Hi Anastasia:
I processed 42 brains on Tracula and it ran without problems. I am now trying to run them individually on DTK to test another hypothesis. [I am using the DTK for the first time]. I loaded the diffusion weighted image, filled the parameters in the GUI and ran one single brain. However, it gave me an error which is as follows:
************ 11/5/15 2:07 PM ************
Steps to do:
1. dti_recon "/Users/afrancis/Desktop/Connectome/101309/Diffusion/data.nii.gz" "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti" -gm "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/matrices/gradient.txt" -b 1000 -b0 1 -p 3 -sn 1 -ot nii
2. dti_tracker "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti" "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" -at 35 -m "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_dwi.nii" -it nii
3. spline_filter "/var/folders/97/_lbh5hkn2b57h_hvks9m2bp80000gq/T/dtk_tmp/track_tmp.trk" 1 "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti.trk"
4. trackvis "/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti.trk"
--------- Launching dti_recon -----------------
Volume dimension: 145 174 145
Voxel size: 1.250 1.250 1.250
Number of b0's: 1
Number of gradient directions: 6
Reading raw data... 100%
Reconstructing... 100%
b0 threshold used to mask background: 951.79 26709
Writing output...
** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_b0.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_dwi.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_fa.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_adc.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_fa_color.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_exp.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_tensor.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_e1.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_e2.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_e3.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_v1.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_v2.nii' ** ERROR (nifti_image_write_hdr_img2): cannot open output file '/Users/afrancis/Desktop/Connectome/101309/Diffusion/dti_v3.nii'
Process aborted due to error.
Thanks so much,
Alan