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
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*From: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu>
*Date: *Monday, March 20, 2017 at 4:54 PM
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, David
Semanek <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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek
<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>
*Date: *Wednesday, March 15, 2017 at 12:47 PM
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, David
Semanek <seman...@nyspi.columbia.edu>
*Cc: *Bruce Fischl <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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of David Semanek
<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> 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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