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-atlases>. 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,
Douglas 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>>>
<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
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:

You can try using bbregister.
Normally, you
don't use
bbregister on a segmentation,
but the
segmentation
index numbers just happen to be
"T1-weighted".
doug
ps. Please remember to copy
the list when
responding.
thanks!

On 7/23/13 9:51 AM, Mark
Plantz wrote:

Hi Doug,

Sorry about that vague
explanation. So
I received
a series of infant brain
atlases
from a
UNC medical
research group

(http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases).
I have a series of infant
MRI's that I
would like to
segment (using the infant
atlases,
instead
of the
default adult atlas in
FreeSurfer).

As a preliminary step,
I was
attempting
to check
the alignment of one of
the atlas
files
('avgseg.mgz') with one of the
input brains
('brain.mgz'). [I attached
these two
files, just in
case].

So my command line would be:

tkmedit $Subject brain.mgz
-segmentation
avgseg.mgz
$FREESURFER_HOME/FreeSurferColorLUT.txt

The result was the
previously attached
image. I was
just wondering if there is
any way to
shift the two
images manually so the
alignment is
better? Or maybe
the two files are simply not
compatible
with one another?

Thanks for all the help!

Best,

Mark

On Mon, Jul 22, 2013 at
3:53 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>>>

<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
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:

Hi Mark, I have no
idea what
you are
doing. Can
you send a command line?
Are either of the images
generated by FS?
doug

On 07/22/2013 03:56
PM, Mark
Plantz wrote:
> Hello FreeSurfers,
>
> I recently
obtained a
set of infant
templates. Out of
curiousity,
> I decided to view
one of the
input
brains with
the provided segmented
> volume file. It
appears that
there
is some
misalignment. I wouldn't
> expect the alignment
to be
perfect,
since I am
basically overlaying an
> average of multiple
brains
onto one.
However,
it looks like this
> misalignment may be
caused by
either: 1.) the
segmentation volume file
> being shifted down
or 2.)
the slices
not lining
up properly (i.e. one
> file starts before
the other).
>
> Any ideas what
could cause a
problem like
this? Could it be that
> the segmented files are
simply not
compatible
with FreeSurfer?
>
> Thanks for the help,
>
> Mark
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.