Hi Donna,
Thank you for your help. From what I understand, the topology files from each subject have to be compiled (using caret_command -metric-composite) into one, and that file is then entered into the ANOVA test. My question however, is regarding the generation of the open topo files for each subject. I have used freesurfer_to_fs_LR pipeline, and I'm wondering if the topo files generated (there is only one for each subject) are indeed the open topo file, because looking at the script for freesurfer_to_fs_LR it looks like it is the closed topo file. Any advice on how to obtain an open topo file? Also, to clarify, the first parameter in the ANOVA test is a fiducial coord file. I have used caret_command -surface-average to generate an average fiducial file for each hemisphere. Is this correct? Please let me know. Thanks, Eshita On Wed, Nov 13, 2013 at 10:50 PM. Donna Dierker wrote: >Hi Eshita, > >I always use the open topology for this purpose (i.e., excludes only medial >wall vertices). The files here will be helpful: >http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k/ >login pub >password download > >You can get them all in this zip file: > >http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2013_11/TFCE_164k.zip > >Just to explain what is going on, the areas in the TFCE/cluster computations >are computed on the Conte69 mean mid thickness, with the open topo file >(excluding medial wall). The distortion maps pump up the areal value where >substantial smoothing occurs as a result of averaging individuals' coordinate >files (e.g., high 3D variability). The intent is to make the areas more like >an individual's area would be in that region. For folks not attuned to what >you are doing, this is during group analysis. > >Cheers, > >Donna > >On Tue, Nov 12, 2013 at 1:18 PM, Eshita Shah <[email protected]> wrote: > Hello, > > Thanks for your input. I successfully was able to use freesurfer_to_fs_LR > Pipeline to import my FreeSurfer files into caret, however when I try > running ANOVA, it asks for certain files that have not been generated by > the pipeline. Specifically, how do I generate the > "distortion-metric-shape-file" that is being asked for? Lastly, is the > .topo file that is generated via the pipeline the open topo file or closed? > Previously I was able generate the closed topo file, so I'm not sure if the > freesurfer_to_fs_LR pipeline does the same. The parameter required for the > ANOVA analysis is the open topo file. > > Thank you, > Eshita Shah > > > On Thu, Nov 7, 2013 at 4:12 PM, Rouhollah Abdollahi <[email protected]>wrote: > >> Hi >> Actually the code import the original data from freesurfer to caret then >> automatically you will have different node number for different subjects >> and hemispheres. To have the same mesh you can use Freesurfer_to_fs_LR >> Pipeline which is available in the caret website. It imports all the data >> to the same mesh which here is fs_LR mesh. >> Hope it helps >> Best >> Rouhi >> On Nov 8, 2013 12:06 AM, "Eshita Shah" <[email protected]> wrote: >> >>> Hello, >>> >>> I have just recently started using Caret, and I am running the >>> freesurfer2caret.sh script in order to import my FreeSurfer files into >>> Caret as well as generate sulcal depth for all subjects. I tried doing a >>> One-Way ANOVA test, but I've realized that the number of nodes in the >>> metric/surface_shape files for the two subjects are different. How is it >>> possible that the same script is creating files with different node >>> numbers? Also, within each subject, sometimes the node numbers for the left >>> and right hemisphere are different as well. How can I resolve this issue so >>> I can successfully run ANOVA on my subjects? >>> >>> Any help would be appreciated. >>> >>> Thank you, >>> Eshita Shah >>> >>> _______________________________________________ >>> 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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