Hi Matt, Thanks for your advise. I found this "connectome workbench" much more useful and liked much better than MRIcron that I mentioned before!! Now I am trying to handle the data, reading "Tutorial," but if I have any difficulty or problems, let me ask again.
Thanks a lot! Ikko 2014-05-04 12:38 GMT+09:00 Glasser, Matthew <[email protected]>: > You should view those files in Connectome Workbench. > > Peace, > > Matt. > > From: 木村一皓 <[email protected]> > Date: Saturday, May 3, 2014 at 10:36 PM > To: "Elam, Jennifer" <[email protected]> > Cc: "[email protected]" <[email protected]> > > Subject: Re: [HCP-Users] Questions about the behavioral data > > Thanks Jenn, > > However I have another problem. > > Though I tried to open the file > "MNINonLinear/Native/100307.L.aparc.native.label.gii" and > "MNINonLinear/100307.aparc.164k_fs_LR.dlabel.nii" you've mentioned, I > have problem in seeing the data. > I of course installed MRIcron from ( > http://www.mccauslandcenter.sc.edu/mricro/mricron/install.html), but the > latter have a problem with warnig"the header file is not in NIfTi > format...". What should I install to see both of the data? > > And ,if there is, please tell me the code to see them in "Matlab." > > Thanks a lot! > > Ikko > > > > > > 2014-05-03 5:57 GMT+09:00 Jennifer Elam <[email protected]>: > >> Hi Ikko, >> >> >> >> The Freesurfer-derived volumes and average thickness of the Desikan ROI >> parcels (e.g. right cuneus) for the individual subjects are also included >> in the behavioral data that you downloaded as a CSV (from Quick Downloads). >> >> >> >> You can also browse these measures by subject in the ConnectomeDB >> dashboard accessible by clicking the Explore [BETA] button for All >> Subjects. Once you are on the Dashboard, click Add Tab on the right and >> select FreeSurfer. Scroll to the right to browse summary volumes, or >> volume, avg thickness, or surface area for each ROI. >> >> >> >> If you want more detailed info than what comes out of FreeSurfer, you can >> get it by working with the individual subjects imaging data, but someone >> else will have to give you advice on how best to do that. >> >> Best, >> >> Jenn >> >> >> >> Jennifer Elam, Ph.D. >> Outreach Coordinator, Human Connectome Project >> Washington University School of Medicine >> Department of Anatomy and Neurobiology, Box 8108 >> 660 South Euclid Avenue >> St. Louis, MO 63110 >> 314-362-9387 >> [email protected] >> www.humanconnectome.org >> >> >> >> *From:*木村一皓 [mailto:[email protected]] >> *Sent:* Thursday, May 01, 2014 9:59 PM >> *To:* Jennifer Elam >> *Cc:* [email protected] >> *Subject:* Re: [HCP-Users] Questions about the behavioral data >> >> >> >> Thanks Jenn, >> >> >> >> I'm always really thankful for your courteous reply. >> >> And, sorry, one more qustion about question 2. >> >> >> >> I am thinking about getting the data of volume or thickness of brain in >> more detail on each subject. >> >> (e.g. volume of gray matter or white matter on rigtht cuneus) >> >> Can I do this through http://surfer.nmr.mgh.harvard. >> edu/fswiki/CorticalParcellation with data of ConnectomeDB? >> >> >> >> Thanks again, >> >> Ikko >> >> >> >> >> >> >> >> 2014-05-02 2:33 GMT+09:00 Jennifer Elam <[email protected]>: >> >> Hi Ikko, >> >> >> >> 1. If you downloaded the behavioral data CSV, the Penn Progressive >> Matrices scores for each subject are listed under the abbreviations >> PMAT24_A_CR, PMAT24_A_SI, PMAT24_A_RTCR. If you open the file in >> Excel or another spreadsheet program these should be columns AR-AT. The key >> to all of the abbreviations used for the HCP behavioral and individual >> difference measures is in the Q3 Reference Manual Appendix >> VII<http://humanconnectome.org/documentation/Q3/HCP_Q3_Release_Appendix_VII.pdf>, >> available on the HCP website (www.humanconnectome.org) though the >> Documentation tab. >> >> >> >> 2. The HCP behavioral data includes the surface area of each >> region in the FreeSurfer Desikan atlas cortical parcellation (more info at >> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and in >> https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf) >> created for each subject in the HCP preprocessing pipelines. >> >> If you download the structural preprocessed package for a particular >> subject, Desikan atlas surface and volume ROI parcel labels generated in >> Freesurfer are included for the volume and different surface meshes in the >> directory tree in NIFTI volume (e.g. T1w/aparc+aseg.nii.gz), GIFTI >> surface (e.g. MNINonLinear/Native/100307.L.aparc.native.label.gii) and >> CIFTI (e.g. MNINonLinear/100307.aparc.164k_fs_LR.dlabel.nii), which >> includes surface labels from both hemispheres). See the Q3 Release Ref >> Manual Appendix >> III<http://humanconnectome.org/documentation/Q3/HCP_Q3_Release_Appendix_III.pdf>, >> Section B: Preprocessed Data Directory Structure, Structural Volume and >> Surface Data for a list of the files provided in the structural >> preprocessed package. >> >> >> >> 3. The HCP recruits twins and their non twin siblings to be >> subjects in the study. The “unrelated” refers to the fact that all subjects >> in the group (e.g. of 80) are not part of the same family, i.e. they are >> not genetically related to one another. We provide groups of unrelated >> subjects to allow researchers to do initial explorations with the open >> access data without being concerned about heritability issues. >> Investigators must apply for restricted >> access<http://humanconnectome.org/data/restricted-access/index.html>to view >> the family structure of subjects in the database. >> >> >> >> Best, >> >> Jenn >> >> Jennifer Elam, Ph.D. >> >> Outreach Coordinator, Human Connectome Project >> >> Washington University School of Medicine >> >> Department of Anatomy and Neurobiology, Box 8108 >> >> 660 South Euclid Avenue >> >> St. Louis, MO 63110 >> >> 314-362-9387 >> >> [email protected] >> >> www.humanconnectome.org >> >> *From:*[email protected] [mailto: >> [email protected]] *On Behalf Of *???? >> *Sent:* Wednesday, April 30, 2014 8:51 AM >> *To:* [email protected] >> *Subject:* [HCP-Users] Questions about the behavioral data >> >> >> >> Hi, >> >> >> >> I am now seeing the data of "behavioral data" from "Quick Downloads," >> having several problems. >> >> >> >> My questions are: >> >> >> >> 1. I know that HCP have datas of "Fluid Intelligence(Pennn Progressive >> Matrices)" on each subjects with number of correct responses, total skipped >> items, and median reaction time, but I can't see them from "behvioral data." >> >> Where can I find them for each subject? >> >> >> >> 2.Downloading the "behavioral data", now I can have the data of "suraface >> area." >> >> Can I have the information of which part they decided as a particular >> region(say right cuneus) in nii files(or else) for all 66 regions? >> >> >> >> 3.From "HCP MR Data Q3 Releases," I can see unrelated subjects(like "80 >> Unrelated Subjects") >> >> Does "unrealted" mean that they are the data of not-so-special people (or >> the data with having Gaussian manner) in U.S.? >> >> >> >> Sorry for taking your time, >> >> Ikko Kimura >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> > > _______________________________________________ > HCP-Users mailing list > [email protected] > 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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