Dwi2response error

rsmith · July 22, 2016, 8:56am

OK just merged a change that should deal with the presence of whitespace characters in the working directory where the script is executed from. But please test it just in case there’s something else funny going on: as Donald noted, those earlier logs didn’t contain any white spaces…

Ralf · July 22, 2016, 1:18pm

Hi,
I am on Ubuntu 16.xx !

As to the white spaces:
I cant really say if I not copied all of it. But if I watch back through our conversation…there are also white spaces.
So I guess I used white spaces all the time and later without.

It can be the error all along.

Now I try the new version without whiote spaces.
I “pulled a git” and “builded” and used a path without spaces right now.
It gives:

ibmi@ibmi-81645:/media/ibmi/Data/bh27_B1000_neu/MRTrix_final$ dwi2response tournier data_reg_ecc.mif response_tournier.txt -grad encoding.b 
dwi2response: 
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response: 
Traceback (most recent call last):
  File "/home/ibmi/mrtrix3/scripts/dwi2response", line 80, in <module>
    grad_import_option = ' -grad ' + getUserPath(lib.app.args.grad, True)
  File "/home/ibmi/mrtrix3/scripts/lib/getUserPath.py", line 7, in getUserPath
    if is_command and (filename.count(' ') or lib.app.workingDir(' ')):
TypeError: 'str' object is not callable
ibmi@ibmi-81645:/media/ibmi/Data/bh27_B1000_neu/MRTrix_final$

I hope I did nothing wrong. The error looks different! I can try one without -grad maybe!

Ralf

rsmith · July 22, 2016, 2:01pm

No sorry, that’s just me being far too trigger-happy with the commit button and not having set up automated testing for the scripts and madly doing other things at the same time… The fix is here, I just need to wait for the tests to complete before I can merge it to the master branch. Sorry

rsmith · July 22, 2016, 2:31pm

OK, the fixed command is there now.

Ralf · July 22, 2016, 4:26pm

It does something. But its not done yet.
You want to have to whole output?

Ralf · July 22, 2016, 4:27pm

Without white spaces:

