You are using some forward slashes ("/") where you should be using backslashes (""). ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Renew Andrade andraderenew@yahoo.com Sent: Saturday, October 26, 2019 5:11 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ERROR: Must specify input table of gradient vectors
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Dear Anastasia Yendiki: I have tried to run TRACULA on 3 subjects as specified in configuration file attached. But the terminal output is:
sh-3.2# trac-all -prep -c dmrirc.IXI domainname: Command not found. Too many ('s. INFO: SUBJECTS_DIR is /Volumes/FREESURFER/freesurfer_preprocessed INFO: Diffusion root is /Volumes/FREESURFER/freesurfer_preprocessed Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local -log /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log -cmd /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Sat Oct 26 23:06:34 CEST 2019 mri_convert --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0506412, -0.996042, 0.0730476) j_ras = (0.00618997, 0.073453, 0.997279) k_ras = (0.998698, 0.0500512, -0.00988522) writing to /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz... ERROR: Must specify input table of gradient vectors Darwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Sat Oct 26 23:06:39 CEST 2019
I don’t understand why? Because I think I have specified everything correctly. May be there is an issue with “bvecs” and “bvals” files because I added .txt format manually for it to be equal to what is specified in the tutorial of TRACULA configuration file.
Sincerely, Andrade.