[Freesurfer] using custom templates

[Jason Tourville]

Greetings,
I have generated custom surface templates from pediatric data sets. To
apply it to the larger data set, is it sufficient to simply run the
autorecon3 steps (perhaps skipping the mris_sphere step)? If so, is there a
handy flag for running this with recon-all and/or a way to run autorecon3
with a flag indicating that the non-default template should be used?

Once I've done this, I'd like to do some form of comparison b/w the
templates. I am considering looking at the overlap of surface labels
generated by the custom templates to a manually labeled "gold standard."
Does that sound reasonable? Do you have any other suggestions?

Best,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] using custom templates

[Jason Tourville]

Hi Bruce,
By template here, I mean the folding pattern .tif files. The intention is
to have  a replacement for the fsaverage template for surfer
co-registration.

Cheers,
Jason


On Thu, Mar 5, 2015 at 3:18 PM, Bruce Fischl 
wrote:

> Hi Jason
>
> I don't think so - you'll probably have to edit the recon-all script. And
> by template do you just mean the folding pattern .tif files, or do you
> meant the parcellation atlases (*.gcs)?
>
> cheers
> Bruce
> On Thu, 5 Mar 2015, Jason Tourville
> wrote:
>
> > Greetings,
> > I have generated custom surface templates from pediatric data sets. To
> apply
> > it to the larger data set, is it sufficient to simply run the autorecon3
> > steps (perhaps skipping the mris_sphere step)? If so, is there a handy
> flag
> > for running this with recon-all and/or a way to run autorecon3 with a
> flag
> > indicating that the non-default template should be used?
> >
> > Once I've done this, I'd like to do some form of comparison b/w the
> > templates. I am considering looking at the overlap of surface labels
> > generated by the custom templates to a manually labeled "gold standard."
> > Does that sound reasonable? Do you have any other suggestions?
> >
> > Best,
> > Jason
> >
> > --
> > Jason A. Tourville, Ph.D.
> > Research Assistant Professor
> > Department of Speech, Language,
> > and Hearing Sciences
> > Boston University
> > 677 Beacon St.
> > Boston, MA 02215
> > Phone: (617)353-9484
> > Fax: (617)353-7755
> >
> >
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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 not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] using custom templates

[Jason Tourville]

Hi Doug,
I've run the steps outlined in the SurfaceRegAndTemplates page so far. So:

make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...

foreach subject (subj1 subj2 subj3 ...)
  cd $SUBJECTS_DIR/subject
  mris_register -curv surf/lh.sphere \
 $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
 surf/lh.sphere.reg.newtemplate
end

mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...

make_average_subject --out newnewtemplate --surf-reg
sphere.reg.newtemplate \
  --subjects subj1 subj2 subj3 ...

My understanding is that the next step is to now register each individual
surface to this new template and then run through the surface (and volume)
labeling steps. Is that correct?

It occurs to me that the fsaverage template used as the target for any .gcs
that I would to label the surface. Will I have to account for this?

Thanks again,
Jason




On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve 
wrote:

>
> If you used make_average_subject to create the template, you can run
> surfreg to do the registration. If/when you run mris_preproc, make sure
> to spec both the target subject and the new spherical registration
>
>
> On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > Hi Jason
> >
> > I don't think so - you'll probably have to edit the recon-all script. And
> > by template do you just mean the folding pattern .tif files, or do you
> > meant the parcellation atlases (*.gcs)?
> >
> > cheers
> > Bruce
> > On Thu, 5 Mar 2015, Jason Tourville
> > wrote:
> >
> >> Greetings,
> >> I have generated custom surface templates from pediatric data sets. To
> apply
> >> it to the larger data set, is it sufficient to simply run the autorecon3
> >> steps (perhaps skipping the mris_sphere step)? If so, is there a handy
> flag
> >> for running this with recon-all and/or a way to run autorecon3 with a
> flag
> >> indicating that the non-default template should be used?
> >>
> >> Once I've done this, I'd like to do some form of comparison b/w the
> >> templates. I am considering looking at the overlap of surface labels
> >> generated by the custom templates to a manually labeled "gold standard."
> >> Does that sound reasonable? Do you have any other suggestions?
> >>
> >> Best,
> >> Jason
> >>
> >> --
> >> Jason A. Tourville, Ph.D.
> >> Research Assistant Professor
> >> Department of Speech, Language,
> >> and Hearing Sciences
> >> Boston University
> >> 677 Beacon St.
> >> Boston, MA 02215
> >> Phone: (617)353-9484
> >> Fax: (617)353-7755
> >>
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
> ___
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> 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.
>
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] using custom templates

[Jason Tourville]

Hi Doug,
Perhaps I should back up and explain our goal. We are using Freesurfer to
recon pediatric data sets and are planning to use the surface labels as
seeds for connectivity studies and for morphometric analyses. We're
concerned that using the fsaverage surface template as the target for
surface registration could introduce errors in the labels due to match with
our pediatric surfaces, so we derived a new surface template from a subset
of our data set.