ibmi@ibmi-81645:/media/ibmi/Data/bh27_B1000_neu/MRTrix_final$ dwi2response tournier data_reg_ecc.mif response_tournier.txt -grad encoding.b 
dwi2response: 
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response: 
dwi2response: Generated temporary directory: /tmp/dwi2response-tmp-ZH8M6W/
Command: mrconvert /media/ibmi/Data/bh27_B1000_neu/MRTrix_final/data_reg_ecc.mif - -stride 0,0,0,1 -grad /media/ibmi/Data/bh27_B1000_neu/MRTrix_final/encoding.b | dwiextract - /tmp/dwi2response-tmp-ZH8M6W/dwi.mif
[['mrconvert', '/media/ibmi/Data/bh27_B1000_neu/MRTrix_final/data_reg_ecc.mif', '-', '-stride', '0,0,0,1', '-grad', '/media/ibmi/Data/bh27_B1000_neu/MRTrix_final/encoding.b', '-quiet'], ['dwiextract', '-', '/tmp/dwi2response-tmp-ZH8M6W/dwi.mif', '-quiet']]
dwi2response: Changing to temporary directory (/tmp/dwi2response-tmp-ZH8M6W/)
Command: dwi2mask dwi.mif mask.mif
[['dwi2mask', 'dwi.mif', 'mask.mif', '-quiet']]
Command: amp2sh dwi.mif dwiSH.mif
[['amp2sh', 'dwi.mif', 'dwiSH.mif', '-quiet']]
Command: dwi2fod csd dwi.mif init_RF.txt iter0_FOD.mif -mask mask.mif -lmax 4
[['dwi2fod', 'csd', 'dwi.mif', 'init_RF.txt', 'iter0_FOD.mif', '-mask', 'mask.mif', '-lmax', '4', '-quiet']]
Command: fod2fixel iter0_FOD.mif -peak iter0_peaks.msf -mask mask.mif -fmls_no_thresholds
[['fod2fixel', 'iter0_FOD.mif', '-peak', 'iter0_peaks.msf', '-mask', 'mask.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter0_FOD.mif
Command: fixel2voxel iter0_peaks.msf split_value iter0_amps.mif
[['fixel2voxel', 'iter0_peaks.msf', 'split_value', 'iter0_amps.mif', '-quiet']]
Command: mrconvert iter0_amps.mif iter0_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter0_amps.mif', 'iter0_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter0_amps.mif iter0_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter0_amps.mif', 'iter0_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter0_amps.mif
Command: fixel2voxel iter0_peaks.msf split_dir iter0_all_dirs.mif
[['fixel2voxel', 'iter0_peaks.msf', 'split_dir', 'iter0_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter0_peaks.msf
Command: mrconvert iter0_all_dirs.mif iter0_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter0_all_dirs.mif', 'iter0_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter0_all_dirs.mif
Command: mrcalc iter0_first_peaks.mif -sqrt 1 iter0_second_peaks.mif iter0_first_peaks.mif -div -sub 2 -pow -mult iter0_CF.mif
[['mrcalc', 'iter0_first_peaks.mif', '-sqrt', '1', 'iter0_second_peaks.mif', 'iter0_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter0_CF.mif', '-quiet']]
dwi2response: Deleting file: iter0_first_peaks.mif
dwi2response: Deleting file: iter0_second_peaks.mif
Command: mrthreshold iter0_CF.mif -top 300 iter0_SF.mif
[['mrthreshold', 'iter0_CF.mif', '-top', '300', 'iter0_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter0_SF.mif iter0_first_dir.mif iter0_RF.txt -lmax 4
[['sh2response', 'dwiSH.mif', 'iter0_SF.mif', 'iter0_first_dir.mif', 'iter0_RF.txt', '-lmax', '4', '-quiet']]
dwi2response: Deleting file: iter0_first_dir.mif
Command: mrthreshold iter0_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter0_SF_dilated.mif
[['mrthreshold', 'iter0_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter0_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter0_CF.mif
Command: dwi2fod csd dwi.mif iter0_RF.txt iter1_FOD.mif -mask iter0_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter0_RF.txt', 'iter1_FOD.mif', '-mask', 'iter0_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter1_FOD.mif -peak iter1_peaks.msf -mask iter0_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter1_FOD.mif', '-peak', 'iter1_peaks.msf', '-mask', 'iter0_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter1_FOD.mif
dwi2response: Deleting file: iter0_SF_dilated.mif
Command: fixel2voxel iter1_peaks.msf split_value iter1_amps.mif
[['fixel2voxel', 'iter1_peaks.msf', 'split_value', 'iter1_amps.mif', '-quiet']]
Command: mrconvert iter1_amps.mif iter1_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter1_amps.mif', 'iter1_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter1_amps.mif iter1_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter1_amps.mif', 'iter1_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter1_amps.mif
Command: fixel2voxel iter1_peaks.msf split_dir iter1_all_dirs.mif
[['fixel2voxel', 'iter1_peaks.msf', 'split_dir', 'iter1_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter1_peaks.msf
Command: mrconvert iter1_all_dirs.mif iter1_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter1_all_dirs.mif', 'iter1_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter1_all_dirs.mif
