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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.shachar@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