Hi Mark
creating a FreeSurfer LUT really isn't that hard. Have you looked at our standard one? Probably we have the names you already want and you just need to change our indices to match the ones in your segmentation file (and save it as a different LUT)
cheers
Bruce
On Tue, 30 Jul 2013, Mark Plantz wrote:
Turns out that the files had been labeled using a color LUT in a program
called MRIcro. I am now installing this program simply to access the LUT.
Will it be as simple as exchanging the index values from this LUT to a
custom LUT in FreeSurfer?
On Tue, Jul 30, 2013 at 12:35 AM, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:
The problem is that you need to create a completely new LUT. The
labels that get displayed with the standard LUT are going to be
totally random with respect to what they should display.
On 7/29/13 2:20 PM, Mark Plantz wrote:
Hi Doug,
Thanks for the reply. I will definitely go into the LUT and
change those values to some specific region. My main concern is
that I think all of these "out of bounds" labels are the
symptoms of some larger problem. The segmentation looks very
strange as compared to a typical segmentation (i.e. an
'aseg.mgz' file). In fact, the segmentation appears to be
labeling "left-<region" in the right hemisphere. Have you seen a
segmentation file that looks like the once I attached before? I
am used to seeing segmentation files such as the one attached to
this e-mail.
- Mark
On Mon, Jul 29, 2013 at 12:28 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu> wrote:
Mark, the only thing that is wrong with the out of
bounds regions is that they are not represented in
the LUT. Once you add an index corresponding to the
index of the segmentation to the LUT, it will not
show up as "out of bounds". The brain mask has
nothing to do with it.
best
doug
On 7/29/13 12:50 PM, Mark Plantz wrote:
Sorry about that. I received the manual
segmentations from a UNC medical group<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atla
ses>. I actually asked the main researcher
about the out of bounds regions. He thinks
that as long as the segmented file lines up
with the input volumes, a few out of bounds
regions might be OK. However, these seg
volumes look very different from a typical
.aseg volume that I am used to seeing after
recon-all is run.
Maybe the segmentation is simply incompatible with
FreeSurfer?
Thanks for the help. These files are a nightmare!
- MP
On Mon, Jul 29, 2013 at 11:40 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
can you cc the list please? Maybe we
should start over. Where did you get the
manual segmentations from?
On Mon, 29 Jul 2013, Mark Plantz wrote:
Ahh, right. So it looks like
the red regions appear to be
averaged around 248. I am
not sure why that is the
case or if it has
any significance. I attached
a screen shot for
reference.
On Mon, Jul 29, 2013 at
11:29 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
it isn't a
registration file. You
should just specify it as a
volume on the freeview
command line, the same as
brainmask.mgz
On Mon, 29 Jul 2013,
Mark Plantz wrote:
I actually tried
to view the brainmask.mgz
file with the segmentation
file [Freeview calls it
'registration
file' I believe].
For some reason,
the file will load without
segmentation, but when I
attempt to add the
registration
file, I get an
error
message:
"Failed to load
MRI
~/.../../../brainmask.mgz
Could this
potentially be part of the
problem?
Thanks
MP
On Mon, Jul 29,
2013 at 10:57 AM, Mark
Plantz
<markplantz2016@u.northwestern.edu>
wrote:
It looks
like the values vary from
20-120 depending on which
region I run the cursor
over.
However, aren't
those the
values
that correspond to the
brain.mgz regions? Is there
another way to find the
segmentation
values?
On Mon, Jul 29,
2013 at 10:37 AM, Bruce
Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
I mean the
segmentation values that
give you the "out of bounds"
message
On Mon, 29
Jul 2013, Mark Plantz wrote:
Hi
Bruce,
Do
you mean the brainmask.mgz
values? I'm not sure what
the segmentation #'s exactly
are.
Thanks!
MP
On
Mon, Jul 29, 2013 at 10:17
AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
wrote:
Hi Mark
what #s are those
segmentations? It should be
trivial to just add them to
the end of
the
LUT.
I wouldn't let them be
out of bounds as there
might be code around that
might ignore them then.
cheers
Bruce
On Mon, 29 Jul 2013, Mark
Plantz wrote:
Hi Doug,
Thanks for
the reply. After doing some
research, it looks like
messing
with the
LUT
might be a
risky decision [and
way
out of my
abilities!].
If I were to use
this segmentation file to
create a .gca atlas using
the
command
mri_ca_train, do you
think it would yield
problems or be
inaccurate? I guess what I
am trying to figure out is
if the
color
lookup values are even
significant when
using
the segmentation
file to create an atlas?
Thanks for all of
the help with this.