Command: mrcalc iter1_first_peaks.mif -sqrt 1 iter1_second_peaks.mif iter1_first_peaks.mif -div -sub 2 -pow -mult iter1_CF.mif
[['mrcalc', 'iter1_first_peaks.mif', '-sqrt', '1', 'iter1_second_peaks.mif', 'iter1_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter1_CF.mif', '-quiet']]
dwi2response: Deleting file: iter1_first_peaks.mif
dwi2response: Deleting file: iter1_second_peaks.mif
Command: mrthreshold iter1_CF.mif -top 300 iter1_SF.mif
[['mrthreshold', 'iter1_CF.mif', '-top', '300', 'iter1_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter1_SF.mif iter1_first_dir.mif iter1_RF.txt
[['sh2response', 'dwiSH.mif', 'iter1_SF.mif', 'iter1_first_dir.mif', 'iter1_RF.txt', '-quiet']]
dwi2response: Deleting file: iter1_first_dir.mif
Command: mrcalc iter1_SF.mif iter0_SF.mif -sub iter1_SF_diff.mif
[['mrcalc', 'iter1_SF.mif', 'iter0_SF.mif', '-sub', 'iter1_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter0_SF.mif
dwi2response: Deleting file: iter1_SF_diff.mif
Command: mrthreshold iter1_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter1_SF_dilated.mif
[['mrthreshold', 'iter1_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter1_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter1_CF.mif
Command: dwi2fod csd dwi.mif iter1_RF.txt iter2_FOD.mif -mask iter1_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter1_RF.txt', 'iter2_FOD.mif', '-mask', 'iter1_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter2_FOD.mif -peak iter2_peaks.msf -mask iter1_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter2_FOD.mif', '-peak', 'iter2_peaks.msf', '-mask', 'iter1_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter2_FOD.mif
dwi2response: Deleting file: iter1_SF_dilated.mif
Command: fixel2voxel iter2_peaks.msf split_value iter2_amps.mif
[['fixel2voxel', 'iter2_peaks.msf', 'split_value', 'iter2_amps.mif', '-quiet']]
Command: mrconvert iter2_amps.mif iter2_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter2_amps.mif', 'iter2_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter2_amps.mif iter2_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter2_amps.mif', 'iter2_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter2_amps.mif
Command: fixel2voxel iter2_peaks.msf split_dir iter2_all_dirs.mif
[['fixel2voxel', 'iter2_peaks.msf', 'split_dir', 'iter2_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter2_peaks.msf
Command: mrconvert iter2_all_dirs.mif iter2_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter2_all_dirs.mif', 'iter2_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter2_all_dirs.mif
Command: mrcalc iter2_first_peaks.mif -sqrt 1 iter2_second_peaks.mif iter2_first_peaks.mif -div -sub 2 -pow -mult iter2_CF.mif
[['mrcalc', 'iter2_first_peaks.mif', '-sqrt', '1', 'iter2_second_peaks.mif', 'iter2_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter2_CF.mif', '-quiet']]
dwi2response: Deleting file: iter2_first_peaks.mif
dwi2response: Deleting file: iter2_second_peaks.mif
Command: mrthreshold iter2_CF.mif -top 300 iter2_SF.mif
[['mrthreshold', 'iter2_CF.mif', '-top', '300', 'iter2_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter2_SF.mif iter2_first_dir.mif iter2_RF.txt
[['sh2response', 'dwiSH.mif', 'iter2_SF.mif', 'iter2_first_dir.mif', 'iter2_RF.txt', '-quiet']]
dwi2response: Deleting file: iter2_first_dir.mif
Command: mrcalc iter2_SF.mif iter1_SF.mif -sub iter2_SF_diff.mif
[['mrcalc', 'iter2_SF.mif', 'iter1_SF.mif', '-sub', 'iter2_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter1_SF.mif
dwi2response: Deleting file: iter2_SF_diff.mif
Command: mrthreshold iter2_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter2_SF_dilated.mif
[['mrthreshold', 'iter2_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter2_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter2_CF.mif
Command: dwi2fod csd dwi.mif iter2_RF.txt iter3_FOD.mif -mask iter2_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter2_RF.txt', 'iter3_FOD.mif', '-mask', 'iter2_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter3_FOD.mif -peak iter3_peaks.msf -mask iter2_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter3_FOD.mif', '-peak', 'iter3_peaks.msf', '-mask', 'iter2_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter3_FOD.mif
dwi2response: Deleting file: iter2_SF_dilated.mif
Command: fixel2voxel iter3_peaks.msf split_value iter3_amps.mif
[['fixel2voxel', 'iter3_peaks.msf', 'split_value', 'iter3_amps.mif', '-quiet']]
