Re: [HCP-Users] spin echo phase encoding direction

The value of PhaseEncodingDirectionPositive in the shadow field (0029,1020) reflects the combination of both Phase enc. dir. on the Routine tab (e.g., AP vs. PA) AND the setting of Invert RO/PE Polarity on the Sequence/Special tab. As long as you have one of each polarity, you can use the

Re: [HCP-Users] spin echo phase encoding direction

Would that be the *.dInPlaneRot value for each slice in the CSA header? From: Harms, Michael [mailto:mha...@wustl.edu] Sent: Monday, December 15, 2014 10:11 AM To: Book, Gregory; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] spin echo phase encoding direction The value of

Re: [HCP-Users] spin echo phase encoding direction

If your phase encoding directions are inverted, I would recommend swapping the SpinEchoPositive and NegativeImage values. This would make the computed field map have the same sign as a typical field map and then the PhaseEncodeList would not have to change. Peace, Matt. From: Book,

[HCP-Users] Integration of FIX cleanup with the minimal preprocessing pipeline

Dear HCP Could you give the details of how you integrated the FIX cleanup with the minimal processing pipelines, to generate the cleaned rsBOLD data? More specifically, MELODIC should be applied in native space after motion correction and correction of distortions with the fieldmap. It seems

Re: [HCP-Users] Integration of FIX cleanup with the minimal preprocessing pipeline

Hi Julien, We simply ran melodic FIX on the MNI space volume results of each resting state run (i.e. the outputs of the minimal preprocessing pipelines). The cleanup was then applied to both the volume timeseries and the CIFTI timeseries. Look in the FIX distribution for a shell script

Re: [HCP-Users] spin echo phase encoding direction

I'm slightly more confused now. So, using the CMRR sequences, if I set the phase encoding direction on my spin echo to AP, and Invert RO/PE Polarity option is checked... a) what is the actual phase direction of the data b) what is recorded in the DICOM header in the *.dInPlaneRot field?

Re: [HCP-Users] spin echo phase encoding direction

Hi, If you had AP with Invert RO/PE Polarity checked, then that would be the same as if you had set PA andInvert RO/PE Polarity was left unchecked. The *dInPlaneRot field does NOT include the impact of theInvert RO/PE Polarity flag. Sorry, I directed you to the wrong shadow field

Re: [HCP-Users] spin echo phase encoding direction

Ok, good to know what that means as to how the data is collected relative to the label. So with the original example of a console entered AP, what does that mean if the PhaseEncodingDirectionPositive is 1 or 0? -G From: Harms, Michael [mha...@wustl.edu] Sent:

Re: [HCP-Users] spin echo phase encoding direction

Hi Greg, Ultimately, getting all the signs right is a complicated combination of (1) how the manufacturer implements its PE gradient blips, (2) the DICOM to NIFTI converter that you use (and whether you 'reorient' the data, e.g., using 'fslreorient2std'), (3) your settings for Phase enc.