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> 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, 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
> 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
>
> Any thoughts?
>
> Thanks,
> Shachar
>
>
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