Re: [Freesurfer] Incomplete and poorly formed tracts

[Anastasia Yendiki]

Hi Susan - Good to hear that you get good results for most of your 
subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical 
registration for the subjects that are failing? I'd check the 
aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if 
there are any holes or misregistration.


a.y

On Mon, 25 Mar 2013, Susan Kuo wrote:


Hi FreeSurfers and Anastasia,   TRACULA is working great for me, generating 
tracts for a sample of 20 subject
brains I'm working with. However, for 3 of the brains, I'm receiving incomplete 
and poorly formed tracts.
I've re-run trac-all at least 2x on each subject in case there was a mistake in 
my original configuration.
However, I am reproducing the same results. Does anybody have an idea why I would see 
these "spotty" tracts? 


Thank you for all your help! 

--
Susie Kuo
NIH

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Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  I did as you recommended and checked the diffusion-to-anatomical
registration, and the overlay of aparc+aseg_mask on FA, and these views
seem to be good. Upon closer inspection, what I find is that there are
incipient 'bits' of all the tracts, but they seem to not have 'grown',
though they are in the proper space (comparing them to good brains that
yielded the full complement of tracts). Is there a configuration in your
TRACULA that controls the growing of the tracts specifically? Perhaps I
should look into that.

  Thank you, btw, for your very prompt reply yesterday- it was much
appreciated!


Sincerely,
Susie Kuo
NIH

On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susan - Good to hear that you get good results for most of your
> subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical
> registration for the subjects that are failing? I'd check the
> aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if
> there are any holes or misregistration.
>
> a.y
>
>
> On Mon, 25 Mar 2013, Susan Kuo wrote:
>
>  Hi FreeSurfers and Anastasia,   TRACULA is working great for me,
>> generating tracts for a sample of 20 subject
>> brains I'm working with. However, for 3 of the brains, I'm receiving
>> incomplete and poorly formed tracts.
>> I've re-run trac-all at least 2x on each subject in case there was a
>> mistake in my original configuration.
>> However, I am reproducing the same results. Does anybody have an idea why
>> I would see these "spotty" tracts?
>>
>>
>> Thank you for all your help!
>>
>> --
>> Susie Kuo
>> NIH
>>
>>
>>
>
> 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.
>



-- 
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly
recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of
Fear*
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,

  I see what you mean. I had previously used the dtifit_FA.nii.gz image and
overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using
freeview. I didn't end up with the same images as you, however. Can you
tell me which images you used to obtain this overlay?

  I am going to run bbregister tonight, and I'll let you know how it goes
-- I'm hopeful!

Thank you again!

Susie Kuo
NIH

On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susie - I'm attaching a snapshot from your subject, showing the
> aparc+aseg overlaid on the FA map. The registration has failed. The frontal
> lobe has spilled out of the brain, the white matter has spilled into the
> ventricles.
>
> I strongly recommend using bbregister for the intra-subject registration,
> which is the default in the latest version of trac-all.
>
> Hope this helps,
> a.y
>
>
> On Tue, 26 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,   I did as you recommended and checked the
>> diffusion-to-anatomical
>> registration, and the overlay of aparc+aseg_mask on FA, and these views
>> seem to be
>> good. Upon closer inspection, what I find is that there are incipient
>> 'bits' of all
>> the tracts, but they seem to not have 'grown', though they are in the
>> proper space
>> (comparing them to good brains that yielded the full complement of
>> tracts). Is there a
>> configuration in your TRACULA that controls the growing of the tracts
>> specifically?
>> Perhaps I should look into that.
>>
>>   Thank you, btw, for your very prompt reply yesterday- it was much
>> appreciated!
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Susan - Good to hear that you get good results for most of your
>>   subjects. Have you checked the aparc+aseg and the
>> diffusion-to-anatomical
>>   registration for the subjects that are failing? I'd check the
>>   aparc+aseg_mask (in the dlabel/diff directory) over the FA map to
>> see if
>>   there are any holes or misregistration.
>>
>>   a.y
>>
>>   On Mon, 25 Mar 2013, Susan Kuo wrote:
>>
>> Hi FreeSurfers and Anastasia,   TRACULA is working great for
>> me, generating tracts for a sample of 20 subject
>> brains I'm working with. However, for 3 of the brains, I'm
>> receiving incomplete and poorly formed tracts.
>> I've re-run trac-all at least 2x on each subject in case there
>> was a mistake in my original configuration.
>> However, I am reproducing the same results. Does anybody have
>> an idea why I would see these "spotty" tracts?
>>
>>
>> Thank you for all your help!
>>
>> --
>> Susie Kuo
>> NIH
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Susie Kuo
>>
>> Mediocrity knows nothing higher than itself, but talent instantly
>> recognizes genius. -
>> Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear
>>
>>


