Re: [caret-users] mapping fMRI data to surface
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 .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 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 > > > > > > > > > [-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 > FWHMFull-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" 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: caret-users-boun...@brainvis.wustl.edu [mailto: > caret-users-boun...@brainvis.wustl.edu] 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" 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: caret-users-boun...@brainvis.wustl.edu [mailto: > caret-users-boun...@brainvis.wustl.edu] 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 > >> > >>
Re: [caret-users] mapping fMRI data to surface
It depends on how you map. See page 25 of this tutorial: http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_Tutorial_Sep22.pdf "In AFM, each node is assigned the value of the voxel in which it resides (or an interpolated value, depending on the specific algorithm chosen). In MFM, each node takes the average value after mapping the volume to each of the 12 contributing hemispheres. MFM gives a smoother map and the best estimate of spatial localization; AFM gives the localization; AFM gives the most likely peak value." While the normalization method does affect the smoothness, the AFM vs MFM choice swamps those differences. On Mar 31, 2014, at 12:43 PM, "Cheng, Hu" wrote: > 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: caret-users-boun...@brainvis.wustl.edu > [mailto:caret-users-boun...@brainvis.wustl.edu] 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 > > > > > > > > > [-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 >FWHMFull-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" 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: caret-users-boun...@brainvis.wustl.edu >> [mailto:caret-users-boun...@brainvis.wustl.edu] 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 direc
Re: [caret-users] mapping fMRI data to surface
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: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] 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 [-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 FWHMFull-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" 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: caret-users-boun...@brainvis.wustl.edu > [mailto:caret-users-boun...@brainvis.wustl.edu] 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" 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: caret-users-boun...@brainvis.wustl.edu >> [mailto:caret-users-boun...@brainvis.wustl.edu] 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 dat
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 [-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 FWHMFull-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" 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: caret-users-boun...@brainvis.wustl.edu > [mailto:caret-users-boun...@brainvis.wustl.edu] 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" 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: caret-users-boun...@brainvis.wustl.edu >> [mailto:caret-users-boun...@brainvis.wustl.edu] 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 a
Re: [caret-users] mapping fMRI data to surface
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: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] 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" 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: caret-users-boun...@brainvis.wustl.edu > [mailto:caret-users-boun...@brainvis.wustl.edu] 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 >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
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" 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: caret-users-boun...@brainvis.wustl.edu > [mailto:caret-users-boun...@brainvis.wustl.edu] 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 >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] mapping fMRI data to surface
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: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] 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 > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
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 > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] mapping fMRI data to surface
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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] mapping fMRI data to surface
Hi Catherine, There are a couple of tutorials that cover mapping fMRI data: PALS tutorial: PDF: http://sumsdb.wustl.edu/sums/download.do?id=6363278 Dataset: http://sumsdb.wustl.edu/sums/download.do?archive_id=6362705 September 2006 tutorial, part 5: http://sumsdb.wustl.edu/sums/directory.do?id=6585200&dir_name=CARET_TUTORIAL_SEPT-06 (scroll to bottom for PDF) PDF: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6594858 Dataset: http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030 Caret doesn't (yet) have any GLMs or time course regression features, so typically users do that using some other tool (e.g., fidl, FSL, AFNI, or SPM) and map the results onto the surface. We are slowly building a statistical toolkit under Attributes: Metric and Surface shape statistical operations, and if you map your subjects "magnitudes" onto the surface, then you can do simple things (e.g., one sample, two sample, or paired t-test). But as Mark McAvoy says, it's better to do your transformation before or after your statistical processing stream -- not in the middle of it. We hope to do everything in surface-land someday. If the tutorials still don't give you the answers you need, feel free to post follow-up questions. On 10/09/2006 01:35 PM, Catherine Hanson wrote: I've just started working with caret and really think it's a great package. The tutorials have also been very useful in understanding the interface and dialogs. That said, I've been able to segment left and right lobes without any problems, but can not figure out how to map fMRI data to a caret generated (version 5.5.) surface. A search of the archives produced: http://brainmap.wustl.edu/caret/html4.6/map_fmri_to_surface/map_fmri_to_surface_dialog.html#MappingAlgorithms http://brainmap.wustl.edu/help/map_individual.html but both seem out of date with caret 5.5 - The "map volumes to surfaces" dialog doesn't look like the ones I'd found. I'm also unclear about how to generate a metric file from the raw bold file. I'm using FSL rather than AFNI or SPM to generate tmaps, so I'm not sure what needs to be done to get the bold image into the appropriate caret space. I'd really appreciate any help you can give me in understanding how I go from a raw bold image to mapping that and/or zmaps onto a care-generated surface. Thanks, Catherine -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
[caret-users] mapping fMRI data to surface
I've just started working with caret and really think it's a great package. The tutorials have also been very useful in understanding the interface and dialogs. That said, I've been able to segment left and right lobes without any problems, but can not figure out how to map fMRI data to a caret generated (version 5.5.) surface. A search of the archives produced: http://brainmap.wustl.edu/caret/html4.6/map_fmri_to_surface/map_fmri_to_surface_dialog.html#MappingAlgorithms http://brainmap.wustl.edu/help/map_individual.html but both seem out of date with caret 5.5 - The "map volumes to surfaces" dialog doesn't look like the ones I'd found. I'm also unclear about how to generate a metric file from the raw bold file. I'm using FSL rather than AFNI or SPM to generate tmaps, so I'm not sure what needs to be done to get the bold image into the appropriate caret space. I'd really appreciate any help you can give me in understanding how I go from a raw bold image to mapping that and/or zmaps onto a care-generated surface. Thanks, Catherine
