Re: [Freesurfer] infant atlas segmentation

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-atlase.... 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.eduwrote:

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 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.**edugreve@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 greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu 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 greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu 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 markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>>> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>>

                                                        <mailto:

markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu 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 markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>>> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>>

                                                        <mailto:

markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu 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 markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>>>

<mailto:markplantz2016@u.**northwestern.edumarkplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu>>

                                                        <mailto:

markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu markplantz2016@u.northwestern.edu> <mailto: markplantz2016@u.**northwestern.edu markplantz2016@u.northwestern.edu <mailto:markplantz2016@u.** northwestern.edu 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:165-124-23-232tel: 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:165-124-23-232tel: 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:165-124-23-232tel: 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:165-124-23-232tel: 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 greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>>

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

                                                        <mailto:

greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu 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-atlaseshttp://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 greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>>

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

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

                                                            <mailto:

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

      >