Re: [HCP-Users] Preprocessing questions

[Glasser, Matthew]

We don’t distribute those images, as they are only pipeline intermediates.  If you download some of the raw data and run the pipelines yourself (https://github.com/Washington-University/Pipelines), you could show these two images: ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef.nii.gz — Original distorted image ${StudyFolder}/${Subject}/${fMRIName}/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased/FieldMap/SBRef_dc.nii.gz — Undistorted image Peace, Matt. From: Anders Eklund <andek...@gmail.com> Date: Thursday, February 12, 2015 at 11:57 AM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Preprocessing questions I'm giving an fMRI course and would like to show the effect of distortion correction (b0 field). - Anders Den 12 feb 2015 18:14 skrev "Glasser, Matthew" <glass...@wusm.wustl.edu>: The code for that derivation (written by Mark Jenkinson) is posted online: https://github.com/Washington-University/Pipelines/blob/master/global/scripts/aff2rigid.py Yes *_restore means the bias field has been removed. Why do you want to see fMRI data with and without distortion correction?  What kind of distortion are you referring to (gradient distortion correction or b0 distortion correction)? Peace, Matt. From: Anders Eklund <andek...@gmail.com> Date: Thursday, February 12, 2015 at 11:08 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Preprocessing questions Dear HCP users/developers, I was reading the NeuroImage paper "The minimal preprocessing pipelines for the Human Connectome Project" and found the sentence below. Can anyone explain how you went from 12 to 6 parameters? Did you for example calculate the SVD of the 3 x 3 transformation matrix (excluding the translations) and set the 3 singular values to 1? "Next, the average T1w and T2w images are aligned to the MNI space template (with 0.7 mm resolution for the HCP data) using a rigid 6 DOF transform, derived from a 12 DOF affine registration." ---- For the preprocessed structural data (in MNINonLinear), what is the difference between T1w.nii.gz and T1w_restore.nii.gz? A bias field removal? ---- Is it possible to see the fMRI data (e.g. the resting state data) with and without distortion correction, excluding all other operations?  If not, can anyone provide the necessary FSL commands to achieve distortion corrected fMRI data from the unprocessed data? ---- Thanks, Anders _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   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. If you have received this email in error, please immediately notify the sender via telephone or return mail.   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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users