Hi,
Looks like the input is a multi frame image. Should only be single frame.
Best Martin
On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk wrote:
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 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 CautionDear 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