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]> 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]> > Date: Tuesday, March 7, 2017 at 2:08 PM > To: Matt Glasser <[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]> > 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]> on behalf of Kajsa >> Igelström <[email protected]> >> Date: Tuesday, March 7, 2017 at 12:40 PM >> To: "[email protected]" <[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]> >> 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] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> 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] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > > > -- > *Jenny Gilbert* > [email protected] | 443.846.3687 <(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] | 443.846.3687 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
