caret_command -volume-map-to-surface-pals
<input-metric-or-paint-file-name>
<output-metric-or-paint-file-name>
<stereotaxic-space-name>
<structure>
<algorithm>
<input-volume-file-name>
[-metric-afm]
[-metric-mfm]
[-metric-min]
[-metric-max]
[-metric-std-dev]
[-metric-std-error]
[-metric-all-cases]
[-paint-afm]
[-paint-most-common]
[-paint-most-common-no-unknown]
[-paint-all-cases]
[-av average-voxel-neighbor-cube-size (mm)]
[-bf brain-fish-max-distance
brain-fish-splat factor]
[-g gaussian-neighbor-cube-size (mm)
sigma-norm
sigma-tang
norm below cutoff (mm)
norm above cutoff (mm)
tang-cutoff (mm)]
[-mv maximum-voxel-neighbor-cube-size (mm)]
[-sv strongest-voxel-neighbor-cube-size (mm)]
Map a volume to the PALS atlas surfaces.
"algorithm" is one of:
METRIC_AVERAGE_NODES
METRIC_AVERAGE_VOXEL
METRIC_ENCLOSING_VOXEL
METRIC_GAUSSIAN
METRIC_INTERPOLATED_VOXEL
METRIC_MAXIMUM_VOXEL
METRIC_MCW_BRAIN_FISH
METRIC_STRONGEST_VOXEL
PAINT_ENCLOSING_VOXEL
METRIC MAPPING OPTIONS
"-metric-afm" Map to the average fiducial surface
(Average Fiducial Mapping).
"-metric-mfm" Multi-Fiducal-Mapping - Output the
average of mapping to all PALS cases (Multi-Fiducial-
Mapping)
"-metric-min" Output the minimum of mapping to all
PALS cases.
"-metric-max" Output the maximum of mapping to all
PALS cases.
"-metric-std-dev" Output the sample standard deviation
of mapping to all PALS cases.
"-metric-std-error" Output the standard error of
mapping to all PALS cases.
"-metric-all-cases" Output the mapping to each of the
PALS cases.
PAINT MAPPING OPTIONS
"-paint-afm" Map to the average fiducial surface
(Average Fiducial Mapping).
"-paint-most-common" Output the most common paint
of mapping to all PALS cases.
"-paint-most-common-no-unknown" Output the most common
paint of mapping to all PALS cases but exclude the
unidentified nodes.
"-paint-all-cases" Output the mapping to all PALS
cases.
Stereotaxic Spaces Supported
711-2B
711-2C
AFNI
FLIRT
MRITOTAL
SPM2
SPM5
SPM95
SPM96
SPM99
"structure" is one of:
LEFT
RIGHT
If the input metric or paint file name is not an empty string
(""), the newly create metric or paint columns will be
appended to the file and then written with the output file
name.
On 12/20/2010 01:30 PM, Koene Van Dijk wrote:
> Hi caret users,
>
> I'm fairly new to caret and am using v5.616 on a linux box.
>
> Since I want to map a large number of volumes (in SPM2 MNI space) to the
> surface I'm using carret command. In particular:
>
> caret_command -volume-map-to-surface
> <coordinate-file-name>
> <topology-file-name>
> <input-metric-or-paint-file-name>
> <output-metric-or-paint-file-name>
> <algorithm>
> <input-volume-file-names>
>
> When I use as "coordinate-file-name" this file
> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord
>
> the result I get is the AFM (average fiducial mapping) version (which is
> correct because I gave it the above coordinate file).
>
> I have figured out that for MFM the GUI uses this list of coordinate files:
> ----------------------
> Multi-Fiducial Mapping (MFM); Volume Comment: FSL3.2beta; MFM using
> surface files:
> Human_Buck_Case01.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case02.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case03.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case04.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case05.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM2.clean.73730.coord
> Human_Buck_Case06.L.F.RegToPALS_B12.LR.FIDUCIAL_SPM2.clean.73730.coord
> Human_Buck_Case07.L.M.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case08.L.M.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case09.L.M.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case10.L.M.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case11.L.M.RegToPALS_B12.LR.FIDUCIAL_SPM2.73730.coord
> Human_Buck_Case12.L.M.RegToPALS_B12.LR.FIDUCIAL_SPM2.clean.73730.coord
> ----------------------
>
>
> My question is:
> How can I use the same command line tool to map a volume to a surface but
> get the MFM (multi-fiducial mapping) version?
>
> Thanks for any tips!
>
> -Koene Van Dijk
>
>
>
>
>
>
>
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> at
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