So at least 30 min with two phase encoding directions (2400 volumes) or best the whole 4800 volumes.
Thank you Matthew 2015-02-02 23:24 GMT+01:00 Glasser, Matthew <[email protected]>: > Probably better to do two phase encoding directions and 30 mins vs one > phase encoding direction and 15 mins. Best to do all four though. > > Peace, > > Matt. > > From: David Hofmann <[email protected]> > Date: Monday, February 2, 2015 at 3:16 PM > To: Matt Glasser <[email protected]> > Cc: Chao Liu <[email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] Phase Encoding Direction > > Hi all, > > I have the same "problem", so I split the 4800 volumes in half and used > only 2400 data points so that I have at least two 15-min sessions (2x 1200) > with both phase encoding directions (I'm using the node timeseries > txt-files). I also thought about looking at the other 2400 data points and > compare the difference between the first two and the last two session. As I > understood, only using 1200 volumes which is only one phase encoding > direction, seems to be problematic. > > What do you guys think? Is it ok to do it this way? > > greetings > > David > > > > 2015-01-23 16:54 GMT+01:00 Glasser, Matthew <[email protected]>: > >> The function wb_command -cifti-correlate allows you to conserve RAM when >> doing a pairwise correlation. Also I doubt doing it one run at a time >> would reduce the RAM requirements much since the main array is the 91282 X >> 91282 dense connectome. >> >> Peace, >> >> Matt. >> >> On 1/23/15, 9:08 AM, "Chao Liu" <[email protected]> wrote: >> >> >Dear Matt., >> > >> >Thanks for your reply. I have only one machine with 16GB RAM and the >> >others with 8GB. for a dtseries.nii file, if I calculate pairwise >> >correlation for a 91282 by 1200 matrix. It would cost 60GB RAM in matlab. >> >Although we find a way to calculate a sparse pairwise correlation matrix, >> >we still can not handle a 91282 by 4800 (or more) matrix easily. >> > >> >Now that using all four files is essential, I plan to first calculate the >> >pairwise correlation matrix for each run, then average the correlation >> >matrix from 4 runs for each subject. Is this ok? >> > >> >Many thanks! >> >Chao >> > >> >> On 23 Jan 2015, at 13:57, Glasser, Matthew <[email protected]> >> >>wrote: >> >> >> >> How much RAM do you have? The CIFTI files use far less RAM than the >> >> volume files, but contain all the grey matter information represented >> >>in a >> >> way that makes combining across subjects more accurate. If you don¹t >> >>use >> >> all the data your estimates of the subject¹s functional connectivity >> >>will >> >> be noisier and generally less stable (one 15 min run looks more >> >>different >> >> than another than if you compared two sets of 1 hour¹s worth of data). >> >> Also there are some left/right asymmetries in the data induced by the >> >> LR/RL phase encoding directions, which some people perceive as a >> problem >> >> (though if we had used AP/PA there would still be asymmetries >> >> posterior/anterior). >> >> >> >> Peace, >> >> >> >> Matt. >> >> >> >> On 1/23/15, 6:44 AM, "Chao Liu" <[email protected]> wrote: >> >> >> >>> Dear HCP Experts, >> >>> >> >>> I am inspecting the HCP rfMRI data. For each subject, there are two >> >>> sessions with 2 runs (LR&RL) in each session, yielding 4 files in >> >>>total. >> >>> Although we can concatenate all the four time series and do the >> >>> correlation, I found the memory needed is more than the memory I have >> >>>on >> >>> lab computer, leading to a very slow calculation. So I am wondering >> the >> >>> difference between using only one run and using all the four runs. >> Will >> >>> it give wrong results if I use only one run? >> >>> >> >>> Many thanks! >> >>> Chao >> >> >> >> >> >> ________________________________ >> >> 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. 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