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]>: > > 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 <(314)%20747-6173> > St. Louis, MO 63110 Email: [email protected] > > From: <[email protected]> on behalf of nailin yao < > [email protected]> > Date: Tuesday, November 29, 2016 at 1:29 PM > To: "Glasser, Matthew" <[email protected]> > > Cc: "[email protected]" <[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]>: > >> 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}.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 >> >> >> ------------------------------ >> >> 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 > > > ------------------------------ > > 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
