So how do I deal with the two hemispheres when comparing
${subj}.MyelinMap.32k_fs_LR.dscalar.nii if the mask is only for one
hemisphere?Thank you! Nailin 2016-11-28 20:07 GMT-05:00 Glasser, Matthew <[email protected]>: > You can use the atlas ROI file: ${StudyFolder}/${Subject}/ > MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}. > atlasroi.32k_fs_LR.shape.gii. > > Peace, > > Matt. > > From: <[email protected]> on behalf of nailin yao < > [email protected]> > Date: Monday, November 28, 2016 at 3:06 PM > To: Timothy Coalson <[email protected]> > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] group comparison > > 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_s >> hortcuts/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 63110Email: [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 > > > ------------------------------ > > 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
