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" <[email protected]>: > 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 <[email protected]> > Date: Thursday, February 12, 2015 at 11:08 AM > To: "[email protected]" <[email protected]> > 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 > [email protected] > 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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