Best,
MP
p.s. I attached the
photo of the segmentation
volume because this e-mail
is sort
of
old
On Wed, Jul 24, 2013
at 2:39 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu>
wrote:
you need a new
LUT. See my comment from a
few emails ago.
On 07/24/2013
03:29 PM, Mark Plantz wrote:
I'm not
actually quite sure what it
means either. When I use the
command
line:
tkmedit
$Subject brain.mgz
-segmentation <seg.mgz>,
I can run the
cursor over various regions
and the name of the region
should pop
up.
For some
reason, the red
regions are
simply labeled as "out of
bounds."
I'll keep
messing with tkmedit and let
you know if I find out what
the
problem
is.
Thanks guys!
MP
On Wed, Jul 24, 2013
at 2:26 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
wrote:
what do you mean
that they are out of bounds?
On 07/24/2013
03:25 PM, Mark Plantz wrote:
I guess the
problem is that those
regions should not be out of
bounds.
Maybe I need to create a new
Lookup Table for the
infant
mri's? Is that possible to
do?
On Wed, Jul
24, 2013 at 2:21 PM, Douglas
N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>
wrote:
Hi Mark,
please post to the list and
not to me.
thanks
doug
On
07/24/2013 03:21 PM, Mark
Plantz wrote:
I
guess the problem is that
those regions should not
be out of
bounds. Maybe I need to
create a new Lookup Table
for the
infant mri's? Is that
possible to do?
On
Wed, Jul 24, 2013 at 2:15
PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
wrote:
what is the problem exactly?
The fact that there
are red
regions
or that that the red regions
are labeled as "Out of
Bounds"? If
the latter, you will need to
create a LUT that
matches your
regions. the out of bounds
means that the index in the
volume does
not match an index in the
LUT.
doug
On 07/24/2013 01:26 PM, Mark
Plantz wrote:
Finally got the
registration to work.
However, it
looks like
the out of bounds
regions (in red) are still
present
(even
though the regions are
well within our
boundaries).
Is
that
expected since they were
labeled in the original
segmentation
volume? Is there anyway
to correct those?
Thanks for all of the
help!
- Mark
p.s. I attached a
picture of the original
brain.mgz
file
viewed with the
corrected segmentation
volume
On Wed, Jul 24, 2013 at
12:22 PM, Mark Plantz
<markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>>>>
wrote:
Finally got the
registration to work.
However, it
looks
like the
out of bound regions
(in red) are still
prevalent.
Is
that
expected since they
were present in the
original
segmentation
volume? Would there
be anyway to correct
those?
Thanks for all the
help!
- MP
On Wed, Jul 24, 2013
at 11:11 AM, Mark Plantz
<markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>>>>
wrote:
Nevermind, it
turned out to be a
permissions
issue.
Thanks!
On Wed, Jul 24,
2013 at 10:12 AM, Mark
Plantz
<markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>
<mailto:markplantz2016@u.northwestern.edu
<mailto:markplantz2016@u.northwestern.edu>>>>>
wrote:
Thanks for
the reply Doug. I
recently ran
the
bbregister
command and
attempted to view the
results
using
tkregister2.
I received the
following
error:
dhcp-165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>
<tel:165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>>
<tel:165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>
<tel:165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>>>:Desktop
IngvalsonLab$ tkregister2
--mov
/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/mri/avgseg.mgz
--reg
/Users/IngvalsonLab/Desktop/register.dat
--surf
tkregister_tcl
/Applications/freesurfer/tktools/tkregister2.tcl
INFO: no
target volume specified,
assuming
FreeSurfer orig
volume.
target
volume orig
movable
volume
/Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-1yr-mgz/mri/avgseg.mgz
reg file
/Users/IngvalsonLab/Desktop/register.dat
LoadVol
1
ZeroCRAS
0
$Id:
tkregister2.c,v 1.121.2.1
2011/03/28
20:25:16
greve Exp $
Diagnostic
Level -1
regio_read_register():
Undefined
error: 0
Error
reading subject from
/Users/IngvalsonLab/Desktop/register.dat
ERROR:
reading
/Users/IngvalsonLab/Desktop/register.dat
dhcp-165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>
<tel:165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>>
<tel:165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>
<tel:165-124-23-232
<tel:165-124-23-232>
<tel:165-124-23-232
<tel:165-124-23-232>>>>:Desktop
IngvalsonLab$
I do not
believe it is a
permissions
issue?
Could it
simply be that the
register was
bad?
Is
there an
easy way to
open up the
register.dat.mincost file
to check
the
registration?
Thanks
again,
MP
On Tue, Jul
23, 2013 at 9:32 PM,