You need to specify the input files to process. Here is the wiki page for recon-all - https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
Best,
Yujing
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Joanna Kidon Sent: Monday, January 8, 2024 3:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Subject does not have a bstampfile
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), as described on the https://secure-web.cisco.com/1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwt..., but I get the following error when I run the recon-all -all -s command:
Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /mnt/c/Users/GCM/Desktop/subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Sun Jan 7 20:48:46 CET 2024 ERROR: no run data found in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://secure-web.cisco.com/1YoN1A69KdRcMav_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwul... Linux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s NowakG exited with ERRORS at Sun Jan 7 20:48:46 CET 2024
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the scripts/recon-all.log in case it's of any use.
Best regards,
Joanna
-- ---------------------------------------------------------------------------------- dr n.med., specjalista fizyki medycznej, neurobiolog Przewodnicząca Sekcji Diagnostyki Obrazowej Polskiego Towarzystwa Fizyki Medycznej Zakład Kardiologii Inwazyjnej i Elektrokardiologii, III Katedra Kardiologii Śląski Uniwersytet Medyczny w Katowicach Kierownik Działu Fizyki Medycznej, Koordynator ds. Ochrony Radiologicznej Z-ca Kierownika Zakładu Diagnostyki Obrazowej Górnośląskie Centrum Medycznego im. prof. L. Gieca SUM w Katowicach
PhD, specialist in medical physics, neurobiologist Chairwoman of the Diagnostic Imaging Section of the Polish Society of Medical Physics Department of Invasive Cardiology and Electrocardiology, 3rd Department of Cardiology, Medical University of Silesia in Katowice Head of the Medical Physics Department, Coordinator for Radiological Protection, Deputy Head of the Department of Diagnostic Imaging Leszek Giec Upper-Silesian Medical Centre of the Medical University of Silesia in Katowice