Dear Eugenio, Using full path solved the problem, thank you very much!

Best Regards Cong

From: "Iglesias Gonzalez, Eugenio" e.iglesias@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-15492520BEBA@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-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?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!