Thanks for your help. - Anders
2015-02-23 23:23 GMT+01:00 Marcus, Dan <[email protected]>: > Actually, the files are in ConnectomeDB but not in the downloadable > packages. You can get to individual subject files using the XNAT REST API, > something like this (after logging in of course): > > > https://db.humanconnectome.org/data/projects/HCP_500/subjects/100307/experiments/100307_3T/resources/tfMRI_WM_RL_preproc/files/MNINonLinear/Results/tfMRI_WM_RL/tfMRI_WM_RL_SBRef.nii.gz > > Replace the subject (100307), session (100307_3T), and series > (tfMRIWMRL_preproc) portions > to get to other data. A little basic scripting, and you should be able to > pull down all of the files. > > -Dan > > From: <Glasser>, Matthew Glasser <[email protected]> > Date: Thursday, February 12, 2015 7:32 PM > To: Anders Eklund <[email protected]> > > Cc: "[email protected]" <[email protected]> > Subject: Re: [HCP-Users] Preprocessing questions > > 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 <[email protected]> > Date: Thursday, February 12, 2015 at 11:57 AM > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > 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" <[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. >> > > ------------------------------ > > 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 > > -- Anders Eklund, PhD _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
