External Email - Use Caution        

It seems like a problem with mri_robust_register.

Martin, any ideas?

 

-- 

Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

Department of Medical Physics and Biomedical Engineering

University College London

http://www.jeiglesias.com

 

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Chen Guoyang (IMH)" <Guoyang_CHEN@imh.com.sg>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 26 October 2018 at 11:35
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

 

        External Email - Use Caution        

Dear Freesurfer experts,

 

I am currently attempting to include an additional T2 MRI scan in the segmentation of our T1 scan. The freesurfer version that I'm using is the freesurfer-darwin-OSX-ElCapitan-dev-20180919-4c582fa (developmental version).

 

However, I ran into this issue, ERROR: cannot find transform file. I've pasted the output below.

 

Will like your advices for the this matter.

 

Thanks!

 

Sincerely,

Guoyang

 

OS Darwin

Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

------------------------------

 

#--------------------------------------------

#@# Hippocampal Subfields processing (T1+T2) left Fri Oct 26 17:50:06 +08 2018

------------------------------------------

Setting up environment variables

---

DYLD_LIBRARY_PATH is .:/Applications/freesurfer_Dev_26Sep18/MCRv84//runtime/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//bin/maci64:/Applications/freesurfer_Dev_26Sep18/MCRv84//sys/os/maci64:/Applications/freesurfer_Dev_26Sep18/lib/gcc/lib:

Registering norm.mgz to additional volume

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register: only pass single frame MRI target /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii.

 

/Applications/freesurfer_Dev_26Sep18/bin//mri_robust_register --mov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/norm.mgz --maskmov /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//wholeBrainMask.mgz --dst /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1_T2.nii --lta /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta --noinit --cost NMI -nosym >/dev/null: Signal 127

ERROR: cannot find transform file /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/mri/transforms/T1_to_T2.v21.lta

gunzip: can't stat: /Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_T2_left//T2resampledLikeT1.mgz (/Users/newfei/Desktop/ECT/ECT_Nifti_ZoomHippo/ECT0003_1.long.ECT0003.t/tmp/hippoSF_T1T2_v21_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 207)

 

 

 

MATLAB:badSwitchExpression

Darwin newfeis-iMac.local 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct  4 00:17:00 PDT 2017; root:xnu-3789.71.6~1/RELEASE_X86_64 x86_64

 

T2 hippocampal subfields exited with ERRORS at Fri Oct 26 17:50:18 +08 2018