Hi Matt, Thanks for the information! I was able to successfully run the PreFreeSurfer pipeline by specifying the T1w image as the T2w image. The FreeSurfer pipeline is running now, and I expect to be able to run the PostFreeSurfer pipeline next, since I have the output files from the PreFreeSurfer pipeline to use as inputs into the PostFreeSurfer pipeline.
The main reason that I am wanting to convert my legacy data into CIFTI space is to map the Glasser et al., 2016 MMP average parcellation scheme to my data. Since the lack of field maps makes accurately registering the BOLD scan to the T1w image problematic, I will apply the subject-specific NIFTI/CIFTI transformation matrix to the parcellated CIFTI file in order to map the parcels onto the subject’s volume space and then do my analysis of the BOLD data in volume space. Thanks again for the help! Best, Kelli > On Oct 4, 2016, at 5:35 AM, Glasser, Matthew <glass...@wustl.edu> wrote: > > The lack of a field map is the larger issue, as it makes accurately > registering the EPI to the T1w image problematic. Some folks have made use > of an “average field map” to attempt to improve upon this situation, but I > don’t have this code or personal experience with this. > > Lacking the T2w image need not necessarily prevent mapping fMRI data to CIFTI > as one can take the non T2w parts of PreFreeSurfer (basically everything > except the T2w to T1w registration and the bias correction), do things like > specifying the T1w image as the T2w image (e.g. for the MNI registration), > run FreeSurfer on its own, and then specify the T1w image as the T2w image > for PostFreeSurfer. A script that does all of this exists, but is not an > “official pipeline.” > > Peace, > > Matt. > > From: Kelli Cannon <kecanno...@gmail.com <mailto:kecanno...@gmail.com>> > Date: Monday, October 3, 2016 at 5:32 PM > To: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>> > Cc: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> > Subject: Converting legacy data to CIFTI format > > Hello, > > I would like to convert a legacy dataset into CIFTI format. The legacy > dataset lacks T2-weighted images or field maps. How does the HCP advise that > investigators go about converting legacy data into CIFTI format? I assume > this must be possible, as we can use FreeSurfer to convert to flat maps with > such data... > > For the structural data, the PreFreeSurfer pipeline requires both a T1w and a > T2w image, so it can not be used on the legacy dataset. One can run the T1w > images through FreeSurfer’s recon-all to approximate the HCP FreeSurfer > pipeline for lower-resolution data. However, the PostFreeSurfer pipeline > requires additional input files (e.g., T1w_acpc_dc_restore.nii.gz) that are > not included in the FreeSurfer output. > > Is there a reasonably straightforward way of converting legacy data without > T2w images into CIFTI format? If not, does HCP plan to create a pipeline for > preprocessing legacy data? > > > Best regards, > > Kelli Cannon > Graduate Student > UAB Department of Vision Science > kecan...@uab.edu <mailto:kecan...@uab.edu> > > > > 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
