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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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-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-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_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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> tjL-U3LQRsdN6UgbGMfC_7WZBab2gNkQTjwNNyX6ASrpu7wv9IP-39nhkFqznIyXzOBqA4
> RGb3euhx3CJJ1MonbJMEudvFDFJPzz1sIosXRL8AdfksucPZRDsBlnr7mWntz82Thyd5M6
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> n%2Flistinfo%2Ffreesurfer
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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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