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> Sent: 14 March 2018 01:14:51 To: Harms, Michael; Stephen Smith; Will Khan Cc: 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. 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