[caret-users] ROIs from freesurfer?
j janssen
joost.janssen76 at gmail.com
Wed Sep 17 12:11:41 CDT 2008
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?
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.
does this make sense?
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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caret_command -file-substitution
caret_command -image-combine
caret_command -image-compare
caret_command -image-format-convert
caret_command -image-insert-text
caret_command -image-resize
caret_command -image-to-web-page
caret_command -image-view
caret_command -metric-clustering
caret_command -metric-composite
caret_command -metric-composite-identified-columns
caret_command -metric-correlation-coefficient-map
caret_command -metric-file-create
caret_command -metric-in-group-difference
caret_command -metric-information
caret_command -metric-math-postfix
caret_command -metric-multiple-correlation-coefficient-map
caret_command -metric-set-column-name
caret_command -metric-set-column-to-scalar
caret_command -metric-smoothing
caret_command -metric-statistics-anova-one-way
caret_command -metric-statistics-anova-two-way
caret_command -metric-statistics-coordinate-difference
caret_command -metric-statistics-interhemispheric-clusters
caret_command -metric-statistics-kruskal-wallis
caret_command -metric-statistics-levene-map
caret_command -metric-statistics-normalization
caret_command -metric-statistics-one-sample-t-test
caret_command -metric-statistics-paired-t-test
caret_command -metric-statistics-shuffled-cross-correlation-map
caret_command -metric-statistics-shuffled-t-map
caret_command -metric-statistics-subtract-group-average
caret_command -metric-statistics-t-map
caret_command -metric-statistics-two-sample-t-test
caret_command -metric-statistics-z-map
caret_command -metric-twin-comparison
caret_command -metric-twin-paired-data-diffs
caret_command -paint-add-columns
caret_command -paint-assign-nodes-relative-to-line
caret_command -paint-assign-to-nodes
caret_command -paint-composite
caret_command -paint-file-create
caret_command -scene-create
caret_command -script-convert
caret_command -script-run
caret_command -script-variable-read
caret_command -script-variable-set
caret_command -show-scene
caret_command -show-surface
caret_command -show-volume
caret_command -spec-file-add
caret_command -spec-file-clean
caret_command -spec-file-copy
caret_command -spec-file-create
caret_command -spec-file-directory-clean
caret_command -spec-file-zip
caret_command -statistic-set-random-seed
caret_command -statistic-unit-test
caret_command -stereotaxic-spaces
caret_command -study-metadata-duplicates
caret_command -surface-affine-regression
caret_command -surface-align-to-standard-orientation
caret_command -surface-apply-transformation-matrix
caret_command -surface-average
caret_command -surface-border-create-parallel-border
caret_command -surface-border-cutter
caret_command -surface-border-delete
caret_command -surface-border-draw-around-roi
caret_command -surface-border-draw-geodesic
caret_command -surface-border-draw-metric
caret_command -surface-border-intersection
caret_command -surface-border-landmark-identification
caret_command -surface-border-link-to-focus
caret_command -surface-border-merge
caret_command -surface-border-nibbler
caret_command -surface-border-projection
caret_command -surface-border-resample
caret_command -surface-border-reverse
caret_command -surface-border-unprojection
caret_command -surface-border-variability
caret_command -surface-crossover-check
caret_command -surface-curvature
caret_command -surface-foci-create
caret_command -surface-foci-delete
caret_command -surface-foci-projection
caret_command -surface-foci-unprojection
caret_command -surface-folding-measures
caret_command -surface-generate-inflated
caret_command -surface-identify-sulci
caret_command -surface-inflate
caret_command -surface-information
caret_command -surface-place-foci-at-limits
caret_command -surface-place-focus-at-extremum
caret_command -surface-region-of-interest-selection
caret_command -surface-roi-coord-report
caret_command -surface-roi-statistical-report
caret_command -surface-smoothing
caret_command -surface-sulcal-depth
caret_command -surface-sulcal-identification-probabilistic
caret_command -surface-to-cerebral-hull
caret_command -surface-to-segmentation-volume
caret_command -surface-to-volume
caret_command -surface-topology-disconnect-nodes
caret_command -surfaces-to-segmentation-volume-mask
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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> 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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