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-bounces@nmr.mgh.harvard.edu> on behalf of Cong <3110103623@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年11月29日
星期三 17时27分20秒
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年11月29日
星期三 17时27分31秒
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!
If you have used results from this software for a publication, please cite:
Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., Player, A., Wright,
M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B., and Van Leemput, K.,
A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution
MRI: Application to adaptive segmentation of in vivo MRI. Neuroimage 115, 2015, 117-137.
In addition, if you have used the segmentation of the nuclei of the amygdala, please also cite:
Saygin, Z.M. & Kliemann, D. (joint 1st authors), Iglesias, J.E., van der Kouwe, A.J.W.,
Boyd, E., Reuter, M., Stevens, A., Van Leemput, K., McKee, A., Frosch, M.P., Fischl, B.,
and Augustinack, J.C., High-resolution magnetic resonance imaging reveals nuclei of the
human amygdala: manual segmentation to automatic atlas. Neuroimage 155, 2017, 370-382.
BrainwaverdeMacBook-Pro:subjects Brainwaver$