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
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*From: *Martin Reuter <mreu...@nmr.mgh.harvard.edu>
*Date: *Tuesday, March 28, 2017 at 1:27 PM
*To: *<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 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
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your cooperation.
*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 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.
*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
>
>
>
> 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.
>
>
>
>
>
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