External Email - Use Caution Let me add that it will not work to use shared mount point from the Windows filesystem as you list below, /mnt/c/Users/GCM/Desktop/subjects/NowakG/mri - for your SUBJECTS_DIR when running a recon-all command. The command will fail because the Windows file system does not support soft-links. Any SUBJECTS_DIR used for recon-all needs to be inside the Linux OS image running freesurfer. You could however copy the files from that mount point to create another SUBJECTS_DIR somewhere inside your Linux image, e.g., under your home directory in linux. .... in your linux terminal window ... $ cd$ mkdir subjects$ export SUBJECTS_DIR=$HOME/subjects$ cd $SUBJECTS_DIR$ cp -p -f -R /mnt/c/Users/GCM/Desktop/subjects/NowakG . - R.
On Jan 8, 2024, at 16:10, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote:You need to specify the input files to process. Here is the wiki page for recon-all - https://secure-web.cisco.com/1hqVY7QioPnD85rxOcGMUcCuynnW47DWZwkPX0Z-CZpPZhsuOE3Dqq56yZOR48pnqlARbSGSU1uJNTssTzOLeJZDej-4B4APtXHQmIDTAeNiz6injsGyGghBE4szgzC-CIvlktYVKAeIFD9vBNBZGTgRtRAfcxOZTJJXzk0kPtE9fSY8vo9o05Q8Lf5La4t7Av6IvB6hkO3ZqlfaDGIxlZfRhNJC0f5oWDNXpfp8nYykG-egLh8zOuhOsHSbWCac7UKV67GamZPc5FS5KwH3vo_4_Omj5v0dIRxZ5O4d9WtJGN0f3IkrLaqnXHmnqhmI4YmYtNQmp-0UBF38a-xfw4w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-allBest,Yujing-----Original Message-----From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Joanna KidonSent: Monday, January 8, 2024 3:33 PMTo: freesur...@nmr.mgh.harvard.eduSubject: [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/1JRIAQtmLphlXIykU3RsSWy2GeEv_y0Em3hHjyX02njKQRMzktRXyIr6AsUKD8-6mfnHs3e3VqgraV5HY65g0kcdnn-c5SO11uj3GmVopw6uBvHuq9nL41NZthselkwcmF1_pfF7tqA1mMsAKXVbGF7kWv-nHwevhhA8F6Ut_G89GsS36wOdw4Qdt0y3NAVk7FFD73D5O1AlLLXsiM0_emjpApIZBLEppGP5jjmBYXvnW-lkYFHOz1Mpazf7b7a-Tkol4Hrp9s-ygaeijb4CyTVrQYXiaqfwLwo5L2QmewMDyINYXoiDYTFnRY1ZnSd75iVr_Rv6sEbBi2merzCpAuQ/https%3A%2F%2Fsecure-web..cisco.com%2F1thysYb_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFCVfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3oztafbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS673v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy_5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gMMBHaDYc4X4fiJjG0re3rdg%2Fhttps%253A%252F%252Fsurfer..nmr.mgh.harvard.edu%252Ffswiki%252FHippocampalSubfieldsAndNucleiOfAmygdala,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.txtSubject FS Version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version DoneINFO: 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 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux#--------------------------------------------#@# MotionCor Sun Jan 7 20:48:46 CET 2024ERROR: 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%2FConversionLinux LAP-LKP 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 521:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s NowakG exited with ERRORS at Sun Jan 7 20:48:46 CET 2024I'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 KatowicachPhD, 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_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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