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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_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3oztafbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS673v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy_5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gMMBHaDYc4X4fiJjG0re3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala, 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_4NI9T7PYgKG5FAtbmkvQ7vxtAUykGwuliarvPShgKfL_ItgaKWWnaYhDjK5FMWmDuPGEEEjW91LA3z7KDEeMiaIfV2jyXtfoUeeAjtPetkV6AuryGQBEKfk8d73IpHcgRIPrySwzLQaUtJT-A3dciz-Ma0n5qP4wsp5g9Tjvw5bGZUJlDFhJwWQrn04-RanD9XSLv0hlRr6ygjNO1BDIi4FgyjW3UWknkdWZwG9r4rG9cdS5Q0g6fBJ_QfVYe1DlgOs71lVji4Q7vMKZoWhEAgKq_5yhthldQEcJLHUmFLDrBcBX1TXcVwnrmkcLYG8z3GWHohA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FConversion
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

<<attachment: scripts.zip>>

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