It worked! 1) First I used mri_convert and converted my sig.nii files to a chache.gii file. 2) I downloaded the files and unpacked them. 3) I went to directory fs_LR and used this command:
caret_command -deformation-map-apply fsaverage.R.registered-to-fs_LR_fix.164k_fs_LR.deform_map METRIC_NEAREST_NODE ../..j/Practice/cache.gii ../../Practice/fsaverage_to_FS1441.nii 4) Then I went to directory pals_R and used this command: caret_command -deformation-map-apply fsaverage.LR.registered-to-pals_R_fix.74k_pals_R.deform_map METRIC_NEAREST_NODE ../../Practice/fsaverage_to_FS1441.nii ../..j/Practice/FS1441_to_PALS1449.nii I did not face any error 5) Then I went to "Map Functional Volumes to Surfaces". I used "Add Volumes From Disk" and I picked the "FS1441_to_PALS1449.nii" file. 6) in "Map to Spec File" I picked the pals.R.register-with-fs_LR.74k_pals.spec that exists in pals_R folder 7) Then when used File>Open Spec File and openned the same spec file (pals.R.register-with-fs_LR.74k_pals.spec) I faced this message: Error map_data_1_8_Nov_2013_15_05_50.metric contains a different number of nodes than PALS_B12.R.AVG-FIDUCIAL_MRITOTAL.74k_pals.coord Any idea what is wrong? On Fri, Nov 8, 2013 at 10:56 AM, David Van Essen <[email protected]> wrote: > Shahin et al., > > In the SumsDB database you can go to > > http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps > > and download > http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=8293223&archive_name=inter-atlas_deformation_maps.zip > > The README.inter-atlas-registration_March2012.txt document (copied below) > provides instructions on how to carry out the inter-atlas deformations > using the accompanying dataset. If this doesn't work for you, please send > another post detailing the problem. > > David > > README.inter-atlas-registration_March2012.txt > > How to convert (register) data between 164k_fs_LR and 74k_pals meshes > > 21 March 2012 > > * Download and unzip inter-atlas_deformation_maps.zip archive: > http://sumsdb.wustl.edu/sums/directory.do?id=8291757&dir_name=Inter-atlas_deformation_maps > > * In a terminal window, change (cd) to whichever target directory (fs_L, > fs_LR, fs_R, pals_L, pals_R) represents the mesh you desire for the output > files. > > * Enter “caret_command –deformation-map-apply”, then follow the displayed > command-line instructions (see below) in order to register the files of > interest. > > > > caret_command -deformation-map-apply > > DEFORMATION MAP APPLY > > caret_command -deformation-map-apply > > <deformation-map-file-name> > > <data-file-type> > > <input-data-file-name> > > <output-data-file-name> > > [source-topology-file-name > > source-deformed-topology-file-name > > target-topology-file-name] > > > > Deform a data file. > > > > Note: "source-topology-file-name", > > "source-deformed-topology-file-name", > > and "target-topology-file-name" are only required when > > deforming coordinate FLAT files. > > > > "data-file-type" is one of: > > AREAL_ESTIMATION > > BORDER_FLAT > > BORDER_PROJECTION > > BORDER_SPHERICAL > > CELL > > CELL_PROJECTION > > COORDINATE > > COORDINATE_FLAT > > FOCI > > FOCI_PROJECTION > > LAT_LON > > METRIC_AVERAGE_TILE > > METRIC_NEAREST_NODE > > PAINT > > PROB_ATLAS > > RGB_PAINT > > SURFACE_SHAPE > > TOPOGRAPHY > > > > NOTE: > > METRIC_AVERAGE_TILE assigns target surface node average > > of nodes from the nearest tile in source surface. > > METRIC_NEAREST_NODE assigns target surface node metric > > value from nearest source node. Use this mode when > > it is important that the metric values are NOT > > modified. > > > > Run "caret_command -help-global-options" > > for parameters available to all commands. > > > On Nov 8, 2013, at 1:11 AM, SHAHIN NASR <[email protected]> > wrote: > > Thanks. Would you tell me where I can get these deformation maps (what's > their exact name)? > On Nov 7, 2013 10:24 PM, "Matt Glasser" <[email protected]> wrote: > >> You need to save the file as a GIFTI .func.gii file. Then you can use >> the fsaverage to FS_LR and FS_LR to PALS deformation maps to resample the >> data onto the PALS mesh. >> >> Peace, >> >> Matt. >> >> From: SHAHIN NASR <[email protected]> >> Reply-To: "Caret, SureFit, and SuMS software users" < >> [email protected]> >> Date: Thursday, November 7, 2013 7:42 PM >> To: <[email protected]> >> Subject: [caret-users] mapping fMRI maps generated in freesurfer on >> >> Hi, >> I have generated a group-averaged fmri activity map in freesurfer to >> be overlaid on fsaverage (freesurfer brain template). Analysis was in the >> surface space (rather than MNI305 space) and output is a sig.nii file. >> Now I want to overlay it on the PALS brain template using caret. As >> far as I see, this is not supported. When I try to use Attribute>Map >> Volumes to surfaces I can load my sig.nii file but when I use "Map to Spec >> File with Atlas", there is no fsaverage space and also when I use SPM5 >> space instead, registration is off. >> Is there any solution? Should I reanalyze my data in MNI305 space? >> Or is there anyway to correct the registration? >> >> -- >> Shahin Nasr >> >> PhD in Cognitive Neuroscience >> Martinos Imaging Center, MGH >> Harvard Medical School >> >> _______________________________________________ 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 > > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
_______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
