taken into account when the surfaces were
generated.
I did not use that flag for the data I uploaded. The wm edits to base did not
influence the base wm surfaces or the cross wm surfaces. The cross wm edits
(not uploaded) did not influence cross, base, or long wm surfaces.
I’ve found no condition under which wm edits have influenced the white matter
surface in any of my data.
Best,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally privileged
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someone who was not authorized to send it to you, you are strictly prohibited
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From: Martin Reuter
<mreu...@nmr.mgh.harvard.edu><mailto:mreu...@nmr.mgh.harvard.edu>
Date: Tuesday, March 28, 2017 at 1:27 PM
To: <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
This is how it should work:
WM edits in the base should affect surfaces in the base, these surfaces should
be used as initialization for the long processing and fix most of the things
there. If not , you need to edit the cross, because WM edits are copied into
long from cross.
Using the -uselongbasewmedits flag is usually not recommended. It copies WM
edits from base to the long and that is only meaningful if there is very little
longitudinal change.
Best, Martin
On 03/23/2017 04:12 PM, David Semanek wrote:
Thanks for taking another look at our data.
I have uploaded another subject in the archive dsemanek2.zip . For this subject
I have:
1) run the cross processing stream on both timepoints
2) created the base
3) edited the wm.mgz on the base
4) rerun –base –autorecon2-wm –autorecon3
5) run the long stream to create the long folders for the two time points
It doesn’t look like the white matter edits were factored into any of the
surfaces at any point in the process. NB: some edits have been exaggerated over
protocol for the purpose of testing the software.
These folders were processed on OSX 10.11. I am running the same subject on
Linux and I will let you know if I get a qualitatively different outcome.
Best,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally privileged
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From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu><mailto:ahoo...@mgh.harvard.edu>
Date: Monday, March 20, 2017 at 4:54 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David
Semanek <seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Hi David,
That is interesting. Sorry to ask you to upload data again, but if you could
upload this subject (with only base wm.mgz edits), I could try to replicate
this and see why no wm changes are showing up in the longs.
best,
Andrew
________________________________
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 David
Semanek<seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu>
Sent: Monday, March 20, 2017 1:59 PM
To: Hoopes, Andrew; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Andrew, thanks for your response. I am still not seeing the white matter edit
performance that I am expecting, or that I have seen from using the cross
stream on 5.3 in the past with a different dataset.
I started with a new subject with two timepoints. I ran recon-all on both for
the cross stream with no edits, and then ran the base. I edited the wm.mgz for
the base, then ran “recon-all –autorecon2-wm –autorecon3 –base xx_base –tp
xx_t1 –tp xx_t2”. I noticed the surfaces didn’t really change in the base, but
I went ahead and ran the two long runs using “recon-all –all –long xx_tx
xx_base” and although there are minor differences in the base and time point
surfaces, the white matter edits I did on the base were largely ignored, and
none of them were included in the time point long run wm.mgz files.
I am tempted to try these same analyses using Linux (I am running this on OSX
10.11 currently), as I experienced a completely different response from the
surface generation modules to my edits in the past when using Linux. I’m
thinking this is a real long shot, but I cannot otherwise figure out why the
software would be behaving so differently from my past experiences.
Any thoughts? Thanks!
Best,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally privileged
or otherwise protected by law. If you received this e-mail in error or from
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PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
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From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu><mailto:ahoo...@mgh.harvard.edu>
Date: Wednesday, March 15, 2017 at 12:47 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>, David
Semanek <seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu>
Cc: Bruce Fischl <fis...@nmr.mgh.harvard.edu><mailto:fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Hi David
Try editing the base wm.mgz first instead of editing the long and cross wm
files. Rerun autorecon2-wm and autorecon3 for the base dir, then completely
rerun the longitudinals. The long surfaces are initialized from the base
surfaces, so this could be why your wm fixes seem to have no effect.
You can find more info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#CheatSheet<https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits>
If editing the base doesn't solve the problem, you can send me the commands you
ran in order and I can look into this further.
best,
Andrew
________________________________
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 David
Semanek<seman...@nyspi.columbia.edu><mailto:seman...@nyspi.columbia.edu>
Sent: Monday, March 13, 2017 11:55 AM
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Thanks, I have uploaded the cross and long stream processing from one subject
which requires numerous white matter edits to correct defects in the white
matter surfaces; the file is on the ftp server as dsemanek.zip.
Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to
both the brainmask as well as the wm files, and autorecon2-wm and autorecon-3
have been run on them, as well as the long folder for the first time point,
s02_t1.long.s02_base.
It was in working with the rerun results of s02_t1.long.s02_base that I noticed
the white matter surfaces after being regenerated with the edited wm.mgz did
not reflect any of the edits. The easiest way to see this is to load the wm.mgz
with the white matter surfaces and scroll through the slices, there are
numerous areas where the contours of the white matter surfaces do not follow
the voxels of the wm.mgz volume, mostly near what should be identified as
hyperintense gray matter. I’m fairly certain the white matter surfaces didn’t
change at all after running autorecon2-wm with the wm.mgz edits.
Thanks for taking a look at our data.
Best,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally privileged
or otherwise protected by law. If you received this e-mail in error or from
someone who was not authorized to send it to you, you are strictly prohibited
from reviewing, using, disseminating, distributing or copying the e-mail.
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
On 3/12/17, 4:13 PM, "Bruce Fischl"
<fis...@nmr.mgh.harvard.edu><mailto:fis...@nmr.mgh.harvard.edu> wrote:
Hi David
if you upload a subject to our ftp site and give us enough detail to
replicate what you tried we will take a look
cheers
Bruce
On Fri, 10 Mar 2017, David
Semanek wrote:
>
> Hello, I have worked quite a bit in the past with fs 5.3 on datasets which
> required a fair number of manual edits to the white matter volume in order
> to correct defects in the white matter surface. Typically, these edits
take
> the form of removing voxels in the wm.mgz volume that have been
incorrectly
> identified as white matter, usually near the pial surface caused by
> intensity artifacts resulting from motion. My experience in the past is
that
> generating the white matter surface after edits to the wm.mgz volume will
> reliably change the geometry of the resulting surfaces.
>
>
>
> However, on my current dataset, 1.5T adolescent brains with pervasive
motion
> artifacts that do not meet the threshold for unusable data, absolutely no
> intervention I have done on the wm.mgz volume has any impact at all on the
> generation of the white matter surfaces. I am really very puzzled by this.
> All of the files that result from wm.mgz reflect the edits, however the
aseg
> does not.
>
>
>
> The resulting white matter surfaces always follow the aseg white matter
> definitions and never the wm.mgz edits. I feel as if there might be
> something I am missing but this protocol has reliably been used to do
white
> matter edits in the past. I thought it may be an issue with fs 6 or the
long
> stream, but I have tried the same edits in 5.3, 6, long and cross streams
> and nothing at all has worked.
>
>
>
> Does anyone have any suggestions, or perhaps a hint that I am overlooking
> something common?
>
>
>
> Thanks,
>
>
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885_______________________________________________
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