External Email - Use Caution Dear Yujing,
Thank you very much for your help, but I still have a problem. I copied the files to create another SUBJECTS_DIR inside my Linux...I get the following error when I run the recon-all -all -s command: gcm@LAP-LKP:~$ recon-all -all -s NowakG fs-check-version --s NowakG --o /tmp/tmp.W9nDpk Sat Mar 2 19:14:18 CET 2024 setenv SUBJECTS_DIR /subjects cd /home/gcm /usr/local/freesurfer/7.3.2/bin/fs-check-version --s NowakG --o /tmp/tmp.W9nDpk -rwxr-xr-x 1 root root 18565 Aug 4 2022 /usr/local/freesurfer/7.3.2/bin/fs-check-version freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 $Id$ 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 pid 2145 Current FS Version freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 bstampfile exists /subjects/NowakG/scripts/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 /subjects Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2 -rw-rw-r-- 1 gcm gcm 89354 Mar 2 18:42 /subjects/NowakG/scripts/recon-all.log 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 Sat Mar 2 19:14:18 CET 2024 ERROR: no run data found in /subjects/NowakG/mri. Make sure to have a volume called 001.mgz in /subjects/NowakG/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://secure-web.cisco.com/1tuieePwmpGJNz-se1po4eAte-Piv-L3dyFVwTAhmaZp1yuYYA6WDplZIn_eOMWSQ6XNWLWosRbbqgelF1dP6cwLzm49NGnC06aPYcm9dVEqiJHPlKBBJdCOCc5UpBZKFISeT2vAsKPmtPe5bSN1PtnI37qzrEzfKZy04iVyZ7gO9j5K9chOEjC-f8PIW5LZ1QreMBW2MF4XAAmUD9cfwmgL-W-Xp87kV3_MnP7BzXmeq7Jcd1g7syzCCfGmQTOgp8StEekKQqnO96-4yhVqPeMcxevRvfvieGQEmdvybuW2fdVKNNP-v_6GslOFvUscl9fCLKOFTtLXKsa3Hnw_gYg/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 Sat Mar 2 19:14:18 CET 2024 For more details, see the log file /subjects/NowakG/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1ufOUDYmRZBZH5OvNEdAvUSqehiGigkQXoMoJ5I3aSHOfsc36kcTvYNgNB3aBZ4jVdHB0nuAnVNJWxdRwzvXmwEPI3gDUdU4QRXnZbUR1wcB5OQxntw7Z5gopDmzqs9na5EBTZln5BzgpoULJxgLdPUVbjXFh90-tX1tjhSxELnft_ckbwlGbLrRKwrBBCKMy_wZKQlYHCq_mwPmJG9BFcPayLVp7kVjiKDvmTBGdY6Zu5EuMOFDJ2P8ZQVDTueZfXLtA67Bvr353l_R5YXyreMeaC-ozgMEC92WM24o5BpFOk4M0MsW9VOofqZy5uFd7nnpikbOdTUnpE4XwkWOz8A/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting Could you please give me advice what is wrong? Best regards, Joanna W dniu 2024-01-08 23:25, fsbuild napisał(a): > 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/1BjMQpgiIYbM2liRLcu1lhuxV-DQbuX4Z-UYpPPptMAbFi-NJiLZF1zFn86PASJOkrN6-GWw1d4D3OrHd1v-GqrcqNMoqsq_voJWaLftiEd-vakjsu5IvQ6kyUg5k7ghDpdCZU14EMBNDP8eYcsCjl1E5D5gNql2i-Y9Zu1Kpc6TuQh3odI2Oietrxyv5hM2H9YDVJ2J51cEZLa2CHRqUpe5QTE89g3k1kNK7jl8nNBK5kqYLoLEuZ-gJrrh_Ac2wDqYS5bIbjvKJN4lXnWjHzt6IJAq6spPNw_wAGm40hlLBAz-b5P1MtR3NajhBpUlpPBt-Yo9PLR0TwzBHrCLiHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all > > Best, > > Yujing > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@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_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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/10zVV5ob8j-xslZI-DDJqj4lnlBCC7oACBlOZSaOFnyh3PBCopWOoIFdE4zoFsjEaZfJeuHT36OuR6YFiU63ygQJREaDl56qXjbibliv0GOv2aMtjL-U3LQRsdN6UgbGMfC_7WZBab2gNkQTjwNNyX6ASrpu7wv9IP-39nhkFqznIyXzOBqA4RGb3euhx3CJJ1MonbJMEudvFDFJPzz1sIosXRL8AdfksucPZRDsBlnr7mWntz82Thyd5M6kM_Sp6CQ2AjoEOhRbuNMC_dbYfr3YFRzXkr33gqeIUOn21hAc3duxfyHOW0wBTddkRmNeOZYqUv19TGgK918yw9Q0TlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/10zVV5ob8j-xslZI-DDJqj4lnlBCC7oACBlOZSaOFnyh3PBCopWOoIFdE4zoFsjEaZfJeuHT36OuR6YFiU63ygQJREaDl56qXjbibliv0GOv2aMtjL-U3LQRsdN6UgbGMfC_7WZBab2gNkQTjwNNyX6ASrpu7wv9IP-39nhkFqznIyXzOBqA4RGb3euhx3CJJ1MonbJMEudvFDFJPzz1sIosXRL8AdfksucPZRDsBlnr7mWntz82Thyd5M6kM_Sp6CQ2AjoEOhRbuNMC_dbYfr3YFRzXkr33gqeIUOn21hAc3duxfyHOW0wBTddkRmNeOZYqUv19TGgK918yw9Q0TlA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately. Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. -- ---------------------------------------------------------------------------------- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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