Hi, I used "wb_shortcuts -cifti-concatenate output.dtseries.nii *.dscalar.nii" to concatenate my 155 subjects' MyelinMap.32k_fs_LR.dscalar.nii files. However, it turn out there are 59412 rows in the output file. What's wrong with my command then? Thank you very much.
Best, Nailin 2016-11-29 13:07 GMT-05:00 Glasser, Matthew <[email protected]>: > If you are using CIFTI you don't need to mask the data/can use a CIFTI > file of all ones. > > Peace, > > Matt. > > > Sent from my Verizon, Samsung Galaxy smartphone > > > -------- Original message -------- > From: nailin yao <[email protected]> > Date: 11/29/16 11:33 AM (GMT-06:00) > To: "Glasser, Matthew" <[email protected]> > Cc: NEUROSCIENCE tim <[email protected]>, [email protected] > Subject: Re: [HCP-Users] group comparison > > 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}/MNIN >> onLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.atlasro >> i.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 > > > ------------------------------ > > 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
