Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-11 Thread Timothy Coalson
gt; MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz@$ > {StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz > 2000 ${StudyFolder}/${Subject}/MNINonLinear/Results/${ > ConcatName}/${ConcatName}.nii.gz > > Peace, > > Matt. > > From: Sang-Young

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-11 Thread Sang-Young Kim
gt;> > Cc: Stephen Smith <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>>, > "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-09 Thread Glasser, Matthew
sers@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding directions Dear Matt: I ran the multi-run ICA+FIX according to your guideline. Bu

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-09 Thread Timothy Coalson
z > > Peace, > > Matt. > > From: Sang-Young Kim <sykim...@gmail.com> > Date: Friday, October 6, 2017 at 4:17 PM > To: Matt Glasser <glass...@wustl.edu> > Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, "hcp-users@humanconnectome.org" > <hcp-user

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-09 Thread Sang-Young Kim
org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding > directions > > Thanks! Matt! > > I have one more

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Sang-Young Kim
@humanconnectome.org>> on behalf of Stephen Smith >> <st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>> >> Date: Friday, October 6, 2017 at 1:49 AM >> To: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>> >> Cc: "hcp-users@humanconnectom

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Glasser, Matthew
tome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding directions Thanks! Matt! I have one more following-up question. In order to run the script "hcp_fix_multi_run", we have to concatenate all the data t

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Glasser, Matthew
:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding directions Hi, Matt and Stephen: Thanks for your responses. So I will try below three options to see

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Sang-Young Kim
<mailto:st...@fmrib.ox.ac.uk>> > Date: Friday, October 6, 2017 at 1:49 AM > To: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>> > Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnect

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-06 Thread Glasser, Matthew
m<mailto:sykim...@gmail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Combining rfMRI data for different phase encoding directions H

Re: [HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-05 Thread Stephen Smith
Hi - I think your main two choices are whether to run FIX on each 5min run separately, or to preprocess and concatenate each pair of scans from each session and run FIX for each of the 4 paired datasets. You could try FIX both ways on a few subjects and decide which is working better. Cheers.

[HCP-Users] Combining rfMRI data for different phase encoding directions

2017-10-05 Thread Sang-Young Kim
Dear Experts: We have acquired rfMRI dataset with A-P and P-A phase encoding direction and the data was acquired in eight 5-minute runs split across four imaging sessions. We have processed the data using HCP pipelines (e.g., PreFreeSurfer, FreeSurfer, PostFreeSurfer, fMRIVolume, fMRISurface