## Note: This page was created with the CommandTemplate ## ## If you're modifying this page please take a look at the ## latest version of CommandTemplate to ensure that you're ## using the latest version of the CommandTemplate ## ## See HelpOnCommandTemplate for description of formatting <> '''Index''' <> = Name = mri_ca_label = Description = This program is used to label subcortical structures based in GCA model. = Synopsis = mri_ca_label [] invol1 [invol2 ...] xform gcafile outvol = Arguments = == Positional Arguments == || invol1 [invol2 ...] || input volume(s) || || xform || transform file || || gcafile || Gaussian classifier atlas file || || outvol || output volume || == Required Flagged Arguments == None == Optional Flagged Arguments == || -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 || || -topo_dist_thresh dist || do not relabel ventricle segments that are disconnected from the main body of the ventricle, are less than dist mm from the largest segment, and have a volume greater than topo_volume_thresh1 || || -topo_volume_thresh1 volume || do not relabel ventricle segments that are disconnected from the main body of the ventricle, are less than dist mm from the largest segment, and have a volume greater than volume. || || -topo_volume_thresh2 volume || do not relabel ventricle segments that are disconnected from the main body of the ventricle and have a volume greater than volume || || -t1 gca_t1 || use file to label thin temporal lobe || || -normpd || normalize PD image to GCA means || || -debug_voxel x y z || debug voxel || || -debug_node x y z || debug node || || -debug_label || debug label || || -tr TR || set TR in msec || || -te TE || set TE in msec || || -alpha ALPHA || set alpha in radians || || -example mri_vol segmentation || use T1 (mri_vol) and segmentation as example || || -pthresh thresh || use p threshold n for adaptive renormalization (default=.7) || || -niter n || apply max likelihood for n iterations (default=2) || || -novar || do not use variance in classification || || -regularize reg || 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 || reenorm 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 n || mean filter n time to conditional densities || || -w n filename || write snapshots of gibbs process every n times to filename || || -m mri_vol || use mri_vol to mask final labeling || || -e n || expand || || -n n || set max iterations to n (default=200) || || -f f thresh || filter labeled volume with threshold thresh (default=.5) mode filter f (default=0)times || || -nowmsa || disables WMSA labels (hypo/hyper-intensities), selects second most probable label for each WMSA labelled voxel || || -write_probs || Write label probabilities to filename. || || -L || Longitudinal processing mri_vol is label from tp1, LTA is registration from tp1 to current data || || -RELABEL_UNLIKELY <1/0> || Reclassify voxels at least standard devs from the mean using a Gaussian window (with standard devs) to recompute priors and likelihoods. || = Outputs = || outvol || output volume || = Bugs = None = See Also = [[mri_cc]] = Links = FreeSurfer, FsFast = Reporting Bugs = Report bugs to = Author/s = BruceFischl