-- 
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly
recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of
Fear*
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Incomplete and poorly formed tracts

[Anastasia Yendiki]

Hi Susie - Everything under dlabel/diff is mapped to DWI space (either 
with flirt or with bbregister, whichever you use). The one in my 
screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.


a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:


Hi Anastasia, 
  I see what you mean. I had previously used the dtifit_FA.nii.gz image and
overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using
freeview. I didn't end up with the same images as you, however. Can you tell
me which images you used to obtain this overlay? 

  I am going to run bbregister tonight, and I'll let you know how it goes --
I'm hopeful! 

Thank you again!

Susie Kuo
NIH

On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
 wrote:

  Hi Susie - I'm attaching a snapshot from your subject, showing
  the aparc+aseg overlaid on the FA map. The registration has
  failed. The frontal lobe has spilled out of the brain, the white
  matter has spilled into the ventricles.

  I strongly recommend using bbregister for the intra-subject
  registration, which is the default in the latest version of
  trac-all.

  Hope this helps,
  a.y

  On Tue, 26 Mar 2013, Susan Kuo wrote:

Hi Anastasia,   I did as you recommended and checked
the diffusion-to-anatomical
registration, and the overlay of aparc+aseg_mask on
FA, and these views seem to be
good. Upon closer inspection, what I find is that
there are incipient 'bits' of all
the tracts, but they seem to not have 'grown',
though they are in the proper space
(comparing them to good brains that yielded the full
complement of tracts). Is there a
configuration in your TRACULA that controls the
growing of the tracts specifically?
Perhaps I should look into that. 

  Thank you, btw, for your very prompt reply
yesterday- it was much appreciated!


Sincerely, 
Susie Kuo
NIH

On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki

wrote:

      Hi Susan - Good to hear that you get good
results for most of your
      subjects. Have you checked the aparc+aseg and
the diffusion-to-anatomical
      registration for the subjects that are
failing? I'd check the
      aparc+aseg_mask (in the dlabel/diff directory)
over the FA map to see if
      there are any holes or misregistration.

      a.y

      On Mon, 25 Mar 2013, Susan Kuo wrote:

            Hi FreeSurfers and Anastasia,   TRACULA
is working great for
            me, generating tracts for a sample of 20
subject
            brains I'm working with. However, for 3
of the brains, I'm
            receiving incomplete and poorly formed
tracts.
            I've re-run trac-all at least 2x on each
subject in case there
            was a mistake in my original
configuration.
            However, I am reproducing the same
results. Does anybody have
            an idea why I would see these "spotty"
tracts? 


            Thank you for all your help! 

            --
            Susie Kuo
            NIH




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.




--
Susie Kuo

Mediocrity knows nothing higher than itself, but
talent instantly recognizes genius. -
Sir Arthur Conan Doyle, Sherlock Holmes- Valley of
Fear




--
Susie Kuo

Mediocrity knows nothing higher than itself, but talent instantly recognizes
genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear

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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 

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  I'm attaching the graphic I arrived at with the command:

> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz -v
/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the subjectID. I could
not detect spill over in these images, mostly because the frontal lobe is a
little cut off. Did you perhaps use a different viewer? I'm hoping to be
able to detect these mis-registrations better for myself in the future.
Thanks for all your help!

