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.
http://dx.doi.org/10.1016/j.neuroimage.2015.04.042
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.
http://doi.org/10.1016/j.neuroimage.2017.04.046
BrainwaverdeMacBook-Pro:subjects Brainwaver$
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