My understanding is that once we've done this, to get the surface labels,
stats, etc. for each scan, we need to then register each scan to this new
target and then run the the various steps to get the labeled surfaces
(e.g., mris_ca_label). So I want to confirm this; more specifically, I'd
like to know which steps of the recon-all pipeline need to be rerun to to
replace completely replace the fsaverage target.

Jason


On Thu, Mar 5, 2015 at 3:58 PM, Douglas N Greve 
wrote:

> The mris_register command is what does the registration and creates a
> new sphere.reg file. surfreg just implements that command mris_register
> command.
>
> I'm not sure what you mean by the labeling steps.
>
>
> On 03/05/2015 03:53 PM, Jason Tourville wrote:
> > Hi Doug,
> > I've run the steps outlined in the SurfaceRegAndTemplates page so far.
> So:
> > make_average_subject --out newtemplate --subjects subj1 subj2 subj3 ...
> >
> > foreach subject (subj1 subj2 subj3 ...)
> >cd $SUBJECTS_DIR/subject
> >mris_register -curv surf/lh.sphere \
> >   $SUBJECTS_DIR/newtemplate/lh.reg.template.tif \
> >   surf/lh.sphere.reg.newtemplate
> > end
> >
> > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s
> subj3 ...
> >
> > make_average_subject --out newnewtemplate --surf-reg
> > sphere.reg.newtemplate \
> >--subjects subj1 subj2 subj3 ...
> >
> > My understanding is that the next step is to now register each
> > individual surface to this new template and then run through the
> > surface (and volume) labeling steps. Is that correct?
> >
> > It occurs to me that the fsaverage template used as the target for any
> > .gcs that I would to label the surface. Will I have to account for this?
> >
> > Thanks again,
> > Jason
> >
> >
> >
> >
> > On Thu, Mar 5, 2015 at 3:26 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > If you used make_average_subject to create the template, you can run
> > surfreg to do the registration. If/when you run mris_preproc, make
> > sure
> > to spec both the target subject and the new spherical registration
> >
> >
> > On 03/05/2015 03:18 PM, Bruce Fischl wrote:
> > > Hi Jason
> > >
> > > I don't think so - you'll probably have to edit the recon-all
> > script. And
> > > by template do you just mean the folding pattern .tif files, or
> > do you
> > > meant the parcellation atlases (*.gcs)?
> > >
> > > cheers
> > > Bruce
> > > On Thu, 5 Mar 2015, Jason Tourville
> > > wrote:
> > >
> > >> Greetings,
> > >> I have generated custom surface templates from pediatric data
> > sets. To apply
> > >> it to the larger data set, is it sufficient to simply run the
> > autorecon3
> > >> steps (perhaps skipping the mris_sphere step)? If so, is there
> > a handy flag
> > >> for running this with recon-all and/or a way to run autorecon3
> > with a flag
> > >> indicating that the non-default template should be used?
> > >>
> > >> Once I've done this, I'd like to do some form of comparison b/w
> the
> > >> templates. I am considering looking at the overlap of surface
> > labels
> > >> generated by the custom templates to a manually labeled "gold
> > standard."
> > >> Does that sound reasonable? Do you have any other suggestions?
> > >>
> > >> Best,
> > >> Jason
> > >>
> > >> --
> > >> Jason A. Tourville, Ph.D.
> > >> Research Assistant Professor
> > >> Department of Speech, Language,
> > >> and Hearing Sciences
> > >> Boston University
> > >> 677 Beacon St.
> > >> Boston, MA 02215
> > >> Phone: (617)353-9484 
> > >> Fax: (617)353-7755 
> > >

[Freesurfer] latest freeview

[Jason Tourville]

Hi there,
Looking over the freeview development page, it looks like there are some
(relatively) new features that would come in handy. Could I get a link to
download the latest freeview beta?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] local intensity inhomogeneity

[Jason Tourville]

Hello freesurfers,
We've seen some poor surface reconstructions due to local inhomogeneities
that remain in the brainmask volume. We see omission of significant
portions of brain tissue due to signal fall off (both gray and white voxels
are darker than in surrounding area) that we are unable to current through
control points or other manual interventions. Can anyone suggest a tool for
correcting latent local inhomogeneities? Is anyone aware of a manual tool
that allows one to "brighten" the voxels from some point outward at some
falloff rate?

Any help would be greatly appreciated.

