Is it CIFTI or GIFTI data? I thought you said CIFTI earlier but you have a GIFTI file there.
Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of nailin yao <[email protected]<mailto:[email protected]>> Date: Wednesday, November 30, 2016 at 11:24 AM To: "Dierker, Donna" <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] group comparison Hi, I have successfully generated statistic result from palm, files are results_dpv_tstat_mfwep_m1_c1.gii etc. But it seems cannot be view by wb_view. May I know how can I view the results properly? Thank you! Best, Nailin 2016-11-29 16:25 GMT-05:00 Dierker, Donna <[email protected]<mailto:[email protected]>>: Try the -transposedata option. > On Nov 29, 2016, at 1:49 PM, Harms, Michael > <[email protected]<mailto:[email protected]>> wrote: > > > Sounds like your design.mat file isn’t set up correctly, or you haven’t > supplied a necessary flag to PALM. Read the PALM documentation carefully. I > believe that there are now examples of using PALM with CIFTI data. > > 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<tel:314-747-6173> > St. Louis, MO 63110 Email: [email protected]<mailto:[email protected]> > > From: nailin yao <[email protected]<mailto:[email protected]>> > Date: Tuesday, November 29, 2016 at 1:41 PM > To: Michael Harms <[email protected]<mailto:[email protected]>> > Cc: "Glasser, Matthew" <[email protected]<mailto:[email protected]>>, > "[email protected]<mailto:[email protected]>" > <[email protected]<mailto:[email protected]>> > Subject: Re: [HCP-Users] group comparison > > Because I need to do group comparison here , and met this error when running > palm: > Error using palm_takeargs (line 2003) > The number of rows in the design matrix does > not match the number of observations in the data. > - Rows in the matrix: 155 > - Observations in the data: 59412 > In file design.mat > > How can I fix this?Thank you! > Best, > Nailin > > 2016-11-29 14:37 GMT-05:00 Harms, Michael > <[email protected]<mailto:[email protected]>>: >> >> Hi, >> Why do you think there is something wrong? 59412 is the expected number of >> rows in the *MyelinMap.32k_fs_LR.dscalar.nii files. >> >> 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<tel:314-747-6173> >> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> >> >> From: >> <[email protected]<mailto:[email protected]>> >> on behalf of nailin yao <[email protected]<mailto:[email protected]>> >> Date: Tuesday, November 29, 2016 at 1:29 PM >> To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> >> >> Cc: "[email protected]<mailto:[email protected]>" >> <[email protected]<mailto:[email protected]>> >> Subject: Re: [HCP-Users] group comparison >> >> 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]<mailto:[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]<mailto:[email protected]>> >>> Date: 11/29/16 11:33 AM (GMT-06:00) >>> To: "Glasser, Matthew" <[email protected]<mailto:[email protected]>> >>> Cc: NEUROSCIENCE tim <[email protected]<mailto:[email protected]>>, >>> [email protected]<mailto:[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]<mailto:[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]<mailto:[email protected]>> >>>> on behalf of nailin yao <[email protected]<mailto:[email protected]>> >>>> Date: Monday, November 28, 2016 at 3:06 PM >>>> To: Timothy Coalson <[email protected]<mailto:[email protected]>> >>>> Cc: "[email protected]<mailto:[email protected]>" >>>> <[email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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<tel:314-747-6173> >>>>>>> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> >>>>>>> >>>>>>> From: nailin yao <[email protected]<mailto:[email protected]>> >>>>>>> Date: Tuesday, November 22, 2016 at 2:14 PM >>>>>>> To: Michael Harms <[email protected]<mailto:[email protected]>> >>>>>>> Cc: >>>>>>> "[email protected]<mailto:[email protected]>" >>>>>>> <[email protected]<mailto:[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]<mailto:[email protected]>>: >>>>>>>> Thank you MH! >>>>>>>> >>>>>>>> Best, >>>>>>>> Nailin >>>>>>>> >>>>>>>> 2016-11-22 13:30 GMT-05:00 Harms, Michael >>>>>>>> <[email protected]<mailto:[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<tel:314-747-6173> >>>>>>>>> St. Louis, MO 63110Email: [email protected]<mailto:[email protected]> >>>>>>>>> >>>>>>>>> From: >>>>>>>>> <[email protected]<mailto:[email protected]>> >>>>>>>>> on behalf of nailin yao <[email protected]<mailto:[email protected]>> >>>>>>>>> Date: Tuesday, November 22, 2016 at 12:07 PM >>>>>>>>> To: >>>>>>>>> "[email protected]<mailto:[email protected]>" >>>>>>>>> <[email protected]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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]<mailto:[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. > _______________________________________________ > HCP-Users mailing list > [email protected]<mailto:[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]<mailto:[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. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
