Hi Zeke, please look this error. Thanks Stefano
recon-all -all -s 150706samspe/T1_STRUCT.nii.gz -i $SUBJECTS_DIR/150706samspe/T1_STRUCT.nii.gz -hippocampal-subfields-T1 Subject Stamp: freesurfer-Darwin-OSX-dev-20151214 Current Stamp: freesurfer-Darwin-OSX-dev-20151214 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/T1_STRUCT.nii.gz \n mri_convert /Applications/freesurfer/subjects/150706samspe/T1_STRUCT.nii.gz /Applications/freesurfer/subjects/T1_STRUCT.nii.gz/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/150706samspe/T1_STRUCT. nii.gz /Applications/freesurfer/subjects/T1_STRUCT.nii.gz/mri/orig/001. mgz
-------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.
-------------------------------------------------------------------------- $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /Applications/freesurfer/subjects/150706samspe/T1_STRUCT. nii.gz... Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
recon-all -s T1_STRUCT.nii.gz exited with ERRORS at Sun Dec 27 14:17: 52 CET 2015
For more details, see the log file /Applications/freesurfer/subjects/T1_STRUCT.nii.gz/scripts/recon-all. log To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting
----Messaggio originale---- Da: zkaufman@nmr.mgh.harvard.edu Data: 27-dic-2015 3.42 A: stdp82@virgilio.it, "Freesurfer support list"<freesurfer@nmr.mgh.
harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: Recon-all error
From the recon-all wiki page under "specify input":
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#Specifyinput
In this case you would use the -i flag to point to dicom file or
nifti.
For example:
recon-all -all -s 150622fracal -i </path/to/input_volume> -hippocampal-subfields-T1
-Zeke
Hi Zeke, I'm sorry but I do not understand how run the correct command line. Where I should use --i? Thanks
Stefano
----Messaggio originale---- Da: zkaufman@nmr.mgh.harvard.edu Data: 26-dic-2015 21.50 A: stdp82@virgilio.it, "Freesurfer support list"<freesurfer@nmr.
mgh.
harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Recon-all error
You need to provide input data for the subject. This would either
go
in
the 150622fracal/mri/orig folder or use the -i flag to point to the
input
file.
-Zeke
After this command recon-all -all -s 150622fracal -hippocampal-subfields-T1
this error come out:
Applications/freesurfer/subjects/150622fracal/scripts/recon-all.
log
Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0:
Tue
Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64
x86_64
Can't locate MNI/Startup.pm in @INC (you may need to install the
MNI::
Startup module) (@INC contains:
/Applications/freesurfer/mni/lib/..
/Library/Perl/Updates/5.10.0 /Library/Perl/5.18/darwin-thread-
multi-
2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-
thread-
multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.
18.2
/System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.
18/darwin-
thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. #-------------------------------------------- #@# MotionCor Sat Dec 26 12:57:51 CET 2015 ERROR: no run data found in /Applications/freesurfer/subjects/150622fracal/mri. Make sure to have a volume called 001.mgz in /Applications/freesurfer/subjects/150622fracal/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard. edu/fswiki/FsTutorial/Conversion Darwin iMac-di-Stefano.local 14.5.0 Darwin Kernel Version 14.5.0:
Tue
Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64
x86_64
recon-all -s 150622fracal exited with ERRORS at Sat Dec 26 12:57:
51
CET 2015
For more details, see the log file /Applications/freesurfer/subjects/150622fracal/scripts/recon-all.
log
To report a problem, see http://surfer.nmr.mgh.harvard. edu/fswiki/BugReporting
----Messaggio originale---- Da: zkaufman@nmr.mgh.harvard.edu Data: 26-dic-2015 1.03 A: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu Cc: emad@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Recon-all error
Hello Emad,
Thank you for reporting this. Its a bug specific to the latest
version
of OS X (El Capitan). I have committed the fix and it will
available
after the nightly build. You can download via this link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
Sorry for the inconvenience and thanks for reporting.
-Zeke
Hi,
I ran recon-all on the dicoms of a subject, obtained at Bay 4,
and
I
received the following error:
mris_calc -o lh.area.mid lh.area add lh.area.pial dyld: lazy symbol binding failed: Symbol not found:
___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
Trace/BPT trap Wed Dec 23 21:59:54 EST 2015 ERROR: vertexvol mris_calc -o lh.area.mid lh.area add lh.area.pial Darwin MGH000844.local 15.2.0 Darwin Kernel Version 15.2.0: Fri
Nov
13
19:56:56 PST 2015; root:xnu-3248.20.55~2/RELEASE_X86_64 x86_64
recon-all -s 3Lt_002 exited with ERRORS at Wed Dec 23 21:59:54
EST
2015
For more details, see the log file /Users/Emad/Projects/3LT/subjDir/3Lt_002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I have attached the log file. I’d truly
appreciate
your
help.
Thank you, and with best wishes for a wonderful holiday season
for
everyone, Emad
Emad Ahmadi, MD
Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu
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