Best,
Jason
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[Freesurfer] restoring wm.mgz

[Jason Tourville]

Hi there,
I'm working on a project in which I manually "erased" voxels (changed to
'1') in the optic chiasm region in the wm.mgz and brainmask.mgz. This was
done to eliminate those voxels from the surface reconstructions. We've
since realized that this isn't necessary...our results are largely
unaffected by the edit. So we've skipped that edit on most (110+) scans.
For the few scans that have the optic chiasm edits, I'd like to regenerate
the original surfaces but would like to retain the numerous other edits
I've made to the brainmask.mgz and wm.mgz volumes outside the optic chiasm
region.

I have tried to do this by "cloning" the voxels from the original brainmask
and wm volumes to the edited version, thereby restoring the original voxel
values in only this region. When I then rerun recon all from the
autorecon2-cp option, the "restored" voxels in the wm volume are set set to
"0" (so no longer the original values and not even the "erased" value of
"1") before the surfaces are generated. The result is that the surfaces in
the optic chiasm area remain "clipped." I've tried this on a couple
different scans and after moving the wm.seg.mgz volume out of the mri/
directory.

Any idea why this is happening? Is there a solution that does not require
me to edit these scans from scratch?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] tksurfer command for saving multiple view tiff

[Jason Tourville]

Is there a command for the "saving multiple views as TIFFs" function in
tksurfer that can be used in a TCL script?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] surface repositioning tool documentation

[Jason Tourville]

Hi,
Is there documentation for the use of freeview's surface repositioning
tool? Including the recon-all steps that should be rerun to ensure that the
surface edits are reflected in the surface stats? Are edits made with this
tool applied to future runs through the recon-all process (like pial and wm
edits)?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] norm2b, norm2n

[Jason Tourville]

Greetings,
I am working with pediatric data and have some early evidence that running
recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior
temporal lobe segmention as suggested in the v5.2 release notes (I am
running this with v5.3). I'd like to experiment more with this parameters
to see if I can further improve the segmentation but have been unable to
find a a description of how these parameters influence the 2nd norm. Can
someone point me to such a description?

Thanks,
Jason


Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] -3T and -mprage flags

[Jason Tourville]

Hi there,
I am working on a project that involves pediatric data, ages 3-12. We are
using Freesurfer to generate cortical surfaces. Information regarding the
T1 acquisition is  listed below. Is it appropriate to use the -3T and
mprage flags for such data? Is there an alternative, pediatric atlas, that
can be used for the Talariach and/or normalization steps that would be an
improvement over the standard (or Schwartz) atlases?

Any input that you can provide would be greatly appreciated.

Cheers,
Jason


Below please see some details on the MPRAGE that is being collected for my
study.

GE 3T Signa® HDx MR scanner (GE Healthcare, Waukesha, WI) with an 8-channel
head coil. During each session, 180 T1-weighted 1-mm3 isotropic volumetric
inversion recovery fast spoiled gradient-recalled images (10 minute scan
time), with cerebrospinal fluid (CSF) suppressed, were obtained to cover
the whole brain with the following parameters: time of echo (TE) = 3.8 ms,
time of repetition (TR) of acquisition = 8.6 ms, time of inversion (TI) =
831 ms, TR of inversion = 2332 ms, flip angle = 8°, field of view (FOV) =
25.6 cm × 25.6 cm, matrix size = 256 × 256, slice thickness = 1 mm, and
receiver bandwidth = ± 20.8 kHz.


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] optimal T1 protocol

[Jason Tourville]

Hello freesurfer experts,

Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical
reconstruction?

For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso"
protocol which has PAT = 2 and a TA = 6:02. 􀀈􀀎

I'm wondering if a faster option at the same resolution is now available
that is recon-approved? For instance, a multi-band option?

Thanks for any feedback,
Jason
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[Freesurfer] pial surface midline fix

[Jason Tourville]

Hi,
I've encountered a recon-all'ed scan in which the pial surface along the
posterior midline "jumps" on cortex in the opposite hemisphere. Is there a
simple fix for this, perhaps using a hemisphere mask?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] freeview surface vertex point save?

[Jason Tourville]

Hi there,
The tksurfer/tkmedit combo allowed one to select and save a point on the
inflated surface and then go to that point in the volume. Does freeview
have a similar capability?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] freeview save error

[Jason Tourville]

Hi there,
Occassionally when using the "save volume" function from the gui to save
edits made to the wm.mgz, freeview crashes (see command line error report
below) and the wm.mgz being deleted from subject's 'mri' directory (the
temp wm.mgz~ is still present...but all edits are lost). I am running
freeview from freesurfer v5.3 on Mac OSX 10.8.4. Any thoughts on the cause?

