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>> 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>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>>>> 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>>>> 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>>>> 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>>>: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>>>: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>>>> 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>>>> 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
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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>>>
Phone Number: 617-724-2358
<tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
<tel:617-724-2358>>>
Fax: 617-726-7422
<tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>
Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto: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
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.
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
<tel:617-726-7422>>
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/