External Email - Use Caution Anastasia,
Upon closer inspection the aparc+aseg we have are analogous to the FS labeling, however, the CC is not segmented, it is simply labelled as cortical WM (labels 2/41). Will using Tracula even work at all or will it generate the other tracts but not include the CC minor/major tracts? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Yendiki, Anastasia Sent: Wednesday, October 20, 2021 2:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA * External Email - Caution * Hi Jim - If the file was called $SUBJECTS_DIR/$subj/mri/aparc+aseg.mgz, included the same labels and followed the same lookup table as the OG aparc+aseg, this could work. Note that, for the new TRACULA (in FS 7.2), we recommend also running the thalamic nuclei segmentation, as it helps with the accuracy of the tracts that terminate or neighbor the thalamus. Anastasia. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios <dimitriosalexopou...@wustl.edu<mailto:dimitriosalexopou...@wustl.edu>> Sent: Wednesday, October 20, 2021 2:54 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA External Email - Use Caution External Email - Use Caution Hi, It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. Is this correct? How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs? For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file). Jim ________________________________ 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.
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