If your groups have subjects who are related, PALM can model the family structure:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide It is a very powerful tool. On Jan 24, 2016, at 11:59 AM, "Glasser, Matthew" <glass...@wustl.edu> wrote: > We’d recommend using FSL’s PALM, which supports CIFTI files for multiple > comparison correction, though randomise can be made to work too. > > Peace, > > Matt. > > From: Anders Eklund <andek...@gmail.com> > Date: Sunday, January 24, 2016 at 11:54 AM > To: Matt Glasser <glass...@wustl.edu> > Cc: mohamad reza <mo7278231r...@yahoo.com>, HCP Listserv > <hcp-users@humanconnectome.org>, "Burgess, Greg" <burge...@pcg.wustl.edu> > Subject: Re: [HCP-Users] why hcp task analysed volume data has been removed? > > Several parametric statistical methods are not valid unless you smooth the > data considerably. Do you only use non-parametric statistics? Does the > randomise function in FSL support cifti files? > > - Anders > > 2016-01-24 18:36 GMT+01:00 Glasser, Matthew <glass...@wustl.edu>: >> You can use a command line script to run level 3 FEAT analyses with CIFTI >> data in FSL. I had thought we had released the latest version of this >> script on github, but it appears to perhaps only be in the HCP course >> materials. I’m hopeful that the folks CCed can help get the latest version >> into the master branch of GitHub so that you can use it. The HCP course >> materials explain how. >> >> By smoothed data I was referring to the CIFTI data with substantial >> smoothing. For my analyses, I use the MSMAll aligned CIFTI data with no >> additional smoothing beyond the 2mm FWHM used in the grayordinates >> projection. I’ve not used volume-based analysis in years. >> >> Peace, >> >> Matt. >> >> From: mohamad reza <mo7278231r...@yahoo.com> >> Reply-To: mohamad reza <mo7278231r...@yahoo.com> >> Date: Sunday, January 24, 2016 at 11:16 AM >> To: Matt Glasser <glass...@wustl.edu>, HCP Listserv >> <hcp-users@humanconnectome.org> >> Subject: Re: [HCP-Users] why hcp task analysed volume data has been removed? >> >> Thanks for your prompt response,i really appreciate it. >> >> FSL feat is not able to run group analysis on CIFTI format,right? >> So how should i do the group analysis using CIFTI data? Does fsl recognize >> CIFTI format? >> >>> I also recommend that you avoid the smoothed data (which still have >>> blurring across brain areas). >> by "smoothed data" you mean the analysed volume data? >> The previous release preprocessed task data are fine? or they have the same >> problems? >> >> I will be grateful for any help you can provide. >> >> Best, >> Mohamad >> >> >> >> >> >> On Sunday, January 24, 2016 7:13 PM, "Glasser, Matthew" <glass...@wustl.edu> >> wrote: >> >> >> They aren’t very neuroanatomically accurate (poor alignment across subjects, >> blurring across tissues and areas from smoothing). We recommend you use the >> CIFTI data (in particular the MSMAll aligned CIFTI data) which have much >> better alignment across subjects. I also recommend that you avoid the >> smoothed data (which still have blurring across brain areas). >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of mohamad reza >> <mo7278231r...@yahoo.com> >> Reply-To: mohamad reza <mo7278231r...@yahoo.com> >> Date: Sunday, January 24, 2016 at 9:34 AM >> To: HCP Listserv <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] why hcp task analysed volume data has been removed? >> >> Dear HCP experts, >> >> Why HCP task analysed volume data have been removed in new release? >> Is there something wrong with them? I downloaded some of them from previous >> release. >> >> Best, >> Mohamad >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-use rs >> >> 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. >> >> >> >> >> 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 >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > > -- > Anders Eklund, PhD > > > > > 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 > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
