Thank you! It worked very well. One more question, is there any process of smoothing in the mapping from volume to surface? The resulted surface already has a FWHM of 14 mm (maybe it's due to the normalization in SPM).
Regards, Hu -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Donna Dierker Sent: Monday, March 31, 2014 12:18 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] mapping fMRI data to surface 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
