mri_ca_label
mri_ca_label [<options>] invol1 [invol2 ...] xform gcafile outvol
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| Argument | Explanation |
|---|---|
| invol1 [invol2 ...] | input volume(s) |
| xform | transform file |
| gcafile | |
| outvol | output volume |
| Argument | Explanation |
|---|---|
| -cross-sequence | label a volume acquired with sequence different than atlas |
| -nogibbs | disable gibbs priors |
| -wm <path> | use wm segmentation |
| -conform | interpolate volume to be isotropic 1mm^3 |
| -normpd | normalize PD image to GCA means |
| -tl <gca_tl> | use file to label thin temporal lobe |
| -debug_voxel <x> <y> <z> | debug voxel |
| -debug_node <x> <y> <z> | debug node |
| -debug_label <int n> | debug label |
| -tr <float n> | set TR in msec |
| -te <float n> | set TE in msec |
| -alpha <float n> | set alpha in radians |
| -example <mri_vol> <segmentation> | use T1 (mri_vol) and segmentation as example |
| -pthresh <float n> | use p threshold n for adaptive renormalization (default=.7) |
| -niter <int n> | apply max likelihood for n iterations (default=2) |
| -novar | do not use variance in classification |
| -regularize <float n> | regularize variance to be sigma+nC(noise) |
| -nohippo | do not auto-edit hippocampus |
| -fwm <mri_vol> | use fixed white matter segmentation from wm |
| -mri <mri_vol> | write most likely MR volume to mri_vol |
| -heq <mri_vol> | use histogram equalization from mri_vol |
| -renorm <mri_vol> | renormalize using predicted intensity values in mri_vol |
| -flash | use FLASH forward model to predict intensity values |
| -flash_params <filename> | use FLASH forward model and tissue params in filename to predict |
| -renormalize <wsize> <iter> | renorm class means <iter> times after initial label with window of <wsize> |
| -r <mri_vol> | set input volume |
| -h | use GCA to histogram normalize input image |
| -a <int n> | mean filter n time to conditional densities |
| -w <int n> <filename> | write snapshots of gibbs process every n times to filename |
| -m <mri_vol> | use mri_vol to mask final labeling |
| -e <int n> | expand |
| -n <int n> | set max iterations to n (default=200) |
| -f <int f> <float t> | filter labeled volume with threshold t (default=.5) mode filter f (default=0)times |
| -L <mri_vol> <LTA> | longitudinal processing: mri_vol is label from tp1, LTA is registration from tp1 to current data |
| -RELABEL_UNLIKELY <1/0> <wsize> <sigma> <thresh> | reclassify voxels at least <thresh> std devs from the mean using a <wsize> Gaussian window (with <sigma> standard dev) to recompute priors and likelihoods |
| Output | Explanation |
|---|---|
| outvol | output volume |
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None
Report bugs to <freesurfer@nmr.mgh.harvard.edu>
mri_cc