Thanks,
Jason



0]PETSC ERROR:

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSCERROR:
or try
http://valgrind.org on linux or man libgmalloc on Apple to find memory
corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR:

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:

[0]PETSC ERROR: Unknown Name on a darwin12. named JayMac.local by jaytour
Mon Jul 22 10:40:30 2013
[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR:

[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0








-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] recon-all after manual edits

[Jason Tourville]

Hi there,
I am doing manual edits on the brainmask.mgz, wm.mgz, and
brain.finalsurfs.manedit.mgz volumes and adding control points. What
autorecon flag or from which stage of processing should I rerun recon-all
such that all of these manual edits are respected?

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] preserve manual edits?

[Jason Tourville]

Hi there,
We have performed manual volume edits on a number of scans. Recently, we
ran those scans through recon-all with a new Tal volume target. The seg and
surfaces are improved using the new target but most of the manual edits
performed on the earlier version would improve the surfaces. Is there an
established means for porting the manually edited voxel values to the
volumes of the new re-con?

Thanks,
Jason


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] preserve manual edits?

[Jason Tourville]

Hi Bruce,
I used Freeview to edit the brainmask.mgz, wm.mgz, and
brain.finalsurfs.manedit.mgz volumes.

Cheers,
Jason


On Fri, Jul 25, 2014 at 9:23 PM, Bruce Fischl 
wrote:

> Hi Jason.
> How were the edits done?
> Cheers
>  Bruce
>
> > On Jul 25, 2014, at 10:40 AM, Jason Tourville  wrote:
> >
> > Hi there,
> > We have performed manual volume edits on a number of scans. Recently, we
> ran those scans through recon-all with a new Tal volume target. The seg and
> surfaces are improved using the new target but most of the manual edits
> performed on the earlier version would improve the surfaces. Is there an
> established means for porting the manually edited voxel values to the
> volumes of the new re-con?
> >
> > Thanks,
> > Jason
> >
> >
> > --
> > Jason A. Tourville, Ph.D.
> > Research Assistant Professor
> > Department of Speech, Language,
> > and Hearing Sciences
> > Boston University
> > 677 Beacon St.
> > Boston, MA 02215
> > Phone: (617)353-9484
> > Fax: (617)353-7755
> > ___
> > 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.
>
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] preserve manual edits?

[Jason Tourville]

Hi Bruce,
Used v5.3 for original edits using the "recon" mode in freeview so edits
used 1 for "off" and 255 for "on".

Jason


On Mon, Jul 28, 2014 at 9:22 AM, Bruce Fischl 
wrote:

> Hi Jason
>
> what version? Did it support recon mode? The edits need to use 1 for "off"
> and 255 for "on", otherwise we can't track them.
>
> cheers
> Bruce
> On Mon, 28 Jul 2014, Jason Tourville wrote:
>
>  Hi Bruce,I used Freeview to edit the brainmask.mgz, wm.mgz, and
>>
>> brain.finalsurfs.manedit.mgz volumes.
>>
>> Cheers,
>> Jason
>>
>>
>> On Fri, Jul 25, 2014 at 9:23 PM, Bruce Fischl > >
>> wrote:
>>   Hi Jason.
>>   How were the edits done?
>>   Cheers
>>Bruce
>>
>>   > On Jul 25, 2014, at 10:40 AM, Jason Tourville
>>wrote:
>>   >
>>   > Hi there,
>>   > We have performed manual volume edits on a number of scans.
>>   Recently, we ran those scans through recon-all with a new Tal
>>   volume target. The seg and surfaces are improved using the new
>>   target but most of the manual edits performed on the earlier
>>   version would improve the surfaces. Is there an established
>>   means for porting the manually edited voxel values to the
>>   volumes of the new re-con?
>>   >
>>   > Thanks,
>>   > Jason
>>   >
>>   >
>>   > --
>>   > Jason A. Tourville, Ph.D.
>>   > Research Assistant Professor
>>   > Department of Speech, Language,
>>   > and Hearing Sciences
>>   > Boston University
>>   > 677 Beacon St.
>>   > Boston, MA 02215
>>   > Phone: (617)353-9484
>>   > Fax: (617)353-7755
>> > ___
>> > 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.
>>
>>
>>
>>
>> --
>> Jason A. Tourville, Ph.D.
>> Research Assistant Professor
>> Department of Speech, Language,
>> and Hearing Sciences
>> Boston University
>> 677 Beacon St.
>> Boston, MA 02215
>> Phone: (617)353-9484
>> Fax: (617)353-7755
>>
>>
> ___
> 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.
>
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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The information in this e-mail is intended only for the person to whom it is
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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] preserve manual edits?

