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bit-warrior
December 06, 2017 04:45PM
Dear Afni experts,

I am executing the command:
fat_proc_filter_dwis -in_dwi /home/ahoxha/Desktop/dti_fatproc/dwi_nii.nii.gz -in_col_matT /home/ahoxha/Desktop/dti_fatproc/dwi_nii_matT.dat -prefix /home/ahoxha/Desktop/dti_fatproc/filt

and the program gives me error:
++ Start script version: 3.1
++ 3dinfo: AFNI version=AFNI_17.3.06 (Dec 5 2017) [64-bit]
++ Found inset DWI file: /home/ahoxha/Desktop/dti_fatproc/dwi_nii.nii.gz
++ Based on prefix, the output directory will be:
/home/ahoxha/Desktop/dti_fatproc/filt
++ Based on prefix, the output prefix will be:
filt
+* Output directory didn't exist. Trying to make '/home/ahoxha/Desktop/dti_fatproc/filt' now.
-----> STARTING fat_proc_filter_dwis ---->
This command:
fat_proc_filter_dwis -in_dwi /home/ahoxha/Desktop/dti_fatproc/dwi_nii.nii.gz -in_col_matT /home/ahoxha/Desktop/dti_fatproc/dwi_nii_matT.dat -prefix /home/ahoxha/Desktop/dti_fatproc/filt/filt
++ Echoing the command to: /home/ahoxha/Desktop/dti_fatproc/filt/filt_cmd.txt
+++ Command Echo:
1dDW_Grad_o_Mat++ -overwrite -in_col_matT /home/ahoxha/Desktop/dti_fatproc/dwi_nii_matT.dat{} -out_col_matT /home/ahoxha/Desktop/dti_fatproc/filt/filt_matT.dat
** FATAL ERROR: Error reading gradient vector file

however if I run the command on its own:
1dDW_Grad_o_Mat++ -overwrite -in_col_matT /home/ahoxha/Desktop/dti_fatproc/dwi_nii_matT.dat{} -out_col_matT /home/ahoxha/Desktop/dti_fatproc/filt/filt_matT.dat
t
++ Have read in data.
++ Have organized the data internally.
++ Maximum bvalue appears to be: 1100.00061
++ My view of grads at the moment (postflip, if asked for):

bval scale bvecs: x y z
0.00000 0.00000 0.00000 0.00000
1099.99988 -0.99978 -0.02094 0.00182
1099.99988 -0.02094 0.99978 -0.00182
1099.99951 -0.03995 0.64796 -0.76063
1099.99951 0.60706 -0.75410 -0.25061
1100.00024 0.22512 0.52953 0.81787
1099.99988 0.88795 0.27747 0.36681
1100.00037 -0.79263 -0.14549 0.59209
1099.99963 -0.21397 -0.93421 0.28541
1099.99976 -0.93203 -0.15942 0.32544
1100.00012 -0.52306 0.83385 -0.17633
1100.00024 -0.36405 0.83957 -0.40323
1100.00000 -0.46967 0.62047 -0.62804
1099.99976 0.47928 0.39938 0.78153
1100.00049 -0.63146 0.65911 -0.40844
1099.99988 -0.57398 -0.11732 0.81042
1100.00024 0.81597 0.53815 0.21115
1099.99951 -0.89378 0.02110 -0.44801
1099.99951 -0.30097 0.53443 -0.78981
1100.00012 -0.13617 0.95955 -0.24643
1099.99988 0.80894 -0.38662 -0.44288
1099.99963 -0.49636 -0.85024 0.17524
1100.00012 0.79240 -0.13687 -0.59444
1099.99963 0.95424 -0.21305 -0.20983
1100.00012 -0.21657 -0.78689 0.57784
1099.99988 -0.01722 -0.18781 0.98206
1100.00024 0.23686 -0.95119 -0.19780
1099.99976 0.78687 -0.58774 -0.18815
1099.99951 -0.16790 0.35198 -0.92083
1100.00012 0.16200 -0.72868 -0.66542
1099.99976 -0.87919 -0.43498 0.19444
1099.99951 0.56722 -0.22004 -0.79363
1099.99951 -0.38317 0.13485 -0.91378
1100.00037 -0.30132 -0.20497 0.93123
1099.99963 0.32993 0.13699 0.93401
1099.99951 0.95755 0.28514 0.04237
1100.00000 -0.96344 0.18447 -0.19429
1100.00061 0.47173 -0.87923 -0.06644
1100.00012 -0.78615 0.61152 -0.08950
1100.00000 -0.69964 -0.42224 0.57639
1099.99976 -0.69233 0.00927 -0.72153
1099.99939 0.67084 0.54331 0.50476
1100.00037 0.12678 0.72863 0.67307
1099.99939 -0.74753 0.37225 -0.55012
1099.99988 -0.12020 0.81883 -0.56131
1100.00037 0.59691 -0.58429 -0.54982
1099.99976 0.08129 0.33698 0.93800
1100.00012 0.53522 0.80440 0.25784
1100.00037 -0.84732 0.44016 -0.29715
1100.00000 0.37501 -0.55402 -0.74325
1100.00024 0.19214 -0.38848 -0.90120
1100.00012 0.70641 0.70776 0.00771
1099.99988 0.41894 0.69172 0.58822
1100.00024 -0.48692 -0.69983 0.52263
1099.99951 -0.16020 -0.51166 0.84412
1100.00012 -0.45330 -0.43208 0.77963
1100.00024 0.40219 -0.80146 -0.44260
1100.00024 0.70842 0.26251 0.65515
1100.00012 0.24141 0.89059 0.38544
1100.00049 0.00070 -0.07688 -0.99704
1100.00024 0.05601 -0.90171 -0.42870
1100.00037 -0.57588 0.29056 -0.76416
1100.00012 0.28577 -0.13922 -0.94813
1099.99976 -0.70785 -0.62267 0.33351
1100.00037 0.24678 0.96547 0.08348

++ Number of ref vec/mats (b<0.000001): 1
Number of diffusion weighted vec/mats: 64
++ Keeping all vec/mats.
++ Output dims to be: 65 x 6
++ DONE with grad/matr. Check output file '/home/ahoxha/Desktop/dti_fatproc/filt_matT.dat'


And I check the filt_matT.dat file, and it is properly done. However I would want to continue the execution of the fat_proc_filter_dwis. Is there a way to fix the script to execute properly?

Thanks
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Subject Author Posted

1dDW_Grad_o_Mat++ in fat_proc_filter_dwis

bit-warrior December 06, 2017 04:45PM

Re: 1dDW_Grad_o_Mat++ in fat_proc_filter_dwis

gang December 06, 2017 07:48PM