Command: mrconvert iter3_amps.mif iter3_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter3_amps.mif', 'iter3_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter3_amps.mif iter3_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter3_amps.mif', 'iter3_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter3_amps.mif
Command: fixel2voxel iter3_peaks.msf split_dir iter3_all_dirs.mif
[['fixel2voxel', 'iter3_peaks.msf', 'split_dir', 'iter3_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter3_peaks.msf
Command: mrconvert iter3_all_dirs.mif iter3_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter3_all_dirs.mif', 'iter3_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter3_all_dirs.mif
Command: mrcalc iter3_first_peaks.mif -sqrt 1 iter3_second_peaks.mif iter3_first_peaks.mif -div -sub 2 -pow -mult iter3_CF.mif
[['mrcalc', 'iter3_first_peaks.mif', '-sqrt', '1', 'iter3_second_peaks.mif', 'iter3_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter3_CF.mif', '-quiet']]
dwi2response: Deleting file: iter3_first_peaks.mif
dwi2response: Deleting file: iter3_second_peaks.mif
Command: mrthreshold iter3_CF.mif -top 300 iter3_SF.mif
[['mrthreshold', 'iter3_CF.mif', '-top', '300', 'iter3_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter3_SF.mif iter3_first_dir.mif iter3_RF.txt
[['sh2response', 'dwiSH.mif', 'iter3_SF.mif', 'iter3_first_dir.mif', 'iter3_RF.txt', '-quiet']]
dwi2response: Deleting file: iter3_first_dir.mif
Command: mrcalc iter3_SF.mif iter2_SF.mif -sub iter3_SF_diff.mif
[['mrcalc', 'iter3_SF.mif', 'iter2_SF.mif', '-sub', 'iter3_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter2_SF.mif
dwi2response: Deleting file: iter3_SF_diff.mif
Command: mrthreshold iter3_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter3_SF_dilated.mif
[['mrthreshold', 'iter3_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter3_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter3_CF.mif
Command: dwi2fod csd dwi.mif iter3_RF.txt iter4_FOD.mif -mask iter3_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter3_RF.txt', 'iter4_FOD.mif', '-mask', 'iter3_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter4_FOD.mif -peak iter4_peaks.msf -mask iter3_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter4_FOD.mif', '-peak', 'iter4_peaks.msf', '-mask', 'iter3_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter4_FOD.mif
dwi2response: Deleting file: iter3_SF_dilated.mif
Command: fixel2voxel iter4_peaks.msf split_value iter4_amps.mif
[['fixel2voxel', 'iter4_peaks.msf', 'split_value', 'iter4_amps.mif', '-quiet']]
Command: mrconvert iter4_amps.mif iter4_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter4_amps.mif', 'iter4_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter4_amps.mif iter4_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter4_amps.mif', 'iter4_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter4_amps.mif
Command: fixel2voxel iter4_peaks.msf split_dir iter4_all_dirs.mif
[['fixel2voxel', 'iter4_peaks.msf', 'split_dir', 'iter4_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter4_peaks.msf
Command: mrconvert iter4_all_dirs.mif iter4_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter4_all_dirs.mif', 'iter4_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter4_all_dirs.mif
Command: mrcalc iter4_first_peaks.mif -sqrt 1 iter4_second_peaks.mif iter4_first_peaks.mif -div -sub 2 -pow -mult iter4_CF.mif
[['mrcalc', 'iter4_first_peaks.mif', '-sqrt', '1', 'iter4_second_peaks.mif', 'iter4_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter4_CF.mif', '-quiet']]
dwi2response: Deleting file: iter4_first_peaks.mif
dwi2response: Deleting file: iter4_second_peaks.mif
Command: mrthreshold iter4_CF.mif -top 300 iter4_SF.mif
[['mrthreshold', 'iter4_CF.mif', '-top', '300', 'iter4_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter4_SF.mif iter4_first_dir.mif iter4_RF.txt
[['sh2response', 'dwiSH.mif', 'iter4_SF.mif', 'iter4_first_dir.mif', 'iter4_RF.txt', '-quiet']]
dwi2response: Deleting file: iter4_first_dir.mif
Command: mrcalc iter4_SF.mif iter3_SF.mif -sub iter4_SF_diff.mif
[['mrcalc', 'iter4_SF.mif', 'iter3_SF.mif', '-sub', 'iter4_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter3_SF.mif
dwi2response: Deleting file: iter4_SF_diff.mif
dwi2response: Convergence of SF voxel selection detected at iteration 4
dwi2response: Deleting file: iter4_CF.mif
dwi2response: Changing back to original directory (/media/ibmi/Data/bh27_B1000_neu/MRTrix_final)
dwi2response: Deleting temporary directory /tmp/dwi2response-tmp-ZH8M6W/
ibmi@ibmi-81645:/media/ibmi/Data/bh27_B1000_neu/MRTrix_final$

