Hi - I would strongly recommend doing the group-ICA and dualregression on the CIFTI versions of the data, not volumetric. However, if you really want volumetric versions of 50-dimensional group-ICA then we could provide those that have been done via group-ICA on CIFTI data which has then been dualregged back into volumetric space and averaged across subjects. Or you could ask your sysadmin to not kill your job after 5 days!
Cheers. > On 28 Mar 2017, at 17:08, Jenny Gilbert <[email protected]> wrote: > > Hi Matt, > > I appreciate your help with working through ICA using HCP data. Following > your recommendation, I converted CIFTI files to NIFTI and am trying to run > through ICA, but I am still experiencing problems. > > Running ICA for 62 participants (rest1_RL session) on a high power computing > server with 72 GB mem and a time limit of 5 days, the ICA times out, and > cannot pass the first stage of removing the mean image and normalizing by the > voxel-wise variance. This is the script I'm using: > melodic -i /projects/niblab/scripts/twin/input_ica.txt --migp --sep_vn -o > /projects/niblab/scripts/twin/ica_out -v --nobet --bgthreshold=10 --tr=1 -d > 50 --report --mmthresh=0.5 --Oall > > From your experience, should we expect ICA to take 5+ days to run, or is > there a way to speed this up? > > Thanks for your help! > Jenny > > On Tue, Mar 7, 2017 at 3:48 PM, Glasser, Matthew <[email protected] > <mailto:[email protected]>> wrote: > Hi Jenny, > > Indeed you can use wb_command -cifti-convert -to-nifti to convert the files > to NIFTI, run melodic, do dual regression, etc, and then when you have your > output maps, you convert them back to CIFTI with wb_command -cifti-convert > -from-nifti and view them in Workbench. The only thing to keep in mind is > that spatial relationships will not be 3D volumetric in these converted CIFTI > files, so things like smoothing would not be appropriate to do on them. ICA > or dual regression doesn’t use spatial neighborhood information (though you > will need to select your own ICA dimensionality). > > Peace, > > Matt. > > From: Jenny Gilbert <[email protected] <mailto:[email protected]>> > Date: Tuesday, March 7, 2017 at 2:08 PM > To: Matt Glasser <[email protected] <mailto:[email protected]>> > > Subject: Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files > > Hi Matt, > > Thanks for your help! How do I complete ICA the CIFTI MSMAII files? Is the > first step to convert the files to NIFTI format in workbench? Also, I planned > to complete dual regression with the ICA generated components, so how does > dual regression work with CIFTI format data? Can all of this be done by > converting CITFI to NIFTI, and then running the usual commands? I'm new to > workbench, and would love all the help that you experts can offer! > > Thank you so much! > Jenny > > On Tue, Mar 7, 2017 at 2:05 PM, Glasser, Matthew <[email protected] > <mailto:[email protected]>> wrote: > I think there is a bug in melodic, which I also encountered. I would report > this to the FSL list, but it is likely the issue will be fixed in the next > FSL release. > > Also, if you are running melodic in the volume and combining across subjects, > this is not recommended because much of the brain is not well aligned in the > volume. It is instead recommended that you use the CIFTI data that has been > aligned with MSMAll. ICA gives very different results depending on whether > the data are well aligned or not. > > Peace, > > Matt. > > From: <[email protected] > <mailto:[email protected]>> on behalf of Kajsa Igelström > <[email protected] <mailto:[email protected]>> > Date: Tuesday, March 7, 2017 at 12:40 PM > To: "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > Subject: Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files > > Hi Jenny and others! > I'm also unable to run these files through Melodic. The most common problem > is that it doesn't converge, and under some circumstances it seems like > Melodic just stops in the middle of normalizing individual files, at points > that are not logical to me, or reproducible. > Best, > Kajsa > > > > On Tue, Mar 7, 2017 at 12:24 PM, Jenny Gilbert <[email protected] > <mailto:[email protected]>> wrote: > Hello HCP! > > I am trying to complete ICA using the volumetric ICA-FIX de noised data > (rfMRI_REST1_RL_hp2000_clean.nii.gz files), and melodic keeps failing. It > looks like melodic gets hung up on some participants cannot progress while > removing the mean image and normalizing by the voxel-wise variance. > > Has anyone come across this same problem? Any advice on how to fix? > > Thank you! > Jenny > _______________________________________________ > HCP-Users mailing list > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > _______________________________________________ > HCP-Users mailing list > [email protected] <mailto:[email protected]> > 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 > [email protected] <mailto:[email protected]> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> > > > -- > Jenny Gilbert > [email protected] <mailto:[email protected]> | 443.846.3687 > <tel:(443)%20846-3687> > > > > 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. > > > > > -- > Jenny Gilbert > [email protected] <mailto:[email protected]> | 443.846.3687 > _______________________________________________ > HCP-Users mailing list > [email protected] > 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) [email protected] 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 [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
