External Email - Use Caution I REGISTERED TO THIS MAILING LIST AND HERE IS WHAT HAPPENED:
1.I'M FLOODED WITH EMAILS - I DONT WANT THAT 2 TWICE I ASKED TO BE UNSUBSCRIBED - SEEMS IT DIDN'T WORK - STILL BEING FLOODED WHO CAN HELP/WHO DO I EMAIL?? Dr Katarzyna Cieśla-Seifer The Baruch Ivcher Institute for Brain, Cognition & Technology, The Baruch Ivcher School of Psychology and the Ruth and Meir Rosental Brain Imaging Center, Reichman University, Herzliya, Israel, World Hearing Center, Warsaw, Poland On Thu, 24 Apr 2025, 05:44 Dorian Pustina, <alb...@gmail.com> wrote: > External Email - Use Caution > > Hi all, I have some questions regarding failed segmentations on > longitudinal data. > > We have large datasets of Huntington's disease with data collected > longitudinally for 3-10 years. Freesurfer is our main tool to extract > volumetric scores, particularly in caudate and putamen. > > I usually QC Freesurfer segmentations and include the fail/pass status for > other researchers to use. I inspect the segmentation of the cross-sectional > pipeline because I noticed that mis-segmentations are clearer and the > longitudinal pipeline does not seem to correct them. For example, a > displaced putamen segmentation in cross-sectional pipeline becomes just > more fuzzy in the longitudinal pipeline with more peppered voxels at the > edges. So basically, my QC of the cross-sectional segmentation decides if > the timepoint is good or not. > > > I have three questions: > 1. Is my understanding correct that a motion corrupted scan (i.e., with > motion rings) is going to affect the other timepoints by compromising the > SST? Thus the only solution would be to exclude the motion > corrupt timepoint from FS processing? And in case the timepoint has been > processed with FS, is the best practice to exclude the entire subject given > that the bad scan have compromised the accuracy of other timepoint > segmentations? > 2. On a different scneario, if a timepoint has a good scan but > Freesurfer's segmentation is simply innacurate or displaced, is this bad > segmentation at the cross-sectional level going to affect the other > timepoints after running the longitudinal pipeline? > 3. This is the most important question: is there a common recommendation > or practice how to deal with failed segmentations in the longitudinal > pipeline? Correcting manually the segmentations is not an option, so I am > asking whether we can just exclude the failed segmentation timepoint from > the analysis or whether we should exclude the entire subject? > > Thank you for sharing any thoughts. I cannot seem to find information on > this topic on papers or the mailing list, so any tips on how you or your > lab deals with these issues can help. > > Dorian > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1dPyJ-H_6lSX1PaFE8CdZjZt87rnXpa5tM0jicN4OCjEoBbuufqk7uvMcXEWPS661IHRStQJq59NcLuoyYVQdteIzQT7bWehD2a86pgTqn0W_bqgAsEfIKja-6PRIfAOTFD9JA8mStZyyJLhvhmIqJrz5V8AHXl7s1IyTtIbcSl7rmZokVoR0aWIHCHpv5VNut8XmB_E8xfc-GUgHoxQ9xLxl7OzlTdndyJz2fi20sNAUdDb8FMsMezfvkeLwQm04qAly35OYaxtMoyRHmfhhViMGe6Ppx_uCdl2TrtFwIUanCoL8MIYwPK1VGzIDLaTo1wTuyT2MWiKCP4owaIZAsA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/10GSO_FccmKv1OZRZgz_HgHOu8POqpO7xq2ofAd5jhq1Tih5Ep0INPhv1Kmcg3A-rc7eJbd9OJj6_KNIjIK9AZVW0wXz6PDxehaqHk9I1ScRTSYZcoyVVTiDlnIOmm_4XkdAWVuOfZY_R8HrITuXczZvL46xNPNoFzsw7-3ZZey7xKYv5jJXGGRsyl5TkqC5MG3poXNhi8chqtHIZheGH4yNtolkMsrdqJl-erjWgZUmoLGx0EoRJDsVrDEXrewAFCHXP9X1Juv10C34Ck2QN8cRZ4vTuUr2gxeABCTQ95hwq0Yoiz3YIT4pDXrIV7JHpoF1iUqFDbn5V7_eQZi1YoQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/10GSO_FccmKv1OZRZgz_HgHOu8POqpO7xq2ofAd5jhq1Tih5Ep0INPhv1Kmcg3A-rc7eJbd9OJj6_KNIjIK9AZVW0wXz6PDxehaqHk9I1ScRTSYZcoyVVTiDlnIOmm_4XkdAWVuOfZY_R8HrITuXczZvL46xNPNoFzsw7-3ZZey7xKYv5jJXGGRsyl5TkqC5MG3poXNhi8chqtHIZheGH4yNtolkMsrdqJl-erjWgZUmoLGx0EoRJDsVrDEXrewAFCHXP9X1Juv10C34Ck2QN8cRZ4vTuUr2gxeABCTQ95hwq0Yoiz3YIT4pDXrIV7JHpoF1iUqFDbn5V7_eQZi1YoQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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