Ralf · July 22, 2016, 4:32pm

With White spaces:

ibmi@ibmi-81645:/media/ibmi/Data/Paper_DWI_Treffen_2016.07.20_Miitwoch/Paper_DWI_Vergleich_B1000-3000 bei 1.4mm iso/bh27_B1000_neu/MRTrix_final$ dwi2response tournier data_reg_ecc.mif response_tournier.txt -grad encoding.b 
dwi2response: 
dwi2response: Note that this script makes use of commands / algorithms that have relevant articles for citation. Please consult the help page (-help option) for more information.
dwi2response: 
dwi2response: Generated temporary directory: /tmp/dwi2response-tmp-Z1YA08/
Command: mrconvert "/media/ibmi/Data/Paper_DWI_Treffen_2016.07.20_Miitwoch/Paper_DWI_Vergleich_B1000-3000 bei 1.4mm iso/bh27_B1000_neu/MRTrix_final/data_reg_ecc.mif" - -stride 0,0,0,1 -grad "/media/ibmi/Data/Paper_DWI_Treffen_2016.07.20_Miitwoch/Paper_DWI_Vergleich_B1000-3000 bei 1.4mm iso/bh27_B1000_neu/MRTrix_final/encoding.b" | dwiextract - /tmp/dwi2response-tmp-Z1YA08/dwi.mif
[['mrconvert', '/media/ibmi/Data/Paper_DWI_Treffen_2016.07.20_Miitwoch/Paper_DWI_Vergleich_B1000-3000 bei 1.4mm iso/bh27_B1000_neu/MRTrix_final/data_reg_ecc.mif', '-', '-stride', '0,0,0,1', '-grad', '/media/ibmi/Data/Paper_DWI_Treffen_2016.07.20_Miitwoch/Paper_DWI_Vergleich_B1000-3000 bei 1.4mm iso/bh27_B1000_neu/MRTrix_final/encoding.b', '-quiet'], ['dwiextract', '-', '/tmp/dwi2response-tmp-Z1YA08/dwi.mif', '-quiet']]
dwi2response: Changing to temporary directory (/tmp/dwi2response-tmp-Z1YA08/)
Command: dwi2mask dwi.mif mask.mif
[['dwi2mask', 'dwi.mif', 'mask.mif', '-quiet']]
Command: amp2sh dwi.mif dwiSH.mif
[['amp2sh', 'dwi.mif', 'dwiSH.mif', '-quiet']]
Command: dwi2fod csd dwi.mif init_RF.txt iter0_FOD.mif -mask mask.mif -lmax 4
[['dwi2fod', 'csd', 'dwi.mif', 'init_RF.txt', 'iter0_FOD.mif', '-mask', 'mask.mif', '-lmax', '4', '-quiet']]
Command: fod2fixel iter0_FOD.mif -peak iter0_peaks.msf -mask mask.mif -fmls_no_thresholds
[['fod2fixel', 'iter0_FOD.mif', '-peak', 'iter0_peaks.msf', '-mask', 'mask.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter0_FOD.mif
Command: fixel2voxel iter0_peaks.msf split_value iter0_amps.mif
[['fixel2voxel', 'iter0_peaks.msf', 'split_value', 'iter0_amps.mif', '-quiet']]
Command: mrconvert iter0_amps.mif iter0_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter0_amps.mif', 'iter0_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter0_amps.mif iter0_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter0_amps.mif', 'iter0_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter0_amps.mif
Command: fixel2voxel iter0_peaks.msf split_dir iter0_all_dirs.mif
[['fixel2voxel', 'iter0_peaks.msf', 'split_dir', 'iter0_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter0_peaks.msf
Command: mrconvert iter0_all_dirs.mif iter0_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter0_all_dirs.mif', 'iter0_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter0_all_dirs.mif
Command: mrcalc iter0_first_peaks.mif -sqrt 1 iter0_second_peaks.mif iter0_first_peaks.mif -div -sub 2 -pow -mult iter0_CF.mif
[['mrcalc', 'iter0_first_peaks.mif', '-sqrt', '1', 'iter0_second_peaks.mif', 'iter0_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter0_CF.mif', '-quiet']]
dwi2response: Deleting file: iter0_first_peaks.mif
dwi2response: Deleting file: iter0_second_peaks.mif
Command: mrthreshold iter0_CF.mif -top 300 iter0_SF.mif
[['mrthreshold', 'iter0_CF.mif', '-top', '300', 'iter0_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter0_SF.mif iter0_first_dir.mif iter0_RF.txt -lmax 4
[['sh2response', 'dwiSH.mif', 'iter0_SF.mif', 'iter0_first_dir.mif', 'iter0_RF.txt', '-lmax', '4', '-quiet']]
dwi2response: Deleting file: iter0_first_dir.mif
Command: mrthreshold iter0_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter0_SF_dilated.mif
[['mrthreshold', 'iter0_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter0_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter0_CF.mif
