Thank you Tim! I have now concatenated the myelin maps and going to do the permutation test with Palm. I plan to do a whole brain vertex level comparison, do you know which existing mask should I use to group level analysis? Thanks!
Best, Nailin 2016-11-22 16:48 GMT-05:00 Timothy Coalson <[email protected]>: > wb_shortcuts comes with the latest release of workbench, v1.2.3 - however, > there are a few bugs in the version that was released that way, and a newer > version is available here: > > https://github.com/Washington-University/wb_shortcuts > > If you want just the script itself, use this link: > > https://raw.githubusercontent.com/Washington-University/wb_ > shortcuts/master/wb_shortcuts > > I noticed you used "./wb_command", suggesting that you don't have the > workbench executables in your $PATH. They will need to be in your $PATH in > order for wb_shortcuts to work. > > As a final note, there is also wb_command -metric-merge and wb_shortcuts > -metric-concatenate, which do the same thing for .func.gii files, in case > you actually do need to use the non-cifti files. > > Tim > > > On Tue, Nov 22, 2016 at 2:57 PM, nailin yao <[email protected]> wrote: > >> where can I download wb_shortcuts command? Thanks! >> >> Best, >> Nailin >> >> 2016-11-22 15:28 GMT-05:00 Harms, Michael <[email protected]>: >> >>> >>> Two things: >>> 1) That is not the proper syntax for using -cifti-merge. You need to >>> repeat the -cifti argument separately for *each* cifti file. I suggest >>> that you use wb_shortcuts -cifti-concatenate instead to make it simpler. >>> 2) A .func.gii is not a CIFTI file. Use the .dscalar.nii version of >>> the myelin maps as input. >>> >>> 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: [email protected] >>> >>> From: nailin yao <[email protected]> >>> Date: Tuesday, November 22, 2016 at 2:14 PM >>> To: Michael Harms <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> Subject: Re: [HCP-Users] group comparison >>> >>> Hi Michael, >>> >>> I tried the command: ./wb_command -cifti-merge >>> L.SmoothedMyelinMap.32k_fs_LR.out.func.gii -cifti >>> *.L.SmoothedMyelinMap.32k_fs_LR.func.gii, >>> >>> but comes the error: >>> >>> ERROR: error reading NIfTI file /gpfs/scratch60/fas/glahn/ny87 >>> /Connectivity_Study/myelinmap_analysis/S0009QPW.L.SmoothedMyelinMap.32k_fs_LR.func.gii: >>> /gpfs/scratch60/fas/glahn/ny87/Connectivity_Study/myelinmap_ >>> analysis/S0009QPW.L.SmoothedMyelinMap.32k_fs_LR.func.gii is not a valid >>> NIfTI file >>> >>> How can I solve this? Thank you ! >>> >>> Best, >>> Nailin >>> >>> 2016-11-22 14:14 GMT-05:00 nailin yao <[email protected]>: >>> >>>> Thank you MH! >>>> >>>> Best, >>>> Nailin >>>> >>>> 2016-11-22 13:30 GMT-05:00 Harms, Michael <[email protected]>: >>>> >>>>> >>>>> By “compress” do you mean merge into a single file? If so, you can >>>>> use wb_command -cifti-merge, or wb_shortcuts -cifti-concatenate. >>>>> (The latter is a wrapper that simplifies the merge call). And you can >>>>> use >>>>> FSL’s PALM to do a permutation test. >>>>> >>>>> If 164k is too dense a sampling, there are 32k versions of the myelin >>>>> maps that you could use instead. >>>>> >>>>> 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 63110Email: [email protected] >>>>> >>>>> From: <[email protected]> on behalf of nailin yao >>>>> <[email protected]> >>>>> Date: Tuesday, November 22, 2016 at 12:07 PM >>>>> To: "[email protected]" <[email protected]> >>>>> Subject: [HCP-Users] group comparison >>>>> >>>>> Hi, >>>>> >>>>> I want to compare group difference of >>>>> *L.SmoothedMyelinMap.164k_fs_LR.func.gii >>>>> of each subjects. How can I compress the myelinmap of all the subjects and >>>>> do the group level permutation test on them? Thank you very much! >>>>> >>>>> Best, >>>>> Nailin >>>>> >>>>> -- >>>>> Nailin Yao, PhD >>>>> >>>>> Postdoctoral Associate >>>>> Department of Psychiatry, Yale University >>>>> >>>>> _______________________________________________ >>>>> 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. 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. >>>>> >>>> >>>> >>>> >>>> -- >>>> Nailin Yao, PhD >>>> >>>> Postdoctoral Associate >>>> Department of Psychiatry, Yale University >>>> >>>> >>> >>> >>> -- >>> Nailin Yao, PhD >>> >>> Postdoctoral Associate >>> Department of Psychiatry, Yale University >>> >>> >>> ------------------------------ >>> >>> 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. >>> >> >> >> >> -- >> Nailin Yao, PhD >> >> Postdoctoral Associate >> Department of Psychiatry, Yale University >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > -- Nailin Yao, PhD Postdoctoral Associate Department of Psychiatry, Yale University _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
