If you know how to do it in ANFI, why not use AFNI? —Greg
> On Oct 26, 2016, at 12:04 PM, Michael F.W. Dreyfuss <[email protected]> > wrote: > > Thank you. Is there a recommended method for beta series correlations in fsl? > In afni, this is fairly straightforward with the -stim_times_IM options for > 3dDeconvovle. Does something comparable exist for FEAT or do I have to code > each time point for each individual as a separate regressor in the subject's > fsf file before running feat_model? > > Thanks, > Michael > From: Burgess, Gregory <[email protected]> > Sent: Wednesday, October 26, 2016 12:41:47 PM > To: Michael F.W. Dreyfuss > Cc: Glasser, Matthew; [email protected] > Subject: Re: [HCP-Users] Connectivity Analysis with Cifti > > In general, if you do a conversion from CIFTI to (fake) NIFTI, you can > conduct any timeseries analyses using any tools you would desire, and then > convert back to CIFTI. Spatial processing (spatial smoothing, defining > clusters, etc.) needs to happen in CIFTI space using wb_command. > > > > --Greg > > > > ____________________________________________________________________ > > Greg Burgess, Ph.D. > > Staff Scientist, Human Connectome Project > > Washington University School of Medicine > > Department of Psychiatry > > Phone: 314-362-7864 > > Email: [email protected] > > > > > On Oct 26, 2016, at 9:56 AM, Michael F.W. Dreyfuss > > <[email protected]> wrote: > > > > > > Well, given that I am interested in events of 500 ms duration, I would like > > to use either beta series correlations or gPPI given the results of this > > paper: > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__pdfs.semanticscholar.org_d9d0_a73109ddaa9c426439e8a1a3f67f66391830.pdf&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=l4iDBJrOREqbhXsQA7BDgvNRodb9S2_BbkDCbDKjckQ&s=_9JFIUUGD--boINqd56Fo4ovajnXT5niZDLVU85S8sA&e= > > > > > > I don't see much documentation on either of these methods in fsl or any > > workbench tools. > > > > > > In the past I have used the gppi method from afni: > > https://www.ncbi.nlm.nih.gov/pubmed/22484411 > > > > > > Implemented using these steps: > > > https://afni.nimh.nih.gov/sscc/gangc/CD-CorrAna.html > > > > > > I wasn't sure if there is a convenient way to do either method simply in > > fsl or specifically with any workbench commands. If not I will hack through > > it, but just wanted to check if there was something already set up such as > > the method described b afni above for gPPI, or a particular recommended > > method with this kind of data at present. > > > > > > Thank you, > > > Michael > > > Context-Dependent Correlation Analysis or Generalized PPI ... > > > afni.nimh.nih.gov > > > Typically subjects perform some tasks, or are under some conditions, or go > > through some stimuli during the scanning session. Thus different from > > simple correlation ... > > > > > > > > > > > > > > > A generalized form of context-dependent psychophysiological interactions > > (gPPI): a comparison to standard approaches. - PubMed - NCBI > > > www.ncbi.nlm.nih.gov > > > Neuroimage. 2012 Jul 16;61(4):1277-86. doi: > > 10.1016/j.neuroimage.2012.03.068. Epub 2012 Mar 30. Comparative Study; > > Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, > > Non-P.H.S. > > > > > > From: Glasser, Matthew <[email protected]> > > > Sent: Tuesday, October 25, 2016 7:07:57 PM > > > To: Michael F.W. Dreyfuss; [email protected] > > > Subject: Re: [HCP-Users] Connectivity Analysis with Cifti > > > > > > If you weren’t using CIFTI how would you do such an analysis? > > > > > > Peace, > > > > > > Matt. > > > > > > From: <[email protected]> on behalf of "Michael F.W. > > Dreyfuss" <[email protected]> > > > Date: Tuesday, October 25, 2016 at 9:41 AM > > > To: "[email protected]" <[email protected]> > > > Subject: [HCP-Users] Connectivity Analysis with Cifti > > > > > > Hi, > > > > > > What is/are the recommended method(s) for performing connectivity analyses > > with cifti data? If I want to look at Amygdala-NAcc or Amyg-cortical > > connectivity, for example, during one condition of a task fMRI relative to > > baseline or another condition, how can I do this? > > > > > > Thank you, > > > Michael > > > _______________________________________________ > > > HCP-Users mailing list > > > [email protected] > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=l4iDBJrOREqbhXsQA7BDgvNRodb9S2_BbkDCbDKjckQ&s=UdEzOtB0b0h2-B-FKIlPIHfk6u34XoqLpa3O8K1v3GQ&e= > > > > > > 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] > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=l4iDBJrOREqbhXsQA7BDgvNRodb9S2_BbkDCbDKjckQ&s=UdEzOtB0b0h2-B-FKIlPIHfk6u34XoqLpa3O8K1v3GQ&e= > > > > > > ________________________________ > > 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