[Jason Tourville]

Got it. Thanks Bruce.


On Mon, Jul 28, 2014 at 11:18 AM, Bruce Fischl 
wrote:

> phew. Then you should be able to copy those over to your new runs if you
> want (that is, copy all the 1s and 255s into the volumes in the new
> directories). I assume you are rerunning recon-all from scratch? Or you
> could just copy the whole directory, and rerun recon-all -all on the new
> directory and it should recreate everything while preserving edits
>
>
> cheers
> Bruce
>
> On Mon, 28 Jul 2014, Jason Tourville wrote:
>
>  Hi Bruce,Used v5.3 for original edits using the "recon" mode in freeview
>> so
>>
>> edits used 1 for "off" and 255 for "on".
>>
>> Jason
>>
>>
>> On Mon, Jul 28, 2014 at 9:22 AM, Bruce Fischl > >
>> wrote:
>>   Hi Jason
>>
>>   what version? Did it support recon mode? The edits need to use 1
>>   for "off" and 255 for "on", otherwise we can't track them.
>>
>>   cheers
>>   Bruce
>>   On Mon, 28 Jul 2014, Jason Tourville wrote:
>>
>> Hi Bruce,I used Freeview to edit the brainmask.mgz,
>> wm.mgz, and
>> brain.finalsurfs.manedit.mgz volumes.
>>
>> Cheers,
>> Jason
>>
>>
>> On Fri, Jul 25, 2014 at 9:23 PM, Bruce Fischl
>> 
>> wrote:
>>   Hi Jason.
>>   How were the edits done?
>>   Cheers
>>Bruce
>>
>>   > On Jul 25, 2014, at 10:40 AM, Jason
>> Tourville
>>wrote:
>>   >
>>   > Hi there,
>>   > We have performed manual volume edits on a
>> number of scans.
>>   Recently, we ran those scans through recon-all
>> with a new Tal
>>   volume target. The seg and surfaces are
>> improved using the new
>>   target but most of the manual edits performed
>> on the earlier
>>   version would improve the surfaces. Is there
>> an established
>>   means for porting the manually edited voxel
>> values to the
>>   volumes of the new re-con?
>>   >
>>   > Thanks,
>>   > Jason
>>   >
>>   >
>>   > --
>>   > Jason A. Tourville, Ph.D.
>>   > Research Assistant Professor
>>   > Department of Speech, Language,
>>   > and Hearing Sciences
>>   > Boston University
>>   > 677 Beacon St.
>>   > Boston, MA 02215
>>   > Phone: (617)353-9484
>>   > Fax: (617)353-7755
>> > ___
>> > 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.
>>
>>
>>
>>
>> --
>> Jason A. Tourville, Ph.D.
>> Research Assistant Professor
>> Department of Speech, Language,
>> and Hearing Sciences
>> Boston University
>> 677 Beacon St.
>>

[Freesurfer] surface template construction

[Jason Tourville]

We are planning to generate a surface template from edited reconstructions
of pediatric cortical surfaces (ages 3-11). We plan use this template for
surface coregistration of a large pediatric dataset that we're accruing of
roughly the same age range. I.e., we aren't simply trying to generate a
template to co-register scans used to derive that template. So the goal is
to generate the equivalent of the fsaverage but for a younger population.

My question is what is a reasonable number of surfaces for generating the
template?

Thanks,
Jason



-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] surface template N

[Jason Tourville]

We are planning to generate a surface template from edited reconstructions
of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum
number of subjects should be used to generate the template?

Thanks,
Jason


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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Re: [Freesurfer] surface template N

[Jason Tourville]

Thanks for the feedback. We may have sufficient numbers for binning.

Regarding template creation, the wiki lists two methods, one that involve
"make_average_subject" and another that involves "mris_make_template". For
our purpose, which is to generate a pediatric surface template for use on a
large dataset across several studies, is one method preferable over the
others? Do you foresee any problems with us using either method to generate
a template based on pediatric data?

Thanks,
Jason



On Thu, Dec 18, 2014 at 5:40 PM, Bruce Fischl 
wrote:
>
> Hi Jason
>
> I would say at least 15, but you can also just check to see when things
> start to asymptote. I think Christophe found there were diminishing returns
> after 12 or so, but things have changed somewhat since then, and of course
> it will depend on the variance on your population.
>
> cheers
> Bruce
>
>
>
>
> On Thu, 18 Dec 2014, Jason Tourville wrote:
>
> > We are planning to generate a surface template from edited
> reconstructions
> > of pediatric cortical surfaces (ages 3-11). Any thoughts on the minimum
> > number of subjects should be used to generate the template?
> >
> > Thanks,
> > Jason[cleardot.gif]
> >
> >
> > --
> > Jason A. Tourville, Ph.D.
> > Research Assistant Professor
> > Department of Speech, Language,
> > and Hearing Sciences
> > Boston University
> > 677 Beacon St.
> > Boston, MA 02215
> > Phone: (617)353-9484
> > Fax: (617)353-7755
> >
> >
> ___
> 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.
>
>

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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Re: [Freesurfer] surface template N

[Jason Tourville]

Thanks for looking into the Bruce. Is there a standard protocol for
checking the surface registrations?