Command: dwi2fod csd dwi.mif iter0_RF.txt iter1_FOD.mif -mask iter0_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter0_RF.txt', 'iter1_FOD.mif', '-mask', 'iter0_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter1_FOD.mif -peak iter1_peaks.msf -mask iter0_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter1_FOD.mif', '-peak', 'iter1_peaks.msf', '-mask', 'iter0_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter1_FOD.mif
dwi2response: Deleting file: iter0_SF_dilated.mif
Command: fixel2voxel iter1_peaks.msf split_value iter1_amps.mif
[['fixel2voxel', 'iter1_peaks.msf', 'split_value', 'iter1_amps.mif', '-quiet']]
Command: mrconvert iter1_amps.mif iter1_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter1_amps.mif', 'iter1_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter1_amps.mif iter1_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter1_amps.mif', 'iter1_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter1_amps.mif
Command: fixel2voxel iter1_peaks.msf split_dir iter1_all_dirs.mif
[['fixel2voxel', 'iter1_peaks.msf', 'split_dir', 'iter1_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter1_peaks.msf
Command: mrconvert iter1_all_dirs.mif iter1_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter1_all_dirs.mif', 'iter1_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter1_all_dirs.mif
Command: mrcalc iter1_first_peaks.mif -sqrt 1 iter1_second_peaks.mif iter1_first_peaks.mif -div -sub 2 -pow -mult iter1_CF.mif
[['mrcalc', 'iter1_first_peaks.mif', '-sqrt', '1', 'iter1_second_peaks.mif', 'iter1_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter1_CF.mif', '-quiet']]
dwi2response: Deleting file: iter1_first_peaks.mif
dwi2response: Deleting file: iter1_second_peaks.mif
Command: mrthreshold iter1_CF.mif -top 300 iter1_SF.mif
[['mrthreshold', 'iter1_CF.mif', '-top', '300', 'iter1_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter1_SF.mif iter1_first_dir.mif iter1_RF.txt
[['sh2response', 'dwiSH.mif', 'iter1_SF.mif', 'iter1_first_dir.mif', 'iter1_RF.txt', '-quiet']]
dwi2response: Deleting file: iter1_first_dir.mif
Command: mrcalc iter1_SF.mif iter0_SF.mif -sub iter1_SF_diff.mif
[['mrcalc', 'iter1_SF.mif', 'iter0_SF.mif', '-sub', 'iter1_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter0_SF.mif
dwi2response: Deleting file: iter1_SF_diff.mif
Command: mrthreshold iter1_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter1_SF_dilated.mif
[['mrthreshold', 'iter1_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter1_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter1_CF.mif
Command: dwi2fod csd dwi.mif iter1_RF.txt iter2_FOD.mif -mask iter1_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter1_RF.txt', 'iter2_FOD.mif', '-mask', 'iter1_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter2_FOD.mif -peak iter2_peaks.msf -mask iter1_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter2_FOD.mif', '-peak', 'iter2_peaks.msf', '-mask', 'iter1_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter2_FOD.mif
dwi2response: Deleting file: iter1_SF_dilated.mif
Command: fixel2voxel iter2_peaks.msf split_value iter2_amps.mif
[['fixel2voxel', 'iter2_peaks.msf', 'split_value', 'iter2_amps.mif', '-quiet']]
Command: mrconvert iter2_amps.mif iter2_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter2_amps.mif', 'iter2_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter2_amps.mif iter2_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter2_amps.mif', 'iter2_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter2_amps.mif
Command: fixel2voxel iter2_peaks.msf split_dir iter2_all_dirs.mif
[['fixel2voxel', 'iter2_peaks.msf', 'split_dir', 'iter2_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter2_peaks.msf
