External Email - Use Caution

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Jackson Lee Sent: Wednesday, July 12, 2023 10:25 PM To: 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 be https://secure-web.cisco.com/1rjzSRM7XyYIrwxdRy5gllQ3MFY6Ekfl5LgAbGYQx3Q_uRj...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 be https://secure-web.cisco.com/1Rbv93YNJu7dRSYcAzatOQnek66Wn2qAlIPnTu_46ZvTAZ1...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