Hi, See the PostFreeSurfer scripts in the just released HCP Pipelines v3.4 https://github.com/Washington-University/Pipelines https://github.com/Washington-University/Pipelines/releases
cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu On 9/11/14 4:28 AM, "K. Wagstyl" <kw...@cam.ac.uk> wrote: >Thanks that's really helpful. Using this info I can load into matlab and >with vertices in the 32k fs_LR space. >The last hurdle is registering subject-space freesurfer vertices surface >to the 32k fs_LR vertices, so that I can transfer the labels over to >workbench. >The caret wiki mentions a freesurfer to 32k pipeline - is it generally >available yet? > >Thanks again for all the help >Konrad > > >On 2014-09-10 23:38, Timothy Coalson wrote: >> -cifti-separate is probably what you want, if you want to use spatial >> and/or surface neighbor information (because the indices in the metric >> files will line up with the relevant surface files). Also, with the >> v1.0 release, the -file-information command will give you a quick >> summary of the mappings, like so: >> >> ALONG_ROW map type: SCALARS >> ALONG_COLUMN map type: BRAIN_MODELS >> CortexLeft: 29696 out of 32492 vertices >> CortexRight: 29716 out of 32492 vertices >> AccumbensLeft: 135 voxels >> AccumbensRight: 140 voxels >> AmygdalaLeft: 315 voxels >> AmygdalaRight: 332 voxels >> BrainStem: 3472 voxels >> CaudateLeft: 728 voxels >> CaudateRight: 755 voxels >> CerebellumLeft: 8709 voxels >> CerebellumRight: 9144 voxels >> DiencephalonVentralLeft: 706 voxels >> DiencephalonVentralRight: 712 voxels >> HippocampusLeft: 764 voxels >> HippocampusRight: 795 voxels >> PallidumLeft: 297 voxels >> PallidumRight: 260 voxels >> PutamenLeft: 1060 voxels >> PutamenRight: 1010 voxels >> ThalamusLeft: 1288 voxels >> ThalamusRight: 1248 voxels >> >> If you need to know the details of how CIFTI indices map to surface >> vertices and/or voxels, there is also this new command, which will >> give text files containing the mapping information: >> >> >>http://www.humanconnectome.org/software/workbench-command.php?function=-c >>ifti-export-dense-mapping >> [2] >> >> Tim >> >> On Wed, Sep 10, 2014 at 10:36 AM, Glasser, Matthew >> <glass...@wusm.wustl.edu> wrote: >> >>> You can look at the header (which is XML) to see, but the typical >>> order is >>> left surface, right surface, and then subcortical. Also, it is not >>> 32492 >>> vertices for the surfaces because the medial wall is excluded. If >>> for >>> some reason you need to process the different components >>> separately, you >>> can use wb_command -cifti-separate as well. >>> >>> Peace, >>> >>> Matt. >>> >>> On 9/10/14, 1:59 AM, "K. Wagstyl" <kw...@cam.ac.uk> wrote: >>> >>>> Thanks Matt - the matlab scripts are working great. >>>> Can I check the structure for grayordinate data? >>>> >>>> Is it the first 32492 vertices are left hemisphere surface, >>>> then left subcortical, >>>> then the next 32492 are right hemisphere surface, >>>> then right subcortical? >>>> >>>> Cheers, >>>> Konrad >>>> >>>> On 2014-09-09 20:48, Glasser, Matthew wrote: >>>>> I¹d recommend option ii. >>>>> >>>>> You can use the surfaces and label data in the >>>>> ${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k folder >>>>> together >>>>> with the dense timeseries data. To load the data into matlab, >>> you can >>>>> use >>>>> these attached matlab functions together with wb_command and the >>> matlab >>>>> GIFTI toolbox: >>>>> >>>>> cii = ciftiopen(Œpath/to/file¹,¹path/to/wb_command¹); >>>>> >>>>> CIFTIdata = cii.cdata; >>>>> >>>>> >>>>> Some lines of analysis code >>>>> >>>>> newcii = cii; >>>>> >>>>> newcii.cdata = AnalysisOutput; >>>>> >>>>> ciftisave(newcii,¹path/to/newfile¹,¹path/to/wb_command¹); >>>>> >>>>> Or if the data matrix is a different size from what you started >>> with >>>>> >>>>> >>> ciftisavereset(newcii,¹path/to/newfile¹,¹path/to/wb_command¹); >>>>> >>>>> And then you can view your result in Connectome Workbench¹s >>> wb_view on >>>>> the >>>>> 32k standard surfaces. >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> On 9/9/14, 10:22 AM, "K. Wagstyl" <kw...@cam.ac.uk> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I'm trying to carry out some analysis on the preprocessed >>>>>> resting-state >>>>>> fMRI but running into some problems with the *.dtseries.nii >>> files. >>>>>> The first part of the analysis was carried out on structural >>> data in >>>>>> freesurfer and matlab (using labels etc) >>>>>> Is there any way of converting the resting-state data into a >>> format >>>>>> for >>>>>> similar analysis? >>>>>> >>>>>> In other words, either >>>>>> i) mapping the time series to individuals' freesurfer-space >>> vertices >>>>>> or >>>>>> ii) importing the grayordinate data into matlab? >>>>>> >>>>>> Thanks, >>>>>> Konrad >>>>>> _______________________________________________ >>>>>> HCP-Users mailing list >>>>>> HCP-Users@humanconnectome.org >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users [1] >>>>> >>>>> >>>>> ________________________________ >>>>> The materials in this message are private and may contain >>> Protected >>>>> Healthcare Information or other information of a sensitive >>> nature. If >>>>> you are not the intended recipient, be advised that any >>> unauthorized >>>>> use, disclosure, copying or the taking of any action in reliance >>> on >>>>> the contents of this information is strictly prohibited. If you >>> have >>>>> received this email in error, please immediately notify the >>> sender via >>>>> telephone or return mail. >>> >>> ________________________________ >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. >>> If you are not the intended recipient, be advised that any >>> unauthorized use, disclosure, copying or the taking of any action in >>> reliance on the contents of this information is strictly prohibited. >>> If you have received this email in error, please immediately notify >>> the sender via telephone or return mail. >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users [1] >> >> >> >> Links: >> ------ >> [1] http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> [2] >> >>http://www.humanconnectome.org/software/workbench-command.php?function=-c >>ifti-export-dense-mapping > >_______________________________________________ >HCP-Users mailing list >HCP-Users@humanconnectome.org >http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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