Command: mrconvert iter2_all_dirs.mif iter2_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter2_all_dirs.mif', 'iter2_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter2_all_dirs.mif
Command: mrcalc iter2_first_peaks.mif -sqrt 1 iter2_second_peaks.mif iter2_first_peaks.mif -div -sub 2 -pow -mult iter2_CF.mif
[['mrcalc', 'iter2_first_peaks.mif', '-sqrt', '1', 'iter2_second_peaks.mif', 'iter2_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter2_CF.mif', '-quiet']]
dwi2response: Deleting file: iter2_first_peaks.mif
dwi2response: Deleting file: iter2_second_peaks.mif
Command: mrthreshold iter2_CF.mif -top 300 iter2_SF.mif
[['mrthreshold', 'iter2_CF.mif', '-top', '300', 'iter2_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter2_SF.mif iter2_first_dir.mif iter2_RF.txt
[['sh2response', 'dwiSH.mif', 'iter2_SF.mif', 'iter2_first_dir.mif', 'iter2_RF.txt', '-quiet']]
dwi2response: Deleting file: iter2_first_dir.mif
Command: mrcalc iter2_SF.mif iter1_SF.mif -sub iter2_SF_diff.mif
[['mrcalc', 'iter2_SF.mif', 'iter1_SF.mif', '-sub', 'iter2_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter1_SF.mif
dwi2response: Deleting file: iter2_SF_diff.mif
Command: mrthreshold iter2_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter2_SF_dilated.mif
[['mrthreshold', 'iter2_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter2_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter2_CF.mif
Command: dwi2fod csd dwi.mif iter2_RF.txt iter3_FOD.mif -mask iter2_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter2_RF.txt', 'iter3_FOD.mif', '-mask', 'iter2_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter3_FOD.mif -peak iter3_peaks.msf -mask iter2_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter3_FOD.mif', '-peak', 'iter3_peaks.msf', '-mask', 'iter2_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter3_FOD.mif
dwi2response: Deleting file: iter2_SF_dilated.mif
Command: fixel2voxel iter3_peaks.msf split_value iter3_amps.mif
[['fixel2voxel', 'iter3_peaks.msf', 'split_value', 'iter3_amps.mif', '-quiet']]
Command: mrconvert iter3_amps.mif iter3_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter3_amps.mif', 'iter3_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter3_amps.mif iter3_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter3_amps.mif', 'iter3_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter3_amps.mif
Command: fixel2voxel iter3_peaks.msf split_dir iter3_all_dirs.mif
[['fixel2voxel', 'iter3_peaks.msf', 'split_dir', 'iter3_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter3_peaks.msf
Command: mrconvert iter3_all_dirs.mif iter3_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter3_all_dirs.mif', 'iter3_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter3_all_dirs.mif
Command: mrcalc iter3_first_peaks.mif -sqrt 1 iter3_second_peaks.mif iter3_first_peaks.mif -div -sub 2 -pow -mult iter3_CF.mif
[['mrcalc', 'iter3_first_peaks.mif', '-sqrt', '1', 'iter3_second_peaks.mif', 'iter3_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter3_CF.mif', '-quiet']]
dwi2response: Deleting file: iter3_first_peaks.mif
dwi2response: Deleting file: iter3_second_peaks.mif
Command: mrthreshold iter3_CF.mif -top 300 iter3_SF.mif
[['mrthreshold', 'iter3_CF.mif', '-top', '300', 'iter3_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter3_SF.mif iter3_first_dir.mif iter3_RF.txt
[['sh2response', 'dwiSH.mif', 'iter3_SF.mif', 'iter3_first_dir.mif', 'iter3_RF.txt', '-quiet']]
dwi2response: Deleting file: iter3_first_dir.mif
Command: mrcalc iter3_SF.mif iter2_SF.mif -sub iter3_SF_diff.mif
[['mrcalc', 'iter3_SF.mif', 'iter2_SF.mif', '-sub', 'iter3_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter2_SF.mif
dwi2response: Deleting file: iter3_SF_diff.mif
Command: mrthreshold iter3_CF.mif -top 3000 - | maskfilter - dilate - -npass 1 | mrcalc mask.mif - -mult iter3_SF_dilated.mif
