Comments (7)
m-reuter
commented on September 2, 2024
hi @zhangcc89claire ,
this is a separate issue which is why I moved it here.
Probably your bash is too old to understand the |& command (which was added in bash 4 I think). You can update your bash to a more recent version or replace all occurrences with the equivalent:
2>&1 |
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zhangcc89claire
commented on September 2, 2024
Thank you very much for your reply. I have checked bash and it is the
latest version as follows：
clairedeiMac:FastSurfer-master claire$ echo $BASH && echo $BASH_VERSION
/usr/local/bin/bash
5.0.17(1)-release
May I ask if there are other possible reasons that need to be investigated?
Martin Reuter <[email protected]> 于2020年7月3日周五 上午4:18写道：
… hi @zhangcc89claire <https://github.com/zhangcc89claire> ,
this is a separate issue which is why I moved it here.
Probably your bash is too old to understand the |& command (which was
added in bash 4 I think). You can update your bash to a more recent version
or replace all occurrences with the equivalent:
2>&1 |
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m-reuter
commented on September 2, 2024
Do you have a working FreeSurfer 6.0 install?
What OS are you running on?
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LeHenschel
commented on September 2, 2024
Hey,
could you paste the exact command you tried to run? And which operating system you are using? I ran it on ubuntu 20.04 with bash 5.0.16(1)-release and could not replicate the error.
In addition, you could try to change just the command in line 227 and 228 as proposed by Martin from
echo $cmd |& tee -a $seg_log
$cmd |& tee -a $seg_log
to
echo $cmd 2>&1 | tee -a $seg_log
$cmd 2>&1 | tee -a $seg_log
and see if you still get the same error.
Thank you
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zhangcc89claire
commented on September 2, 2024
Thanks very much for your reply.My operating system is macOS High Sierra
10.13.6 (17G65)
The errors I encountered are as follows：
(base) clairedeiMac:~ claire$ echo $BASH_VERSION
5.0.17(1)-release
(base) clairedeiMac:~ claire$ export
FREESURFER_HOME=/Applications/freesurfer
(base) clairedeiMac:~ claire$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
…-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /usr/local/fsl
(base) clairedeiMac:~ claire$ cd
/Users/claire/Downloads/FastSurfer-masterdatadir=/Users/claire/Downloads/FastSurfer-master/my_mri_data
*./run_fastsurfer.sh --fs_license /Users/claire/Downloads/license.txt \*
* --t1
/Users/claire/Downloads/FastSurfer-master/my_mri_data/subject1/orig.mgz \*
* --seg
/Users/claire/Downloads/FastSurfer-master/my_fastsurfer_analysis/subject1/aparc.DKTatlas+aseg.deep.mgz
\*
* --sid subject1 --sd
/Users/claire/Downloads/FastSurfer-master/my_fastsurfer_analysis *
*./run_fastsurfer.sh:line 1: #!/bin/bash: No such file or director*
*./run_fastsurfer.sh: line 227: syntax error near unexpected token `&'*
Best,
Claire
LeHenschel <[email protected]> 于2020年7月3日周五 下午3:21写道：
Hey,
could you paste the exact command you tried to run? And which operating
system you are using? I ran it on ubuntu 20.04 with bash 5.0.16(1)-release
and could not replicate the error.
Thank you
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m-reuter
commented on September 2, 2024
Currently we do not support MacOS. You would have to use docker for now. Sorry.
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m-reuter
commented on September 2, 2024
Update: in our upcoming release we added support for Mac (Intel cpu-based and M Apple Silicon also GPU on mps device) for the segmentation. Furthermore, we updated install instructions (especially to update the bash shell) and modified recon-surf slightly in #198 to run through. We do not do any testing on the Mac, so you should inspect results.
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