Sincerely,
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susie - Everything under dlabel/diff is mapped to DWI space (either
> with flirt or with bbregister, whichever you use). The one in my screenshot
> was dlabel/diff/aparc+aseg.flt.**nii.gz.
>
> a.y
>
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,
>>   I see what you mean. I had previously used the dtifit_FA.nii.gz image
>> and
>> overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using
>> freeview. I didn't end up with the same images as you, however. Can you
>> tell
>> me which images you used to obtain this overlay?
>>
>>   I am going to run bbregister tonight, and I'll let you know how it goes
>> --
>> I'm hopeful!
>>
>> Thank you again!
>>
>> Susie Kuo
>> NIH
>>
>> On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Susie - I'm attaching a snapshot from your subject, showing
>>   the aparc+aseg overlaid on the FA map. The registration has
>>   failed. The frontal lobe has spilled out of the brain, the white
>>   matter has spilled into the ventricles.
>>
>>   I strongly recommend using bbregister for the intra-subject
>>   registration, which is the default in the latest version of
>>   trac-all.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Tue, 26 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,   I did as you recommended and checked
>> the diffusion-to-anatomical
>> registration, and the overlay of aparc+aseg_mask on
>> FA, and these views seem to be
>> good. Upon closer inspection, what I find is that
>> there are incipient 'bits' of all
>> the tracts, but they seem to not have 'grown',
>> though they are in the proper space
>> (comparing them to good brains that yielded the full
>> complement of tracts). Is there a
>> configuration in your TRACULA that controls the
>> growing of the tracts specifically?
>> Perhaps I should look into that.
>>
>>   Thank you, btw, for your very prompt reply
>> yesterday- it was much appreciated!
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Susan - Good to hear that you get good
>> results for most of your
>>   subjects. Have you checked the aparc+aseg and
>> the diffusion-to-anatomical
>>   registration for the subjects that are
>> failing? I'd check the
>>   aparc+aseg_mask (in the dlabel/diff directory)
>> over the FA map to see if
>>   there are any holes or misregistration.
>>
>>   a.y
>>
>>   On Mon, 25 Mar 2013, Susan Kuo wrote:
>>
>> Hi FreeSurfers and Anastasia,   TRACULA
>> is working great for
>> me, generating tracts for a sample of 20
>> subject
>> brains I'm working with. However, for 3
>> of the brains, I'm
>> receiving incomplete and poorly formed
>> tracts.
>> I've re-run trac-all at least 2x on each
>> subject in case there
>> was a mistake in my original
>> configuration.
>> However, I am reproducing the same
>> results. Does anybody have
>> an idea why I would see these "spotty"
>> tracts?
>>
>>
>> Thank you for all your help!
>>
>> --
>> Susie Kuo
>> NIH
>>
>>
>>
>>
>> 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
>>   

Re: [Freesurfer] Incomplete and poorly formed tracts

[Anastasia Yendiki]

Hi Susie - The -tv (tract volume) option of freeview is designed 
specifically to display the merged*.mgz output files of tracula. For a 
regular volume, use -v or no option at all. For best displaying the 
aparc+aseg, select it in freeview and choose "Lookup Table" from the Color 
map menu.


Hope this helps,
a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:


Hi Anastasia,   I'm attaching the graphic I arrived at with the command: 

> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz -v
/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not 
detect
spill over in these images, mostly because the frontal lobe is a little cut 
off. Did
you perhaps use a different viewer? I'm hoping to be able to detect these
mis-registrations better for myself in the future. Thanks for all your help!

Sincerely, 
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki 

wrote:

  Hi Susie - Everything under dlabel/diff is mapped to DWI space (either
  with flirt or with bbregister, whichever you use). The one in my
  screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.

  a.y

  On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia, 
  I see what you mean. I had previously used the
dtifit_FA.nii.gz image and
overlaid that with the aparc+aseg+2mm.nii.gz image in
/dlabel/diff, using
freeview. I didn't end up with the same images as you,
however. Can you tell
me which images you used to obtain this overlay? 

  I am going to run bbregister tonight, and I'll let you know
how it goes --
I'm hopeful! 

Thank you again!

