Hi - if you don't have your data in CIFTI then you would have to dualregress NIFTI/volumetic existing RSN maps into your data, as I think Michael said - which isn't as optimal. Cheers.
> On 20 Mar 2018, at 01:53, Will Khan <khan.wa...@florey.edu.au> wrote: > > Dear HCP members/Users, > > Thanks so much for your prompt advice and suggestions! > > Steve, if I were to perform ICA on the grayordinates would I still be able to > dualregress this onto a patient nifti dataset? Like others have suggested, > wouldn't my patient data need to be in cifti? > > Cheers :) > > Will > > > From: Glasser, Matthew <glass...@wustl.edu <mailto:glass...@wustl.edu>> > Sent: 14 March 2018 01:14:51 > To: Harms, Michael; Stephen Smith; Will Khan > Cc: hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>; > Erin W. E. Dickie > Subject: Re: [HCP-Users] Melodic ICA idle > > I would recommend the ciftify toolbox if your patient data do not meet HCP > Pipelines acquisition requirements (lacking highres T2w scan and or > Fieldmap). The ciftify toolbox is currently beta, but should be fully > available in the very near future (Erin Dickie the author is CCed and can > give more details). It is intended to assist users with legacy data in > processing using HCP-Style analyses including dual regression in CIFTI. If > you need volume maps for your patients too, as Steve says you can do the > first stage of dual regression in CIFTI to get the timecourses and then > regress these into both the CIFTI and volume data. We do this all the time > if we need to see what is going on outside the greymatter (e.g. we are > denoising data). > > I will note that even fMRI data with coarse voxel resolution (e.g. 4mm > isotropic) will still benefit from HCP-Style analyses over traditional > analyses (see in the attached figure that the 4mm dots are essentially all > above the line of equality between volume and surface). The attached figure > does not consider the effects of volume-based smoothing which are even more > serious than volume-based alignment > (https://www.biorxiv.org/content/early/2018/01/29/255620 > <https://www.biorxiv.org/content/early/2018/01/29/255620>). > > Of course in the future we recommend acquiring HCP Style data (fMRI 2.4mm > isotropic or better, 1s TR or better; T1w and T2w 0.8mm isotropic or better, > and phase reversed field maps) and processing with the HCP Pipelines or an > equivalent or better approach. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" > <mha...@wustl.edu <mailto:mha...@wustl.edu>> > Date: Tuesday, March 13, 2018 at 7:48 AM > To: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>, Will > Khan <khan.wa...@florey.edu.au <mailto:khan.wa...@florey.edu.au>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Melodic ICA idle > > > I think the issue, as I read it, is that Will’s data is only NIFTI currently, > so he doesn’t have any subject CIFTI that he could use for the stage 1 of > dual reg. > > Our suggestion of course to remedy that would be that you process your data > into CIFTI, using the HCP Pipelines. ☺ > > Cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Associate Professor of Psychiatry > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > <mailto:mha...@wustl.edu> > > From: <hcp-users-boun...@humanconnectome.org > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Stephen Smith > <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> > Date: Tuesday, March 13, 2018 at 2:31 AM > To: Will Khan <khan.wa...@florey.edu.au <mailto:khan.wa...@florey.edu.au>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Melodic ICA idle > > Hi Will > > I'm not aware of any outstanding bugs in melodic that would cause it to > silently hang. Are you sure it's not just that you've run out of RAM and are > swapping? > > Yes it's better to do group-ICA on grayordinates. You can still dual-regress > that (step one into subject CIFTI, step two back into either CIFIT and/or > volume) to get volume maps back, like we did for the most recent group-ICA > HCP release. > > Cheers. > > > > > > On 13 Mar 2018, at 04:52, Will Khan <khan.wa...@florey.edu.au > <mailto:khan.wa...@florey.edu.au>> wrote: > > Dear HCP Users, > > I am currently using the ICA-FIX denoised volumetric data for 100 unrelated > subjects. I come across an issue where melodic appears to 'choke' or remain > idle for a considerable amount of time at the variance normalisation step. I > am running a group-ICA within a mask of the PCC. > > I understand this issue has been reported by others and appears to be a bug > with the melodic command. > > I know Steve Smith and others have cautioned against the use of the > volumetric data - but I am using the HCP dataset to generate group-ICA maps > that I later wish to dualreg onto a patient dataset. Since all my patient > data is in NIFTI format I am initially hesitant to use CIFTI (please correct > me if I am wrong here). > > Am I right to be using the volumetric data in this case? > > Many Thanks! > > Regards, > > Will > > > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Head of Analysis, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk> > http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet <http://smithinks.net/> > > > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <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. > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve <http://www.fmrib.ox.ac.uk/~steve> --------------------------------------------------------------------------- Stop the cultural destruction of Tibet <http://smithinks.net/> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
