[HCP-Users] Data processing with SPM

Hi there, I've encountered a problem when dealing with preprocessed r-fMRI HCP data by SPM8. To be specific, data on many time points can not be recognized by SPM, and the MATLAB command window showed an error "file too small" . Beside this, the last few frames of a run looked weird when viewing

[HCP-Users] ICA problem

Hello every one I ran FSL MELODIC single session ica on connectome project Q1- single subject preprocessed rest-fMRI data, but in the result MELODIC report page,the ICA tab is empty.  I didn't change default options in fsl melodic except in pre-stats tab, i disabled all the preprocessing optio

Re: [HCP-Users] ICA problem

Hi - what's in the report_log.html file? Cheers > On 26 May 2015, at 05:22, mo mo wrote: > > Hello every one > > > I ran FSL MELODIC single session ica on connectome project Q1- single subject > preprocessed rest-fMRI data, but in the result MELODIC report page,the ICA > tab is empty. >

Re: [HCP-Users] Data processing with SPM

Hi - I think you probably need to take this query to the SPM email list I'm afraid - we haven't used SPM so far in the HCP, so don't have experience with how it performs on HCP data. Cheers, Steve. > On 26 May 2015, at 04:01, 李勋 wrote: > > Hi there, I've encountered a problem when dealing wit

[HCP-Users] L-R or R-L phase encoding?

hi all In connectome fMRI data,what is difference between R-L phase encoding and L-R phase encoding? which one should i use in my analysis?or should i combine them somehow? there is also an other file named rfMRI_REST1_LR_hp2000_clean.nii,i am confused,which file should i use in my analysis? tha

Re: [HCP-Users] L-R or R-L phase encoding?

We use all four resting state runs and we use the CIFTI ${fMRIName}_Atlas_hp2000_clean.dtseries.nii data which has been cleaned with ICA+FIX.  When using runs with a different phase encoding direction, it is important to remove the mean image first.  We then temporally concatenate multiple runs

Re: [HCP-Users] SBref Distortion Correction

Looking at the WarpFields in the DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap directory, the "WarpField" looks good and has data, The "WarpField_01" and "WarpField_02" are both empty From: hcp-users-boun...@humanconnectome.or

Re: [HCP-Users] SBref Distortion Correction

Are there only two of those files? It¹s not really possible for WarpField to have a warpfield in it (that looks like a field map with a vaguely brain shape inside it) but for the WarpField_01 and Warpfield_02 not to have any data in them (did you check all their volumes)? Peace, Matt. On 5/26/1

Re: [HCP-Users] Creating a parcellation for the HCP data

Hi Stuart, I have fewer answers than questions, but it seems like at the end of this, you want your source (fsaverage) parcellation mapped onto the HCP subjects' surfaces, and then projected from surface to volume (subject's orig/magnet space or MNINonlinear stereotaxic space?). The HCP pipeli

Re: [HCP-Users] SBref Distortion Correction

There are 6 files in the subject I am looking at, labeled Warpfield_01 to 06, in additino to Warpfield.nii.gz.All have 3 volumes, with the 2nd volume having the fieldmap/brain image in each. Warpfield images 4-6 look much like the final Warpfield image, whereas Warpfield images 1-3 appear t

Re: [HCP-Users] SBref Distortion Correction

Okay, that sounds like things are producing the expected outputs. As to why the correction isn’t quite as good, you could check to see how different the corrected spin echo images look. These should give you an idea of how well the distortion correction worked: ${StudyFolder}/${Subject}/${fMRINa

Re: [HCP-Users] Data processing with SPM

When you email the SPM list, you will need to provide the following: (1) What specific files could not be opened? (2) What size are the files? (3) What did you mean by "weird"? I suspect the files are more than 2GB, which has been known to cause issues with some functions in SPM8. These should res