Susie Kuo
NIH

On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
 wrote:

      Hi Susie - I'm attaching a snapshot from your subject,
showing
      the aparc+aseg overlaid on the FA map. The registration
has
      failed. The frontal lobe has spilled out of the brain,
the white
      matter has spilled into the ventricles.

      I strongly recommend using bbregister for the
intra-subject
      registration, which is the default in the latest version
of
      trac-all.

      Hope this helps,
      a.y

      On Tue, 26 Mar 2013, Susan Kuo wrote:

            Hi Anastasia,   I did as you recommended and
checked
            the diffusion-to-anatomical
            registration, and the overlay of aparc+aseg_mask
on
            FA, and these views seem to be
            good. Upon closer inspection, what I find is that
            there are incipient 'bits' of all
            the tracts, but they seem to not have 'grown',
            though they are in the proper space
            (comparing them to good brains that yielded the
full
            complement of tracts). Is there a
            configuration in your TRACULA that controls the
            growing of the tracts specifically?
            Perhaps I should look into that. 

              Thank you, btw, for your very prompt reply
            yesterday- it was much appreciated!


            Sincerely, 
            Susie Kuo
            NIH

            On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
            
            wrote:

                  Hi Susan - Good to hear that you get good
            results for most of your
                  subjects. Have you checked the aparc+aseg
and
            the diffusion-to-anatomical
                  registration for the subjects that are
            failing? I'd check the
                  aparc+aseg_mask (in the dlabel/diff
directory)
            over the FA map to see if
                  there are any holes or misregistration.

                  a.y

                  On Mon, 25 Mar 2013, Susan Kuo wrote:

                        Hi FreeSurfers and Anastasia,  
TRACULA
            is working great for
                        me, generating tracts for a sample of
20
            subject
                        brains I'm working with. However, for
3
            of the brains, I'm
                        receiving incomplete and poorly formed
            tracts.
                        I've re-run trac-

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  Thank you! I can see that the aparc+aseg spilled over badly. I am going
to try bbregister, and then re-betting (Brain Extraction Tool-ing) the
original image, since the dtifit_FA looks to include non-brain near the
frontal lobe. I'll keep you and the FS community updated on the results, in
case anybody is curious.


Sincerely,
Susie Kuo
NIH


On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Susie - The -tv (tract volume) option of freeview is designed
> specifically to display the merged*.mgz output files of tracula. For a
> regular volume, use -v or no option at all. For best displaying the
> aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
> map menu.
>
> Hope this helps,
> a.y
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,   I'm attaching the graphic I arrived at with the command:
>>
>> > freeview -tv /dlabel/diff/aparc+**aseg.flt.nii.gz -v
>> /dmri/dtifit_FA.**nii.gz
>>
>> Here, I used the subject I send you (Sa69845.5) for the subjectID. I
>> could not detect
>> spill over in these images, mostly because the frontal lobe is a little
>> cut off. Did
>> you perhaps use a different viewer? I'm hoping to be able to detect these
>> mis-registrations better for myself in the future. Thanks for all your
>> help!
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Susie - Everything under dlabel/diff is mapped to DWI space
>> (either
>>   with flirt or with bbregister, whichever you use). The one in my
>>   screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz.
>>
>>   a.y
>>
>>   On Wed, 27 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,
>>   I see what you mean. I had previously used the
>> dtifit_FA.nii.gz image and
>> overlaid that with the aparc+aseg+2mm.nii.gz image in
>> /dlabel/diff, using
>> freeview. I didn't end up with the same images as you,
>> however. Can you tell
>> me which images you used to obtain this overlay?
>>
>>   I am going to run bbregister tonight, and I'll let you know
>> how it goes --
>> I'm hopeful!
>>
>> Thank you again!
>>
>> Susie Kuo
>> NIH
>>
>> On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Susie - I'm attaching a snapshot from your subject,
>> showing
>>   the aparc+aseg overlaid on the FA map. The registration
>> has
>>   failed. The frontal lobe has spilled out of the brain,
>> the white
>>   matter has spilled into the ventricles.
>>
>>   I strongly recommend using bbregister for the
>> intra-subject
>>   registration, which is the default in the latest version
>> of
>>   trac-all.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Tue, 26 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,   I did as you recommended and
>> checked
>> the diffusion-to-anatomical
>> registration, and the overlay of aparc+aseg_mask
>> on
>> FA, and these views seem to be
>> good. Upon closer inspection, what I find is that
>> there are incipient 'bits' of all
>> the tracts, but they seem to not have 'grown',
>> though they are in the proper space
>> (comparing them to good brains that yielded the
>> full
>> complement of tracts). Is there a
>> configuration in your TRACULA that controls the
>> growing of the tracts specifically?
>> Perhaps I should look into that.
>>
>>   Thank you, btw, for your very prompt reply
>> yesterday- it was much appreciated!
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Susan - Good to hear that you get good
>> results for most of your
>>   subjects. Have you checked the aparc+aseg
>> and
>> the diffusion-to-anatomical
>>   registration for the subjects that are
>> failing? I'd check the
>>   aparc+aseg_mask (in the dlabel/diff
>