[['mrthreshold', 'iter3_CF.mif', '-top', '3000', '-', '-quiet'], ['maskfilter', '-', 'dilate', '-', '-npass', '1', '-quiet'], ['mrcalc', 'mask.mif', '-', '-mult', 'iter3_SF_dilated.mif', '-quiet']]
dwi2response: Deleting file: iter3_CF.mif
Command: dwi2fod csd dwi.mif iter3_RF.txt iter4_FOD.mif -mask iter3_SF_dilated.mif
[['dwi2fod', 'csd', 'dwi.mif', 'iter3_RF.txt', 'iter4_FOD.mif', '-mask', 'iter3_SF_dilated.mif', '-quiet']]
Command: fod2fixel iter4_FOD.mif -peak iter4_peaks.msf -mask iter3_SF_dilated.mif -fmls_no_thresholds
[['fod2fixel', 'iter4_FOD.mif', '-peak', 'iter4_peaks.msf', '-mask', 'iter3_SF_dilated.mif', '-fmls_no_thresholds', '-quiet']]
dwi2response: Deleting file: iter4_FOD.mif
dwi2response: Deleting file: iter3_SF_dilated.mif
Command: fixel2voxel iter4_peaks.msf split_value iter4_amps.mif
[['fixel2voxel', 'iter4_peaks.msf', 'split_value', 'iter4_amps.mif', '-quiet']]
Command: mrconvert iter4_amps.mif iter4_first_peaks.mif -coord 3 0 -axes 0,1,2
[['mrconvert', 'iter4_amps.mif', 'iter4_first_peaks.mif', '-coord', '3', '0', '-axes', '0,1,2', '-quiet']]
Command: mrconvert iter4_amps.mif iter4_second_peaks.mif -coord 3 1 -axes 0,1,2
[['mrconvert', 'iter4_amps.mif', 'iter4_second_peaks.mif', '-coord', '3', '1', '-axes', '0,1,2', '-quiet']]
dwi2response: Deleting file: iter4_amps.mif
Command: fixel2voxel iter4_peaks.msf split_dir iter4_all_dirs.mif
[['fixel2voxel', 'iter4_peaks.msf', 'split_dir', 'iter4_all_dirs.mif', '-quiet']]
dwi2response: Deleting file: iter4_peaks.msf
Command: mrconvert iter4_all_dirs.mif iter4_first_dir.mif -coord 3 0:2
[['mrconvert', 'iter4_all_dirs.mif', 'iter4_first_dir.mif', '-coord', '3', '0:2', '-quiet']]
dwi2response: Deleting file: iter4_all_dirs.mif
Command: mrcalc iter4_first_peaks.mif -sqrt 1 iter4_second_peaks.mif iter4_first_peaks.mif -div -sub 2 -pow -mult iter4_CF.mif
[['mrcalc', 'iter4_first_peaks.mif', '-sqrt', '1', 'iter4_second_peaks.mif', 'iter4_first_peaks.mif', '-div', '-sub', '2', '-pow', '-mult', 'iter4_CF.mif', '-quiet']]
dwi2response: Deleting file: iter4_first_peaks.mif
dwi2response: Deleting file: iter4_second_peaks.mif
Command: mrthreshold iter4_CF.mif -top 300 iter4_SF.mif
[['mrthreshold', 'iter4_CF.mif', '-top', '300', 'iter4_SF.mif', '-quiet']]
Command: sh2response dwiSH.mif iter4_SF.mif iter4_first_dir.mif iter4_RF.txt
[['sh2response', 'dwiSH.mif', 'iter4_SF.mif', 'iter4_first_dir.mif', 'iter4_RF.txt', '-quiet']]
dwi2response: Deleting file: iter4_first_dir.mif
Command: mrcalc iter4_SF.mif iter3_SF.mif -sub iter4_SF_diff.mif
[['mrcalc', 'iter4_SF.mif', 'iter3_SF.mif', '-sub', 'iter4_SF_diff.mif', '-quiet']]
dwi2response: Deleting file: iter3_SF.mif
dwi2response: Deleting file: iter4_SF_diff.mif
dwi2response: Convergence of SF voxel selection detected at iteration 4
dwi2response: Deleting file: iter4_CF.mif
dwi2response: Changing back to original directory (/media/ibmi/Data/Paper_DWI_Treffen_2016.07.20_Miitwoch/Paper_DWI_Vergleich_B1000-30

Ralf · July 22, 2016, 4:34pm

I dont know if its right, but it does something.
At the end I have a text file with 6 numerals. I hope its worth it.

Thanks for the help again,

Ralf

jdtournier · July 22, 2016, 5:12pm

Sounds like it worked just fine then! You might want to remove the edit to the script that @rsmith suggested, it does add quite a bit of noise to the output…

Surprised you’d get 6 numbers in the response file though, you should only get 5 by default…?

Ralf · July 22, 2016, 5:34pm

You are right. Its 5. The editor showed some stuf, but its not part of the txt.
How do I remove the edit?

Ralf

jdtournier · July 22, 2016, 7:03pm

You just need to revert @rsmith’ previous suggestion - i.e. remove print (cmdstack) from this line.

Ralf · July 22, 2016, 7:08pm

Sorry, didnt remeber. I know…from the python script.