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}.atlasro >> i.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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
