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}/ > MNINonLinear/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_ > 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]> > 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
