Dear Eugenio,
Using full path solved the problem, thank you very much!
Best Regards
Cong
> From: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk>
> Subject: Re: [Freesurfer] error in segmentHA_T2.sh
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <2706b24c-1442-46b9-8a8b-15492520b...@ucl.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Cong,
> This totally looks like a problem with absolute/relative paths. Can you
> please try again, but using the full path to the T2? Something like:
> segmentHA_T2.sh control004 /Users/cong/data/subjects/control004/mri/T2.nii
> T2 1
> If this works, let me know and I?ll fix the code.
> Cheers,
> /E
>
>
> --
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Cong
> <3110103...@zju.edu.cn>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, 29 November 2017 at 09:55
> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] error in segmentHA_T2.sh
>
> Dear freesurfer experts
> I am trying segment hippocampal and amygdala subregions in dev
> version(freesurfer-i386-apple-darwin11.4.2-dev-20171024), the segmentHA_T1.sh
> works well. However, when I try to add a T2 propeller sequence it doesn?t
> work. I am sure the T2.nii file is in mri folder, and this T2.nii file works
> well in 6.0.0 version for segmenting hippocampal subregion. I pasted the
> wrong scripts, could you tell me what?s wrong? Thanks!
>
> Best Regards
> Cong
>
>
> BrainwaverdeMacBook-Pro:subjects Brainwaver$ segmentHA_T2.sh control004
> control004/mri/T2.nii T2 1
> #--------------------------------------------
> #@# Hippocampal Subfields processing (T1+T2) left 2017?11?29? ??? 17?27?20?
> CST
> ------------------------------------------
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is
> .:/Users/Brainwaver/Documents/freesurfer/MCRv80//runtime/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//bin/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//sys/os/maci64:
> Warning: application is running on a locale different from the original
> platform locale.
> Registering norm.mgz to additional volume
> znzreadInt: znzread failed
> znzreadInt: znzread failed
> niiRead(): error opening file control004/mri/T2.nii
> mri_robust_register.bin: could not open MRI target control004/mri/T2.nii.
>
> /Users/Brainwaver/Documents/freesurfer/bin//mri_robust_register --mov
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/norm.mgz
> --maskmov
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//wholeBrainMask.mgz
> --dst control004/mri/T2.nii --lta
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta
> --noinit --cost NMI -nosym >/dev/null: Signal 127
> ERROR: cannot find transform file
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta
> gunzip: can't stat:
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//T2resampledLikeT1.mgz
>
> (/Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_left//T2resampledLikeT1.mgz.gz):
> No such file or directory
> ERROR: problem reading fname
> SWITCH expression must be a scalar or string constant.
>
> Error in myMRIread>load_mgh (line 550)
>
>
>
> Error in myMRIread>myMRIread_aux (line 92)
>
>
>
> Error in myMRIread (line 63)
>
>
>
> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 198)
>
>
>
> MATLAB:badSwitchExpression
> #--------------------------------------------
> #@# Hippocampal Subfields processing (T1+T2) right 2017?11?29? ??? 17?27?31?
> CST
> ------------------------------------------
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is
> .:/Users/Brainwaver/Documents/freesurfer/MCRv80//runtime/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//bin/maci64:/Users/Brainwaver/Documents/freesurfer/MCRv80//sys/os/maci64:
> Warning: application is running on a locale different from the original
> platform locale.
> Registering norm.mgz to additional volume
> znzreadInt: znzread failed
> znzreadInt: znzread failed
> niiRead(): error opening file control004/mri/T2.nii
> mri_robust_register.bin: could not open MRI target control004/mri/T2.nii.
>
> /Users/Brainwaver/Documents/freesurfer/bin//mri_robust_register --mov
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/norm.mgz
> --maskmov
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//wholeBrainMask.mgz
> --dst control004/mri/T2.nii --lta
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta
> --noinit --cost NMI -nosym >/dev/null: Signal 127
> ERROR: cannot find transform file
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/mri/transforms/T1_to_T2.v20.lta
> gunzip: can't stat:
> /Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//T2resampledLikeT1.mgz
>
> (/Users/Brainwaver/Documents/freesurfer/subjects/control004/tmp/hippoSF_T1T2_v20_T2_right//T2resampledLikeT1.mgz.gz):
> No such file or directory
> ERROR: problem reading fname
> SWITCH expression must be a scalar or string constant.
>
> Error in myMRIread>load_mgh (line 550)
>
>
>
> Error in myMRIread>myMRIread_aux (line 92)
>
>
>
> Error in myMRIread (line 63)
>
>
>
> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 198)
>
>
>
> MATLAB:badSwitchExpression
>
> All done!
>
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