Re: [Freesurfer] Incomplete and poorly formed tracts

[Anastasia Yendiki]

Actually the brain mask used on the diffusion data *is* the aparc+aseg 
mapped to diffusion space, so the reason you see that extra non-brain 
stuff in the FA map is because the aparc+aseg was not aligned well to it.


So you just need to switch on bbregister and switch off flirt in your 
configuration file, and then rerun trac-all. If the DWI-to-T1 registration 
is good, then the masking issue will be solved too.


Good luck!
a.y

On Wed, 27 Mar 2013, Susan Kuo wrote:


Hi Anastasia,   Thank you! I can see that the aparc+aseg spilled over badly. I 
am
going to try bbregister, and then re-betting (Brain Extraction Tool-ing) the 
original
image, since the dtifit_FA looks to include non-brain near the frontal lobe. 
I'll keep
you and the FS community updated on the results, in case anybody is curious. 


Sincerely, 
Susie Kuo
NIH


On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki 

wrote:

  Hi Susie - The -tv (tract volume) option of freeview is designed
  specifically to display the merged*.mgz output files of tracula. For a
  regular volume, use -v or no option at all. For best displaying the
  aparc+aseg, select it in freeview and choose "Lookup Table" from the Color
  map menu.

  Hope this helps,
  a.y

  On Wed, 27 Mar 2013, Susan Kuo wrote:

Hi Anastasia,   I'm attaching the graphic I arrived at with
the command: 

> freeview -tv /dlabel/diff/aparc+aseg.flt.nii.gz
-v
/dmri/dtifit_FA.nii.gz

Here, I used the subject I send you (Sa69845.5) for the
subjectID. I could not detect
spill over in these images, mostly because the frontal lobe is
a little cut off. Did
you perhaps use a different viewer? I'm hoping to be able to
detect these
mis-registrations better for myself in the future. Thanks for
all your help!

Sincerely, 
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki

wrote:

      Hi Susie - Everything under dlabel/diff is mapped to DWI
space (either
      with flirt or with bbregister, whichever you use). The
one in my
      screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.

      a.y

      On Wed, 27 Mar 2013, Susan Kuo wrote:

            Hi Anastasia, 
              I see what you mean. I had previously used the
            dtifit_FA.nii.gz image and
            overlaid that with the aparc+aseg+2mm.nii.gz image
in
            /dlabel/diff, using
            freeview. I didn't end up with the same images as
you,
            however. Can you tell
            me which images you used to obtain this overlay? 

              I am going to run bbregister tonight, and I'll
let you know
            how it goes --
            I'm hopeful! 

            Thank you again!

            Susie Kuo
            NIH

            On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
             wrote:

                  Hi Susie - I'm attaching a snapshot from
your subject,
            showing
                  the aparc+aseg overlaid on the FA map. The
registration
            has
                  failed. The frontal lobe has spilled out of
the brain,
            the white
                  matter has spilled into the ventricles.

                  I strongly recommend using bbregister for
the
            intra-subject
                  registration, which is the default in the
latest version
            of
                  trac-all.

