Correction: "It faced this error" Procedure:
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 3:11 PM, SHAHIN NASR <[email protected]>wrote: > 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 > -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
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