On Fri, Dec 19, 2014 at 4:21 PM, Bruce Fischl 
wrote:
>
> Hi Jason
>
> as I discovered today poking through the code, make_average_subject calls
> mris_make_template and also creates a bunch of other useful things (average
> volumes and asegs and such), so I would use it
>
> cheers
> Bruce
>
> On Fri, 19 Dec 2014, Jason Tourville wrote:
>
> > Thanks for the feedback. We may have sufficient numbers for binning.
> >
> > Regarding template creation, the wiki lists two methods, one that involve
> > "make_average_subject" and another that involves "mris_make_template".
> For
> > our purpose, which is to generate a pediatric surface template for use
> on a
> > large dataset across several studies, is one method preferable over the
> > others? Do you foresee any problems with us using either method to
> generate
> > a template based on pediatric data?
> >
> > Thanks,
> > Jason
> >
> >
> > On Thu, Dec 18, 2014 at 5:40 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   Hi Jason
> >
> >   I would say at least 15, but you can also just check to see when
> >   things
> >   start to asymptote. I think Christophe found there were
> >   diminishing returns
> >   after 12 or so, but things have changed somewhat since then, and
> >   of course
> >   it will depend on the variance on your population.
> >
> >   cheers
> >   Bruce
> >
> >
> >
> >
> >   On Thu, 18 Dec 2014, Jason Tourville wrote:
> >
> >   > We are planning to generate a surface template from edited
> >   reconstructions
> >   > of pediatric cortical surfaces (ages 3-11). Any thoughts on
> >   the minimum
> >   > number of subjects should be used to generate the template?
> >   >
> >   > Thanks,
> >   > Jason[cleardot.gif]
> >   >
> >   >
> >   > --
> >   > Jason A. Tourville, Ph.D.
> >   > Research Assistant Professor
> >   > Department of Speech, Language,
> >   > and Hearing Sciences
> >   > Boston University
> >   > 677 Beacon St.
> >   > Boston, MA 02215
> >   > Phone: (617)353-9484
> >   > Fax: (617)353-7755
> >   >
> >   >
> >   ___
> >   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.
> >
> >
> >
> > --
> > Jason A. Tourville, Ph.D.
> > Research Assistant Professor
> > Department of Speech, Language,
> > and Hearing Sciences
> > Boston University
> > 677 Beacon St.
> > Boston, MA 02215
> > Phone: (617)353-9484
> > Fax: (617)353-7755
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
___
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dispose of the e-mail.

[Freesurfer] using custom surface template

[Jason Tourville]

External Email - Use Caution

Hello FreeSurfers,
We use a custom surface template, generated according to the instructions
in the SurfaceRegAndTemplates

instructions for inter-subject co-registration. We then do cortical
labeling and extract surface and volume stats. In the past, I would re-run
mris_register, then jump to labeling using the resulting ?h.sphere.reg
(using either a custom atlas or the labeled template surface), and then
extract stats. However, I now see that there are steps in -autorecon3 stage
of the recon-all workflow, including the pial surface generation step, that
are done after the -surfreg step, but prior to stat extraction, that depend
on ?h.sphere.reg. So it seems like I should be running the essentially the
entire -autorecon3 stage (minus -sphere and the default surface labeling
and stat extraction steps) with the custom surface template as input. Is
that the case? If so, is there an "expert flag" to run these steps of
-autorecon3 with a custom surface template (analogous to the
-custom-tal-atlas flag for early stages?)

Thanks,
Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] using custom surface template

[Jason Tourville]

External Email - Use Caution

Thanks Bruce. I was considering playing around with doing it both
ways...seeing if the parcellation based on our template makes a difference,
but sounds like it would be small. If I do and find any appreciable
difference, will let you know.

Always appreciate the speedy replies.

