Is python being called from matlab here? It probably has to do with how matlab
sets DYLD_LIBRARY_PATH. I would maybe try using pip to uninstall and reinstall
the fslpython scipy package, but that might be dangerous - I’m not sure how fsl
sets up its python env. I’ll look into it a bit more and get back to you
Andrew
From: Shachar Gal <gal.shac...@gmail.com>
Date: Thursday, February 14, 2019 at 4:31 AM
To: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu>, "ts...@rcmd.org"
<ts...@rcmd.org>, FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] problem using recon-all
External Email - Use Caution
you can ignore the nifti errors in the beginning of the error message, because
it was just a small glitch that I solved. the rest of the errors still stand,
and are unclear to me..
On Thu, 14 Feb 2019 at 11:09, Shachar Gal
<gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> wrote:
Hey,
So I disabled SIP, and tried to run the subject from the beginning, and sadly I
encountered an error while running the PreFreesurfer Pipeline, which worked
fine until disabling SIP.
This is the error message:
** ERROR (nifti_image_read): short header read
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR:
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
bad header info
ERROR: failed to open file
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
** ERROR (nifti_image_read): short header read
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR:
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
bad header info
ERROR: failed to open file
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslreorient2std: line 99: [: too many arguments
/usr/local/fsl/bin/fslreorient2std: line 108: [: =: unary operator expected
** ERROR (nifti_image_read): short header read
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR:
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
bad header info
ERROR: failed to open file
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
(standard_in) 1: parse error
** ERROR (nifti_image_read): short header read
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR:
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
bad header info
ERROR: failed to open file
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 107: [: =: unary operator expected
** ERROR (nifti_image_read): short header read
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR:
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
bad header info
ERROR: failed to open file
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 115: [: -gt: unary operator expected
** ERROR (nifti_image_read): short header read
'/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11.nii'
** ERROR:
nifti_image_open(/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11):
bad header info
ERROR: failed to open file
/Volumes/homes/Shachar/piano_hcp/101/unprocessed/3T/T1w_MPR1/11_T1w_MPRAGE_RL_T1w_MPRAGE_RL_20180819094115_11
ERROR: Could not open file
/usr/local/fsl/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot use RLAPSI notation for nifti files without either sform or qform set
Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: Not Averaging T1w
Images
Thu Feb 14 11:04:26 IST 2019 - PreFreeSurferPipeline.sh: ONLY ONE AVERAGE
FOUND: COPYING
Traceback (most recent call last):
File "/usr/local/fsl/bin/imcp", line 11, in <module>
load_entry_point('fslpy==1.7.0', 'console_scripts', 'imcp')()
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
line 479, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
line 2703, in load_entry_point
return ep.load()
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
line 2321, in load
return self.resolve()
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py",
line 2327, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/scripts/imcp.py",
line 26, in <module>
import fsl.utils.imcp as imcp
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/utils/imcp.py",
line 24, in <module>
import fsl.data.image as fslimage
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/data/image.py",
line 44, in <module>
import scipy.ndimage as ndimage
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/ndimage/__init__.py",
line 161, in <module>
from .filters import *
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/ndimage/filters.py",
line 37, in <module>
from scipy.misc import doccer
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/misc/__init__.py",
line 67, in <module>
from scipy.interpolate._pade import pade as _pade
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/interpolate/__init__.py",
line 175, in <module>
from .interpolate import *
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/interpolate/interpolate.py",
line 21, in <module>
import scipy.special as spec
File
"/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/__init__.py",
line 640, in <module>
from ._ufuncs import *
ImportError:
dlopen(/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-darwin.so<http://ufuncs.cpython-36m-darwin.so>,
2): Symbol not found: __gfortran_stop_numeric_f08
Referenced from:
/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-darwin.so<http://ufuncs.cpython-36m-darwin.so>
Expected in: /Applications/MATLAB_R2017b.app/sys/os/maci64/libgfortran.3.dylib
in
/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/special/_ufuncs.cpython-36m-darwin.so<http://ufuncs.cpython-36m-darwin.so>
Any thoughts?
Thanks,
Shachar
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
