wb_command -metric-smoothing does have better smoothing methods, particularly GEO_GAUSS_AREA, which takes into account variation in vertex area.
You will also need to rename the converted file to <something>.func.gii if you want to view it in workbench rather than caret. I would also suspect that your volume was smooth to begin with for your metric to be that smooth after mapping, but I haven't used MFM, so I don't know what smoothness to expect from that, if that is what you did. Tim On Mon, Mar 31, 2014 at 11:17 AM, Donna Dierker <[email protected]>wrote: > I definitely would NOT write to the caret/data_files directory. You can > copy from it, but messing with those files is not a good idea, even if the > permissions allow you to do so. Caret uses files in that directory to do > its job, so if you modify them, things will break. > > Under Attributes: Metric there are many smoothing options, but > caret_command has this feature: > > caret_command -metric-smoothing > <coordinate-file-name> > <topology-file-name> > <input-metric-file-name> > <output-metric-file-name> > <smoothing-algorithm> > <smoothing-number-of-iterations> > <smoothing-strength> > > [-geo-gauss sigma] > > [-fwhm desired-full-width-half-maximum] > > [-gauss spherical-coordinate-file-name > sigma-norm > sigma-tang > norm below cutoff (mm) > norm above cutoff (mm) > tang-cutoff (mm)] > > [-parallel] > > Smooth metric data. > > "smoothing-algorithm" is one of: > AN Average Neighbors > DILATE Dilation > FWHM Full-Width Half-Maximum > GAUSS Gaussian, requires -gauss > GEOGAUSS Geodesic Gaussian, uses -geo-gauss, default 2.0 > WAN Weighted Average Neighbors > > NOTE: Geodesic Gaussian IGNORES the strength parameter, > amount of smoothing is controlled solely by sigma and > iterations. The intent is to do one iteration of > smoothing, with the sigma specifying how much smoother > the metric is desired to be. > > I suspect wb_command has even better smoothing (seem to recall Tim C > saying something along those lines, but I can't recall the details). This > command line utility is part of Caret Workbench and needs a different > format -- GIFTI or CIFTI. You can convert caret5 metric to GIFTI by doing: > > caret_command -file-convert -format-convert XML_BASE64_GZIP my_file.metric > > At least I think that is what Tim C. told me. ;-) > > > On Mar 31, 2014, at 10:38 AM, "Cheng, Hu" <[email protected]> wrote: > > > Hi Donna, > > > > I loaded the atlas first, then I was able to see the mapping using "Map > to Caret". In the software it shows the metric file is added to the spec > file if using "Map to Spec File With Atlas", maybe it's forbidden to add > file to caret/data_files/standard_mesh_atlases/Human.PALS.LEFT? > > Now I have the metric file, could you tell me how to smooth it or is > there any way to convert it back to freesurfer which I know how to do > smoothing? > > Many thanks! > > > > Regards, > > > > Hu > > > > > > -----Original Message----- > > From: [email protected] [mailto: > [email protected]] On Behalf Of Donna Dierker > > Sent: Monday, March 31, 2014 11:07 AM > > To: Caret, SureFit, and SuMS software users > > Subject: Re: [caret-users] mapping fMRI data to surface > > > > Hi Hu, > > > > No, there's no log file, but if you check Debug Enabled (File: > Preferences), all sorts of stuff will scroll to the terminal window from > which Caret was launched. > > > > I assume you have made sure your working directory is writable by the > user running Caret. File: Set Working Directory can show you what Caret > thinks the working directory is. > > > > Donna > > > > > > On Mar 31, 2014, at 9:54 AM, "Cheng, Hu" <[email protected]> wrote: > > > >> Hi Donna, > >> > >> Thank you! There is no non-English character set on the mac. I just > wonder if there is a log file so that I can see what's wrong. > >> > >> Regards, > >> > >> Hu > >> > >> > >> -----Original Message----- > >> From: [email protected] [mailto: > [email protected]] On Behalf Of Donna Dierker > >> Sent: Friday, March 28, 2014 5:07 PM > >> To: Caret, SureFit, and SuMS software users > >> Subject: Re: [caret-users] mapping fMRI data to surface > >> > >> Do you have a non-English character set installed on this computer? We > have had issues with writing metric files when a non-English character set > was installed, but the error I recall was worded slightly different. > >> > >> > >> On Mar 28, 2014, at 1:22 PM, Cheng, Hu wrote: > >> > >>> Dear Caret users, > >>> > >>> I'm trying to map fMRI data to surface template and do surface based > smoothing. The fMRI data I used were already normalized in spm8. I ran > attribute "Map Volumes(s) to Surface(s)" accordingly to > http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MapVolumeToSurface, > I selected "Map to Spec File With Atlas" using " > Human.PALS_B12.B1-12.DEPTH_ANALYSES_LEFT.73730" SPEC file and chose "SPM5" > space. The program ran smoothly at the beginning but an error popped out in > the end showing :Unable to save metric file ...". This was done in Windows. > I repeated the same process on Mac, the program seemed to terminated > without any error except a sound, there is no metric file created in the > working directory. > >>> Thanks for your help. > >>> > >>> Regards, > >>> > >>> Hu > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> caret-users mailing list > >>> [email protected] > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> _______________________________________________ > >> caret-users mailing list > >> [email protected] > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > > caret-users mailing list > > [email protected] > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users >
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