[caret-users] ROIs from freesurfer?
Donna Dierker
donna at brainvis.wustl.edu
Wed Sep 17 13:45:51 CDT 2008
On 09/17/2008 12:11 PM, j janssen wrote:
> Hi,
>
> thanks Donna for your great reply to my previous mail. 2 additional
> questions: if i had a (binary) mask of adjacent cortical (grey matter)
> segmentations from freesurfer (for example, superior and middle
> temporal gyrus).
>
> could i use this mask as a ROI in caret? if so, how would i go about
> creating a Caret-readable-usable ROI from this binary nifti mask?
cd my_subject/mri
mri_convert aseg.mgz aseg.nii
caret_command -volume-map-to-surface rh.MIDTHICKNESS.coord
rh.CLOSED.topo "" outfile.paint METRIC_ENCLOSING_VOXEL aseg.nii
Enter caret_command -volume-map-to-surface with no other arguments to
get the full usage on that command.
I am not sure whether mapping it as a paint (ROI) will work properly,
since Caret might want the parcellation intensity values to be like 1,
2, 3, ... There are some gaps in the attached Freesurfer aseg LUT.
At worst, you can map it as a metric, and then use Surface: ROI and
threshold the metric value such that only the STS nodes are selected.
Then you can assign a paint to them. Alternatively, you can threshold
the aseg.nii volume itself and pull out the desired ROIs in volume-land
somehow. Then map.
>
> thus, i would import pial, white, and inflated surfaces from FSS into
> caret, do the necessary steps to make the surface-shape file and then
> -surface-roi-statistical-report using the ROI mask.
If you have used "caret_command -surface-identify-sulci", then you have
already used something like this to import your surfaces from Freesurfer
into Caret:
http://pub:download@brainmap.wustl.edu/pub/donna/SCRIPTS/FREESURFER/freesurfer2caret.sh
login pub
password download
Along with caret_command -surface-roi-statistical-report, you'll also
need caret_command -surface-region-of-interest-selection, in order to
generate the ROI file that is input to the
-surface-roi-statistical-report function. This is where your paint file
(from the above mapping) will be used.
>
> does this make sense?
I think so -- at least for some questions, although I confess I haven't
read Alex's paper as thoroughly as I'd like.
>
> thanks,
> -joost
>
>
> Hi Joost,
>
>
> The Fornito paper used a ROI approach, i.e., the cingulate sulcus. It
> looks like they took great pains to define the region consistently
> across subjects, as is the norm; ROI definition (and consistent
> delineation) is often the hard part. Assuming Freesurfer 4.05 is new
> enough to have the cortical parcellation, perhaps you can use it to
> define your cingulate sulcus.
> In caret-land, you can then approach things two ways:
>
>
> * Without registration: Skip registration. Somehow export a
> parcellation from Freesurfer that, for each node, assigns 0 to nodes
> outside the ROI, 1 to nodes inside it. Then, use caret_command
> -surface-roi-statistical-report and each subject's surface_shape file
> to output the mean depth in the ROI. * With registration: Register
> your subjects to the PALS atlas. Somehow represent the ROI in the PALS
> standard mesh (perhaps by creating a probabilistic atlas of registered
> Freesurfer parcellations and then thresholding it). Then, use
> caret_command -surface-roi-statistical-report and each subject's
> surface_shape file to output the mean depth in the ROI. The advantage
> of this route is that you can do more than just output a summary stat
> for an entire region, which may not be very informative. You can
> instead create a t-map (or f-map) across groups/hemispheres, which
> gives you greater spatial specificity (e.g., see tmap figure in
> http://dx.doi.org/10.1016/j.neuroimage.2008.07.034). The latter can be
> done on either an entire hemisphere or restricted to a ROI (the latter
> being represented by a custom CUT topo file that excludes nodes
> outside the region). While registration gives you more analytic
> options, it also is work. We have an automated border drawing script,
> but it's not ready for public consumption yet. For now, you still need
> to register as defined here:
> http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html/
> http://brainmap.wustl.edu/caret/pdf/Caret_5.5_Tutorial_Segment.pdf
>
>
> Attached is a list of potentially useful caret_command features.
>
> Donna
>
> On 09/05/2008 08:35 AM, j janssen wrote:
>
>
> Hi,
>
> i´m using Caret5.6.
>
> i´ve used Freesurfer (4.05) to create white and pial surfaces.
>
>
> my goal is to use these surfaces to get measures of sulcal depth
> for a brain region (either a hemisphere or a specific sulcus), so
> that these can be statistically compared, such as in Fornito et al
> 2008, HBM 29: 478-489. after various steps i´ve succesfully used
> "caret_command -surface-identify-sulci" on the brains in my
> dataset. does anybody have some pointers as how to proceed from
> this point?
>
> thanks a lot,
> -joost
>
> ------------------------------------------------------------------------
>
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>
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>
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> * [caret-users] Question
> <http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00223.html>
> r.mtibaa
> o Re: [caret-users] Question
> <http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00224.html>
> Donna Hanlon
> o Re: [caret-users] Question
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> Donna Hanlon
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> j janssen
> +
> Re: [caret-users] question Donna Dierker
>
> Reply via email to
>
>
>
> On Fri, Sep 5, 2008 at 3:35 PM, j janssen <joost.janssen76 at gmail.com
> <mailto:joost.janssen76 at gmail.com>> wrote:
>
> Hi,
>
> i´m using Caret5.6.
>
> i´ve used Freesurfer (4.05) to create white and pial surfaces.
> my goal is to use these surfaces to get measures of sulcal depth
> for a brain region (either a hemisphere or a specific sulcus), so
> that these can be statistically compared, such as in Fornito et al
> 2008, HBM 29: 478-489. after various steps i´ve succesfully used
> "caret_command -surface-identify-sulci" on the brains in my
> dataset. does anybody have some pointers as how to proceed from
> this point?
>
> thanks a lot,
> -joost
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>
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