Best,
Jason

On Wed, Dec 19, 2018 at 2:49 PM Bruce Fischl 
wrote:

> Hi Jason
>
> we use the parcellation to figure out where we don't need to deform the
> pial surface. I expect our standard parcellation is good enough for this,
> so maybe you can just run your own posthoc?
>
> cheers
> Bruce
>
>
> On Wed, 19 Dec 2018, Jason Tourville wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfers,We use a custom surface template, generated according
> to the instructions in the
> > SurfaceRegAndTemplates instructions for inter-subject co-registration.
> We then do cortical labeling
> > and extract surface and volume stats. In the past, I would re-run
> mris_register, then jump to
> > labeling using the resulting ?h.sphere.reg (using either a custom atlas
> or the labeled template
> > surface), and then extract stats. However, I now see that there are
> steps in -autorecon3 stage of
> > the recon-all workflow, including the pial surface generation step, that
> are done after the -surfreg
> > step, but prior to stat extraction, that depend on ?h.sphere.reg. So it
> seems like I should be
> > running the essentially the entire -autorecon3 stage (minus -sphere and
> the default surface labeling
> > and stat extraction steps) with the custom surface template as input. Is
> that the case? If so, is
> > there an "expert flag" to run these steps of -autorecon3 with a custom
> surface template (analogous
> > to the -custom-tal-atlas flag for early stages?)
> >
> > Thanks,
> > Jason
> >
> > --
> > Jason A. Tourville, Ph.D.
> > Research Assistant Professor
> > Department of Speech, Language,
> > and Hearing Sciences
> > Boston University
> > 677 Beacon St.
> > Boston, MA 02215
> > Phone: (617)353-9484
> > Fax: (617)353-7755
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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Re: [Freesurfer] DKT vs. DK Freesurfer atlases

[Jason Tourville]

External Email - Use Caution

I was searching the FS list archives and came across this now very old
question. For the record, the DKT40 classifier in the FreeSurfer
distribution is the same as the one described in the paper. The DK and DKT
atlases are very similar. The goal for constructing the DKT atlas was to
create a cortical classifier that would reliably label the major cortical
gyri. We modified some of the DK region definitions to rely on boundaries
well suited to FreeSurfer’s classifier algorithm, such as sulcal fundi that
are approximated by surface depth and curvature. The boundary definitions
were also made less ambiguous, making it easier to apply them in the
training dataset more consistently.

Jason Tourville

On Thu, Jun 15, 2017 at 5:15 AM Gabor Perlaki 
wrote:

> Dear all,
>
>
> I've found an article comparing DK and DKT atlas based automatic
> segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012;
> 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/). It seems
> that using DKT40 works better than DK in most of the cortical regions
> (based on Dice).
> Does anybody know that the DKTatlas related results created by Freesurfer
> (e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the
> same DKT40 atlas used in the article and whether the DKT40 atlas related
> results were also created by Freesurfer in the article by Klein and
> Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats
> generally more reliable than the results in lh.aparc.stats?
>
>
>
> --
> Gabor Perlaki
> research associate
> Diagnostic Center of Pécs
> H-7623 Pécs, Rét str. 2.
> Tel.: 0036-30-2084367
> E-mail: petzinger.ga...@gmail.com
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> dispose of the e-mail.
>


-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] Custom templates and longitudinal processing

[Jason Tourville]

External Email - Use Caution

Hi Freesurfers,

We are collaborating with a group at Michigan that planss to use
Freesurfer's longitudinal pipeline to process T1 data collected from
children (see brief project summary below) at multiple time points. Our
role is to oversee recon QA and application of a custom cortical
parcellation labeling system. As we move to longitudinal processing, we
have a couple questions about when/how/if to apply various custom templates
that we're using.


In preparing the cross-sectional recons, we used a custom tal atlas
generated from our sample with help from Avi Snyder.


Question 1: When creating the base or running longitudinal processing,
should this atlas be specified in some manner?


We also generated a custom pediatric surface template and cortical
classifier; we co-register each subject to this template and apply the
classifier (we actually just use surf2surf to map the labeled template to
the individual subject surfaces) to generate cortical labels.


Question 2: how should we do this in the longitudinal stream? would we
register the subject's base to the pediatric surface template then use the
the resulting sphere.reg in the call to mris_ca_label?


In the longitudinal work flow, it looks like cortical labeling is done in
the longitudinal stream.


Question 3: If we notice a labeling error and correct it, is there a means
of propagating that correction across all the time points?


Question 4: If we've labeled and reviewed all the cross-sectional
time-point-one data, is there a way to map those labels to the longitudinal
stream time points that doesn't compromise the resulting labels?


Question 5: Given the project summary below, are there any other concerns
that we should be aware of when applying the longitudinal pipeline?