                  Hope this helps,
                  a.y

                  On Tue, 26 Mar 2013, Susan Kuo wrote:

                        Hi Anastasia,   I did as you
recommended and
            checked
                        the diffusion-to-anatomical
                        registration, and the overlay of
aparc+aseg_mask
            on
                        FA, and these views seem to be
                        good. Upon closer inspection, what I
find is that
                        there are incipient 'bits' of all
                        the tracts, but they seem to not have
'grown',
                        though they are in the proper space
                        (comparin

Re: [Freesurfer] Incomplete and poorly formed tracts

[Susan Kuo]

Hi Anastasia,
  I saved out some of the completed trac-all.cmds following each TRACULA
'step', and I see where aparc+aseg is mapped to diffusion space. Thank you
again for all your help - my project is starting to look a lot better!


Sincerely,
Susie Kuo
NIH

On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Actually the brain mask used on the diffusion data *is* the aparc+aseg
> mapped to diffusion space, so the reason you see that extra non-brain stuff
> in the FA map is because the aparc+aseg was not aligned well to it.
>
> So you just need to switch on bbregister and switch off flirt in your
> configuration file, and then rerun trac-all. If the DWI-to-T1 registration
> is good, then the masking issue will be solved too.
>
> Good luck!
>
> a.y
>
> On Wed, 27 Mar 2013, Susan Kuo wrote:
>
>  Hi Anastasia,   Thank you! I can see that the aparc+aseg spilled over
>> badly. I am
>> going to try bbregister, and then re-betting (Brain Extraction Tool-ing)
>> the original
>> image, since the dtifit_FA looks to include non-brain near the frontal
>> lobe. I'll keep
>> you and the FS community updated on the results, in case anybody is
>> curious.
>>
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>>
>> On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>   Hi Susie - The -tv (tract volume) option of freeview is designed
>>   specifically to display the merged*.mgz output files of tracula.
>> For a
>>   regular volume, use -v or no option at all. For best displaying the
>>   aparc+aseg, select it in freeview and choose "Lookup Table" from
>> the Color
>>   map menu.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Wed, 27 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,   I'm attaching the graphic I arrived at with
>> the command:
>>
>> > freeview -tv /dlabel/diff/aparc+**
>> aseg.flt.nii.gz
>> -v
>> /dmri/dtifit_FA.**nii.gz
>>
>> Here, I used the subject I send you (Sa69845.5) for the
>> subjectID. I could not detect
>> spill over in these images, mostly because the frontal lobe is
>> a little cut off. Did
>> you perhaps use a different viewer? I'm hoping to be able to
>> detect these
>> mis-registrations better for myself in the future. Thanks for
>> all your help!
>>
>> Sincerely,
>> Susie Kuo
>> NIH
>>
>> On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki
>> 
>> wrote:
>>
>>   Hi Susie - Everything under dlabel/diff is mapped to DWI
>> space (either
>>   with flirt or with bbregister, whichever you use). The
>> one in my
>>   screenshot was dlabel/diff/aparc+aseg.flt.**nii.gz.
>>
>>   a.y
>>
>>   On Wed, 27 Mar 2013, Susan Kuo wrote:
>>
>> Hi Anastasia,
>>   I see what you mean. I had previously used the
>> dtifit_FA.nii.gz image and
>> overlaid that with the aparc+aseg+2mm.nii.gz image
>> in
>> /dlabel/diff, using
>> freeview. I didn't end up with the same images as
>> you,
>> however. Can you tell
>> me which images you used to obtain this overlay?
>>
>>   I am going to run bbregister tonight, and I'll
>> let you know
>> how it goes --
>> I'm hopeful!
>>
>> Thank you again!
>>
>> Susie Kuo
>> NIH
>>
>> On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Susie - I'm attaching a snapshot from
>> your subject,
>> showing
>>   the aparc+aseg overlaid on the FA map. The
>> registration
>> has
>>   failed. The frontal lobe has spilled out of
>> the brain,
>> the white
>>   matter has spilled into the ventricles.
>>
>>   I strongly recommend using bbregister for
>> the
>> intra-subject
>>   registration, which is the default in the
>> latest version
>> of
>>   trac-all.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Tue, 26 Mar 2013, Susan Kuo wrote:
>>
>> Hi A