I'm not sure what files you copied over. For the initial run of recon-all, you need to specify input files using '-i <input image>' option. See recon-all wiki help page for detail: 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: Saturday, March 2, 2024 1:37 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] lack of volume called 001.mgz
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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-L3dyFVwTAhmaZp1yuY... 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/1ufOUDYmRZBZH5OvNEdAvUSqehiGigkQXoMoJ5I3aSHOfsc3...
Could you please give me advice what is wrong?
Best regards, Joanna
W dniu 2024-01-08 23:25, fsbuild napisał(a):
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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 YHUANG43@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-UYpPPpt MAbFi-NJiLZF1zFn86PASJOkrN6-GWw1d4D3OrHd1v-GqrcqNMoqsq_voJWaLftiEd-vak jsu5IvQ6kyUg5k7ghDpdCZU14EMBNDP8eYcsCjl1E5D5gNql2i-Y9Zu1Kpc6TuQh3odI2O ietrxyv5hM2H9YDVJ2J51cEZLa2CHRqUpe5QTE89g3k1kNK7jl8nNBK5kqYLoLEuZ-gJrr h_Ac2wDqYS5bIbjvKJN4lXnWjHzt6IJAq6spPNw_wAGm40hlLBAz-b5P1MtR3NajhBpUlp PBt-Yo9PLR0TwzBHrCLiHA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswi ki%2Frecon-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 CautionHello 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_zO3z1vpgSTaPhhhrJHE6mFgjDwcJg3vFC VfZAwtvXgTVrtcAutSPTrtciZPyxNbynvc15Hs2QuWbY_5s83lqlEQoYQJki7l_TF3ozta fbzs30sHpSw0h-eZSPjzJ5uVCT29lxgi-ynPEhcVbMEKprxj8oqXGxzhvsFrvGlrQlowS6 73v0V1k05awg3ja96pJZpAes0ADbo-3Cdp-F5Ia5oD5q7fabDh5N202LPH9PNC1ruPvKvy _5987OSpV7RTftXJev5hauvVESrxnACVsA0f5bGY-t55yLWz2a-Tkq1eIulXgNxAa228gM MBHaDYc4X4fiJjG0re3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswi ki%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_4NI9T7PYgKG5FAtbmkvQ7vxtAU ykGwuliarvPShgKfL_ItgaKWWnaYhDjK5FMWmDuPGEEEjW91LA3z7KDEeMiaIfV2jyXtfo UeeAjtPetkV6AuryGQBEKfk8d73IpHcgRIPrySwzLQaUtJT-A3dciz-Ma0n5qP4wsp5g9T jvw5bGZUJlDFhJwWQrn04-RanD9XSLv0hlRr6ygjNO1BDIi4FgyjW3UWknkdWZwG9r4rG9 cdS5Q0g6fBJ_QfVYe1DlgOs71lVji4Q7vMKZoWhEAgKq_5yhthldQEcJLHUmFLDrBcBX1T XcVwnrmkcLYG8z3GWHohA/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
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-- ---------------------------------------------------------------------------------- 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
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