*Brief summary of the longitudinal study of childhood stuttering at
University of Michigan (Soo-Eun Chang)*

Over the last few years, we have collected yearly structural and functional
MRI scans from around 300 children who do and do not stutter. These are
children between the ages of 3-10 at initial scan. Scans were acquired each
year for up to 4 years (some children do not have all 4 years, but many
do). Data from year 1 has been published (Garnett et al., 2018) using a
custom labeling system and atlas. We have just finished manual editing of
the scans from years 2 – 4 and are preparing to conduct a longitudinal
analysis with all 4 years of scans in FreeSurfer.

We plan to extract cortical and subcortical measures of thickness, area,
volume, LGI, etc. and compare developmental trajectories of these measures
in the stuttering group vs. the control group. Also, because of the
longitudinal design, we have information on whether children in the
stuttering group went on to recover or if their stuttering persisted. All
children were considered stuttering at their initial visit, and based on
evaluations each year, we are able to retrospectively assign them to the
persistent group or the recovered group. In this way, in addition to
comparing morphometric measures between children who stutter and controls,
we also hope to find neural markers that help predict persistence vs.
recovery in childhood stuttering.


Many thanks for your input.

Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] VGL error

[Jason Tourville]

Hello FreeSurferers,

I run tksurfer remotely from a linux machine running CentOS (Boston
University) using Virtual GL/TurboVNC. I have been able to do this
successfully for years but have recently encountered the following error
when calling tksurfer:

surfer: tkoInitWindow(RMAUT015)
[VGL] ERROR: OpenGL error 0x0502
[VGL} ERROR: in readpixels - -
[VGL] 624: Could not Read Pixels

The error occurs after the tksurfer image window is started but before a
brain surface is displayed. I have confirmed that the error does not depend
upon what ssh tunneling tool I am using nor on what time of machine I am
using locally. Does anyone have experience with this problem? Suggested
solutions?

Cheers,
Jason



-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-6181
Fax: (617)353-7755
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[Freesurfer] FreeSurfer ROI masks for DTI tractograpy

[Jason Tourville]

Hi FreeSurfers,
I would like to use cortical surface ROIs generated in FreeSurfer to perform
inter-regional WM tractography using FSL's probtrackx tool. My understanding
is that start  seeds and targest are typically defined by mapping the
labeled gray-white surface to the DTI volume. I.e., voxels that intersect
the surface are given labeled with the appropriate ROI. Is that the case? If
so, it seems like this could potentially result in false negatives if the
alignment between the surface and a particular voxel is particularly
troublesome. For instance, if an intersected voxel (call this Voxel 1) is
primarily within the cortex, the adjacent voxel deeper within the white
matter (Voxel 2) might have a low FA. In this case, a tract starting from
Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA
threshold. No tracts would therefore be generated from Voxel 1.
Alternatively, tracts on their way to this ROI from other other regions
might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this
is, particularly given typical DTI resolution. Has anyone else had this
concern or looked into to the likelihood of it occurring.

One solution that should be fairly easy to implement would be to label both
the voxels that intersect the gray-white surface and their nearest neighbor
within the white matter. Has anyone attempted this?

Many thanks for any feedback you can provide.

Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Cognitive and Neural Systems
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-6181
Fax: (617)353-7755
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] FreeSurfer ROI masks for DTI tractograpy

[Jason Tourville]

Hi FreeSurfers,
I would like to use cortical surface ROIs generated in FreeSurfer to perform
inter-regional WM tractography using FSL's probtrackx tool. My understanding
is that start  seeds and targest are typically defined by mapping the
labeled gray-white surface to the DTI volume. I.e., voxels that intersect
the surface are given labeled with the appropriate ROI. Is that the case? If
so, it seems like this could potentially result in false negatives if the
alignment between the surface and a particular voxel is particularly
troublesome. For instance, if an intersected voxel (call this Voxel 1) is
primarily within the cortex, the adjacent voxel deeper within the white
matter (Voxel 2) might have a low FA. In this case, a tract starting from
Voxel 1 might terminate in Voxel 2 because it doesn't reach a minimum FA
threshold. No tracts would therefore be generated from Voxel 1.
Alternatively, tracts on their way to this ROI from other other regions
might stop at Voxel 2 before reaching the ROI. I'm not sure how likely this
is, particularly given typical DTI resolution. Has anyone else had this
concern or looked into to the likelihood of it occurring.

One solution that should be fairly easy to implement would be to label both
the voxels that intersect the gray-white surface and their nearest neighbor
within the white matter. Has anyone attempted this?

Many thanks for any feedback you can provide.

Jason

-- 
Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Cognitive and Neural Systems
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-6181
Fax: (617)353-7755
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] surface label generation from vertex?

[Jason Tourville]

External Email - Use Caution

Hi Freesurfers,
I would like to generate a label that extends some distance from a chosen
vertex on the surface. Is this possible in the freeview gui? Otherwise?

Many thanks for you feedback.

Best,
Jason
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