On Tue, Jul 30, 2013 at 8:47 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

the UNC one? No, you should ask them
On Tue, 30 Jul 2013, Mark Plantz wrote:

---------- Forwarded message ----------
From: Mark Plantz <markplantz2016@u.northwestern.edu>
Date: Tue, Jul 30, 2013 at 8:39 AM
Subject: Re: [Freesurfer] infant atlas segmentation
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Just opened up the default FreeSurferColorLUT.txt file. So it looks like all
I have to change is the #No. column of the file, to match the ones in the
other LUT used.
I actually just received the MRIcro .lut file from the UNC group. [attached]

Hopefully this will help with the conversion. However, I still have to
figure out how to open the file. Any ideas?

On Tue, Jul 30, 2013 at 8:25 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
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 medicalgroup<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>