I have made some changes in the default behavior of the FSFAST preproc-sess command in anticipation of pending updates to FSFAST. These will be live in the next update to dev (probably Monday):
1. It will now only run a stage if the input is newer than the output. Eg, if you are running MC and smoothing, it will check whether the raw data has changed before rerunning MC, and it will check whether MC has changed before rerunning smoothing. If the output of a stage does not exist, it will of course run that stage. Automatic update can be turned off with -force or -no-update. This feature can be quite convenient as you can pass preproc-sess all of your sessions and it will only rerun the stages that are needed.
2. INorm will NOT be run by default. The new version of selxavg (selxavg3-sess) performs intensity normalization in a different way that does not require the mean intensity (.meanval) to be computed in advance. You can turn on INorm with the -inorm flag.
3. In addtion to these default changes, I've added slice-timing correction to preproc-sess. It is not on by default. You turn it on by specifying a slice order with -sliceorder.
See preproc-sess -help for more info.
I'll keep you posted as I make more changes.
doug
On Tuesday, I will change the default FSFAST output format to NIFTI. This will be done by setting an environment variable in the DEV environment, namely
setenv FSF_OUTPUT_FORMAT nii
If you want to continue to use bshort/bfloat, then set the following in your own environment:
setenv FSF_OUTPUT_FORMAT bhdr
Note that this only affects the output format. The tools should read any format as input (ie, you do not need to change exising data to NIFTI).
You can also unpack directly to NIFTI with unpacksdcmdir (or mri_convert).
You can also use any of these formats:
setenv FSF_OUTPUT_FORMAT nii.gz setenv FSF_OUTPUT_FORMAT mgh setenv FSF_OUTPUT_FORMAT mgz
Doubtless there will be some glitches along the way, so be patient:).
doug
freesurfer@nmr.mgh.harvard.edu
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Doug Greve