To add some context, the _acpc_dc_restore_brain versions of the files are *outputs* of the structural pipelines. We do not run freesurfer on masked T1w images.
Matt is asking for the exact arguments you provided to FreeSurferPipeline.sh, by providing the full command line that was run that contains "FreeSurferPipeline.sh" (not the ...Batch.sh). Tim On Tue, Apr 9, 2019 at 9:21 AM Glasser, Matthew <glass...@wustl.edu> wrote: > How did YOU call the FreeSurfer Pipeline in your subject with an issue? > > Matt. > > From: Aaron C <aaroncr...@outlook.com> > Date: Tuesday, April 9, 2019 at 8:42 AM > To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" < > hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Some questions about the HCP structural > processing pipeline > > Hi Matt, > > I called the FreeSurfer pipeline using the script > "FreeSurferPipelineBatch.sh" in the "Examples" folder. Do you mean that > these brain extracted T1w and T2w images "T1w_acpc_dc_restore_brain.nii.gz" > and "T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the > FreeSurfer pipeline? Thank you. > > Aaron > > ------------------------------ > *From:* Glasser, Matthew <glass...@wustl.edu> > *Sent:* Monday, April 8, 2019 10:50 PM > *To:* Aaron C; hcp-users@humanconnectome.org > *Subject:* Re: [HCP-Users] Some questions about the HCP structural > processing pipeline > > The brain masked file should not be used for surface estimation. How are > you calling the FreeSurfer pipeline? > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Aaron C < > aaroncr...@outlook.com> > Date: Monday, April 8, 2019 at 9:41 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Some questions about the HCP structural processing > pipeline > > Dear HCP experts, > > I have some questions about the HCP structural processing pipeline. > > 1. The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the > T1w folder has excessive voxels removed in the cortical surface, which > resulted in erroneous pial surface estimation. Is there a way that I could > adjust any parameters of brain extraction in the PreFreeSurfer.sh file to > have a larger brain mask? > 2. There is another file "brainmask_fs.nii.gz". Is this the same mask > derived from "T1w_acpc_dc_restore_brain.nii.gz" and > "T2w_acpc_dc_restore_brain.nii.gz"? > 3. In the structural processing QC scene, is there a way that I could > also display the boundary of the extracted brain alongside with pial and > white surfaces in the coronal brain? > > Thank you. > > _______________________________________________ > 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
