Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

Thanks Matt That's correct that the --migp option (see a recent post from me to the FSL list about this new option) inside melodic is still single-threaded. However the journal paper (linked below by Matt) includes simple matlab code for doing MIGP and that can easily be parallelised as well as

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

Yeah, I sort of need to do whole-brain. -Micah On Thu, Jan 29, 2015 at 7:33 PM, Glasser, Matthew wrote: > Finally I’ll note that MIGP and lots of RAM are not needed when using > parcellated datasets (though if you want ICA, you probably aren’t planning > to run it on parcellated data). > > Pe

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

Finally I’ll note that MIGP and lots of RAM are not needed when using parcellated datasets (though if you want ICA, you probably aren’t planning to run it on parcellated data). Peace, Matt. From: , Matt Glasser Date: Thursday, January 29, 2015 at 9:32 PM To: Mic

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

http://www.sciencedirect.com/science/article/pii/S105381191400634X We’re working on some improvements for it when used for functional connectivity (i.e. all to all correlations), but it works fine as is for ICA.   Peace, Matt. From: Micah Chambers Date: Thursday,

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

8GB is probably going to be tough to do modern neuroimaging analysis with.  I’d recommend 32GB minimum and 64GB if possible for analysis machines (can get away with 8GB for viewing machines).   Also you can save quite a bit of RAM using the CIFTI data (which will give you better registered res

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

Thanks Matthew, I'll check out the latest version of FSL. Is there a paper the discusses the MIGP method? On Thu, Jan 29, 2015 at 7:24 PM, Micah Chambers wrote: > Well the resting state data provided through the HCP around 1GB each so > I'm guessing the memory requirement is a good bit more than

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

Well the resting state data provided through the HCP around 1GB each so I'm guessing the memory requirement is a good bit more than 8GB now, unless the PCA is performed per subject. Has anyone done Group ICA on datasets this size? -Micah On Thu, Jan 29, 2015 at 6:40 PM, Glasser, Matthew wrote:

Re: [HCP-Users] Group ICA with Melodic on 20 or more subjects

If you update to the latest version of FSL the MIGP algorithm may be in there and is designed to help with this.  The main limitation with melodic has been that it was single threaded.  I don’t know if that has been addressed yet. Peace, Matt. From: Micah Chambers D

[HCP-Users] Group ICA with Melodic on 20 or more subjects

Has anyone on the run group-wise analysis on the HCP resting state data, and if so what tools did you use? I am having memory issues when running more than 10 subjects and I was wondering if anyone has a way of getting around the large memory requirements when concatenating in time. Thanks! -Mica

Re: [HCP-Users] Plot analysis results on HCP resting state fMRI data

We need to know what format your data is currently in to give a definitive answer, but I'm going to guess matlab, as we have provided code for it to load cifti files, which you appear to have done. The matlab code we provide also allows for saving data back out into cifti files, latest version and

Re: [HCP-Users] Resolving an issue

Please see my response of just a few moments ago to dkumar.in...@gmail.com on this same mailing list. It appears that you two are having the same issue. Best Regards, Tim On Thu, Jan 29, 2015, at 09:39, Allwyn cctoc wrote: > Hi all, > While running freesurfer I encountered this problem > Mris_ma

Re: [HCP-Users] mris_make_surfaces: undefined symbol ncerr in FreesurferPipelineBatch.sh

Devakumar, Since you got the mris_make_surfaces binary as part of the 5.3.0-HCP version of FreeSurfer, it is "dynamically linked to shared libraries", which means that it is looking for libraries on your system that it needs to perform some of its work (instead of having all the code from those l

[HCP-Users] Resolving an issue

Hi all, While running freesurfer I encountered this problem Mris_make_surfaces: symbol lookup error: Mris_make_surfaces: undefined symbol :ncerr (Standard_in)2 : error : comparison in expression Can you pls help me fix these issue ? ___ HCP-Users mail

[HCP-Users] Re: mris_make_surfaces: undefined symbol ncerr in FreesurferPipelineBatch.sh

Downloaded from the link ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/. This link was given in https://github.com/Washington-University/Pipelines/wiki/v3.4.0-Release-Notes,-Installation,-and-Usage#prerequisites link. Thanks Devakumar Sent from Windows Mail From:

Re: [HCP-Users] mris_make_surfaces: undefined symbol ncerr in FreesurferPipelineBatch.sh

That doesn’t seem too old.  Where did you get FreeSurfer from (including that binary)? Peace, Matt. From: "dkumar.in...@gmail.com" Date: Thursday, January 29, 2015 at 1:02 AM To: Matt Glasser , "hcp-users@humanconnectome.org"