External Email - Use Caution Hi Yujing,
Thanks for your reply – I have a follow up query (see email thread below): I have both a cross-sectional aim and a longitudinal aim I am hoping to explore with FreeSurfer. While they are separate aims, some participants are present in both the cross-sectional and longitudinal arm. Currently I have run recon-all on all participants for my study using the standard recon-all command. As mentioned, I am hoping to do hippocampal subfield analysis (both cross-sectional and longitudinal). I have read both the hippocampal subfield and longitudinal pipelines available from FreeSurfer (linked below): https://secure-web.cisco.com/1_iq2Ortiz8d4uJhrtEXKZ_Row3SgFJsQNSJUW3b3hm3Fpyvv5sgZR-m4xdjP3Z6_2isSOMQhCU8MRxYVOpq-wsDe0LhbN8SiW48hsAGJdad_Q9Rtk_v2ev-vu6dTtSwkmEAg4sMTudXxhQ6l_omqdcZ5t9qUqJ-XsyszO_Dm0lqUbyrbPT0cSp2Nfp3K8nocfh7Lb8kgqsSzV_zXgsGscmSj-8CPjJkIIWzAkN_JDX41FMLqJgCiScG73AwWrhMnJ4Wb9tYZDCilC-2Fup0qu1J0PKTp0EavwmpjblLt8caLhQS2VUUca2hYZFQ1ApYKgG4hOXqj1JYHXI00qmSMlw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing https://secure-web.cisco.com/1K3vQAJc_XjPimaagPX_W_n-ig3v4kt3fgvsYNoj9HGxxFdrBKEtytPLhzNPZ7fx6uNnvYfnFqO8u95gLEQpxAOqEuVbVywv3kN4vmxyNnk-IHZtg_7o2B-xXyQdhbviDAJ5BaIWX7KoXao8dkm7YTvh4YiaT8yA1q9TEMy66c6OuXiFjYcXmmGyJjt0vUpEUBwTBw0QNwh-vEEN0OzvT7qBwdqESofUTjMHDGJjIDtEROwCtYWn8xvd0Z79-fD1MFHtJgp3Gd7DfuIbMc3oFy3KFk-5i0SEAMKzfdyY6x3Me3ABEWBNvXQmLvd1EbCvfaMQqmq6waaOx98qxVev3eA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala I was planning on running the longitudinal recon-all pipeline as it seems that running longitudinal pipeline allows for greater reliability as "the subject is used as their own control". But if I do this, then the subjects that are also in the cross-sectional arm will potentially have different outputs (even though they are the same scan) compared to outputs from the longitudinal pipeline. This would be the same for the subfield analysis. What is the best approach here? Would I be better off running all participants (even those with one T1-weighted scan) with the longitudinal pipeline so that every participant is treated the homogenously? Let me know if I need to clarify anything! Warm regards, Jack Hi Jack, Longitudinal recon-all pipeline is available in Freesurfer 7.3.2. To do longitudinal segmentation using the hippocampal subfield pipeline, it is a requirement that the data have been processed with the longitudinal stream Freesurfer. Best, Yujing 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 Jackson Lee Sent: Wednesday, July 12, 2023 10:25 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2) External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipeline available in FreeSurfer: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalChangeLog<https://secure-web.cisco.com/1Y9uqixBqGC2B0XHSMg2zr4QS96oUVSkkZcMdhRqdEkVD1KblmslkRndxPSvHW3LBNES_IqNsfYFPgJ0qwhvc1bNFhpnjhfJbHFnw_JsG65hDnTYTh0tH7f-TFks6LnM0ShLPbcTaqRM3Ot0icc5Qz_q6LdCD7ArrMeBy-ZAdoU36C3aO2YWeJUSYV7V1ziGk9n8wLoM3ExyKYNOgnUc1ECoCPAxei2kkH5NycZEWbOU3lH1BrNSjGuSyBOv-39-ZdPFU28SYlq9ASUOR3nT6_1bci2ZeViPVJ1yWa4fuw2q150BmfUOtkpMHpCeEh8c_XtRYiQTDNa9dwtnGNQeSNA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalChangeLog> Will this pipeline work for FreeSurfer v7.3.2? I cannot see any resources to suggest this is the case. Additionally, I am hoping to conduct some longitudinal analysis using the hippocampal subfield pipeline: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala<https://secure-web.cisco.com/1ILqdmv74otr5LeRS7UQz83p5UDddkh5pv-Luvs5PHnW-6BfivGurDffrJ3MLUO6_g51fdQTLLVgIlCbkxz5HvAXXSVsYl5DXzxX7vuZYuXle0lC8SiAlMxablGmyrpj5kLiT4ur9kz0mN3fPEMReUKCskogc5WXK6BMHzhCAT8xCcztE2TUmLJDn6PZN5XiYr_4CE3ZPhwUrzW3qtPXA6aBDo11WlFO7kBKH5exeJUJ2i66Ot29HyeIuOKUQ-suEyIZKsZQ4iyRJMNCLSXJpr-ryBfctpn-E6mEynv9KcCJmJG3V6eJtPJnv5EdktzlUirApmR8nLA-iMVNLDVlJAg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala> Would the best course of action be to run recon-all with the longitudinal pipeline first (assuming it is applicable for freeSurfer v7.3.2) and then use the longitudinal command for post-hoc subfield analysis?: segmentHA_T1_long.sh <baseID> [SUBJECTS_DIR] Thank you, Jack
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