External Email - Use Caution
Dear Freesurfer devs,
I tried to run the thalamic nuclei segmentation (T1 and T2 as input) using the freesurfer dev version and the terminal gave to me the following error
rmnlab1:~ neucoga$ segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS BBREGISTER_MODE t2
Setting ITK threads to 1
#--------------------------------------------
#@# Thalamic Nuclei processing domingo, 8 de diciembre de 2019, 20:55:24 CET
------------------------------------------
Setting up environment variables
---
DYLD_LIBRARY_PATH is .:/Applications/freesurfer_dev/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib
Error using SegmentThalamicNuclei (line 138)
Additional volume does not exist
255
Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
Thalamic nuclei exited with ERRORS at domingo, 8 de diciembre de 2019, 20:55:31 CET
For more details, see the log file /Applications/freesurfer_dev/freesurfer/subjects/4001/scripts/thalamic-nuclei-BBREGISTER_MODE.log
Is the command right? I think that I have followed correctly the instructions of the website.
Best regards,
Please try: segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/ /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii T2_THALAMUS t2 Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Miguel Ángel Rivas Fernández miguelrivasfdez@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, 8 December 2019 at 15:00 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Thalamic nuclei segmentation
segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS BBREGISTER_MODE t2
freesurfer@nmr.mgh.harvard.edu