On Thu, Aug 1, 2013 at 2:28 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

glad it worked out
Bruce
On Thu, 1 Aug 2013, Mark Plantz wrote:

Just as an update, it turns out that my segmentation volume had been
slightly altered during the conversion from .nii to .mgz. I completely
forgot to use the -rt nearest flag to prevent the labels from becoming
distorted. That is why the segmentation looked so fuzzy with various regions
labeled incorrectly.
Apparently, I should check the basics before overcomplicating the problem,
haha. Thanks for the help everyone!

On Thu, Aug 1, 2013 at 9:36 AM, Mark Plantz
<markplantz2016@u.northwestern.edu> wrote:
Sounds good. I also just realized that the segmentation values
are varying from 0-255, which makes me think that the file is
only designed for the grayscale/heat/etc. settings [where 0 is
darkest regions and 255 is brightest regions]. Is that a valid
assumption? Also, if this is the case, would it be impossible to
create a .gca file using mri_ca_train with these files?
Thanks for the help.

MP

On Wed, Jul 31, 2013 at 8:43 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu> wrote:

Just make sure that you create a new file and do not
repeat index numbers.

On 7/31/13 2:02 PM, Mark Plantz wrote:
That makes sense. Wouldn't that cause there to be
some overlap between different regions, since the
same index #'s used by the two programs (FreeSurfer
& MRIcro) correspond to different brain regions?

On Tue, Jul 30, 2013 at 12:50 PM, Douglas Greve
<greve@nmr.mgh.harvard.edu> wrote:

for every line in that file, you will need to
create a line in the new LUT, something like

8 Frontal_Mid_R 0 255 0 0

This will make the right mid frontal green =
(0,255,0)

On 7/30/13 9:55 AM, Mark Plantz wrote:
Hmm, so I received the text part of the
LUT. Looks like this is completely
different from the segmented regions
that we would want. [attached]. Can't
seem to understand how this text file
could be related to the default
FreeSurfer LUT. It looks like the
labeling for an AAL map. This probably
wont' work will it?
- Mark

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 UNCmedicalgroup<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infan
t-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>>