The -metric-reduce command outputs a metric file. You should alter the wb_command line so that the output file has extension .func.gii.
Tim On Fri, Dec 9, 2016 at 1:38 PM, nailin yao <[email protected]> wrote: > Hi, > > I'm trying to run "palm -i data_L.func.gii -d design.mat -t design.con -o > results_L_cort -T -tfce2D -s L_midthickness.surf.gii L_area.dscalar.nii > -logp " according to PALM website. In the file preparation, the > L_midthick_va.func.gii file looks fine in wb_view, but the > L_area.dscalar.nii which generated by "wb_command -metric-reduce > L_midthick_va.func.gii MEAN L_area.dscalar.nii " cannot be open in wb_view. > Both of the files are attached, do you know why? > > Thank you! > Nailin > L_area.dscalar.nii > <https://drive.google.com/file/d/0B1u0DtG5Jo-NcG9vT1BzMHowQVE/view?usp=drive_web> > > L_midthick_va.func.gii > <https://drive.google.com/file/d/0B1u0DtG5Jo-NQ3hyaG84RDdNdWs/view?usp=drive_web> > > > 2016-11-30 13:43 GMT-05:00 Glasser, Matthew <[email protected]>: > >> Perhaps you have to add .func.gii instead of .gii to the extension names >> for wb_view to know what kind of file it is. Do you actually need to do >> the CIFTI separate part though? I thought PALM supported CIFTI files >> natively now. >> >> Peace, >> >> Matt. >> >> From: nailin yao <[email protected]> >> Date: Wednesday, November 30, 2016 at 11:35 AM >> To: Matt Glasser <[email protected]> >> Cc: "Dierker, Donna" <[email protected]>, "[email protected]" < >> [email protected]> >> >> Subject: Re: [HCP-Users] group comparison >> >> Hi Matt, >> >> The result is generated by the command: >> >> wb_command -cifti-separate data.dtseries.nii COLUMN (-volume-all >> data_sub.nii) -metric CORTEX_LEFT data_L.func.gii -metric CORTEX_RIGHT >> data_R.func.gii >> >> palm -i data_L.func.gii -i data_R.func.gii -d design.mat -t design.con -o >> results -corrmod -logp >> >> And the result files are : >> >> results_dpv_tstat_fwep_m1_c1.gii >> >> results_dpv_tstat_fwep_m1_c2.gii >> >> results_dpv_tstat_fwep_m2_c1.gii >> >> results_dpv_tstat_fwep_m2_c2.gii >> >> etc. >> >> best, >> >> Nailin >> >> 2016-11-30 12:30 GMT-05:00 Glasser, Matthew <[email protected]>: >> >>> Is it CIFTI or GIFTI data? I thought you said CIFTI earlier but you >>> have a GIFTI file there. >>> >>> Peace, >>> >>> Matt. >>> >>> From: <[email protected]> on behalf of nailin yao < >>> [email protected]> >>> Date: Wednesday, November 30, 2016 at 11:24 AM >>> To: "Dierker, Donna" <[email protected]> >>> >>> Cc: "[email protected]" <[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]>: >>> >>>> Try the -transposedata option. >>>> >>>> >>>> > On Nov 29, 2016, at 1:49 PM, Harms, Michael <[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 >>>> > St. Louis, MO 63110 Email: [email protected] >>>> > >>>> > From: nailin yao <[email protected]> >>>> > Date: Tuesday, November 29, 2016 at 1:41 PM >>>> > To: Michael Harms <[email protected]> >>>> > Cc: "Glasser, Matthew" <[email protected]>, " >>>> [email protected]" <[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]>: >>>> >> >>>> >> 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 >>>> >> St. Louis, MO 63110Email: [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.3 >>>> 2k_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 >>>> > >>>> > >>>> > >>>> > 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 >>>> >>>> >>>> ________________________________ >>>> 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 >> >> >> ------------------------------ >> >> 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
