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. >>> 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 >>> > >>> > >>> > >>> > 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
