Dear FreeSurfers,
I am trying to run trac-all -prep on a single subject, and get the following error:
dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs -b /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals -o /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit Error: bvecs and bvals don't have the same number of entries
I have searched the message thread, and cannot seem to find a solution applicable to my situation: it seems that the trac-all process generates transposed bvec and bval files. Therefore, I tried transposing these manually and specifying the location to these files (as explained in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but attempting to run trac-all again still leads to the same result: new bval and bvec files are generated, and I receive the same error message.
Does anyone know how I can solve this problem?
Thank you, Joy-Loi
********************* My configuration file:
setenv SUBJECTS_DIR /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
set dtroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
set subjlist = id101 set runlist = 1
set dcmroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set dcmlist = id101/orig/1.dcm
set bvalfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
set bvecfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
set nb0 = 10
set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
#set trainfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP)
set ncpts = 5
set usetrunc = 1
********************* My bvals:
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000
********************* My bvecs:
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.9998760 0.0011040 0.0157340 -0.7705615 0.6320276 0.0823114 -0.2461791 0.0273479 0.9688392 -0.7953558 0.1076421 0.5965091 0.4620816 -0.8755928 0.1407778 0.2261090 -0.8553081 -0.4661796 0.2601186 0.4095102 -0.8744363 -0.7969547 -0.5877791 0.1392076 -0.5028073 -0.5104712 0.6975709 -0.3073035 0.1334521 -0.9422074 0.7957742 0.1950272 -0.5733304 0.8041493 0.5924478 -0.0484727 -0.1867079 -0.9528833 0.2390659 0.3898569 -0.1063898 0.9147088 0.1341999 -0.6614532 0.7378819 0.3382555 0.8823941 0.3270553 -0.7688307 -0.3139264 -0.5570900 -0.4086013 0.6653325 0.6248017 -0.2933309 0.7581020 -0.5824408 0.7689370 -0.4282441 0.4747016 0.1800972 0.5296402 0.8288835 0.7680658 0.3158178 0.5570763 -0.2214999 0.9744585 0.0370050 -0.4175692 -0.8418782 -0.3418731 -0.1784475 -0.4817282 -0.8579599 0.3361637 0.8554551 -0.3939400 0.7858656 -0.5091907 -0.3509137 0.4194232 -0.2589429 -0.8700761 -0.7760561 0.3511497 -0.5238622 0.9987836 -0.0413076 0.0269219
Hi Joy - How were your bvecs and bvals files generated? In the past some people have had problems with files exported from Excel b/c it generates text files with Windows-specific end-of-line characters that cannot be read properly on Linux. Do the files look normal when you run "more" on them on the system where you ran trac-all?
a.y
On Wed, 26 Sep 2012, Loi wrote:
Dear FreeSurfers,
I am trying to run trac-all -prep on a single subject, and get the following error:
dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs -b /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals -o /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit Error: bvecs and bvals don't have the same number of entries
I have searched the message thread, and cannot seem to find a solution applicable to my situation: it seems that the trac-all process generates transposed bvec and bval files. Therefore, I tried transposing these manually and specifying the location to these files (as explained in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but attempting to run trac-all again still leads to the same result: new bval and bvec files are generated, and I receive the same error message.
Does anyone know how I can solve this problem?
Thank you, Joy-Loi
My configuration file:
setenv SUBJECTS_DIR /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
set dtroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
set subjlist = id101 set runlist = 1
set dcmroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set dcmlist = id101/orig/1.dcm
set bvalfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
set bvecfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
set nb0 = 10
set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
#set trainfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP)
set ncpts = 5
set usetrunc = 1
My bvals:
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000
My bvecs:
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.9998760 0.0011040 0.0157340 -0.7705615 0.6320276 0.0823114 -0.2461791 0.0273479 0.9688392 -0.7953558 0.1076421 0.5965091 0.4620816 -0.8755928 0.1407778 0.2261090 -0.8553081 -0.4661796 0.2601186 0.4095102 -0.8744363 -0.7969547 -0.5877791 0.1392076 -0.5028073 -0.5104712 0.6975709 -0.3073035 0.1334521 -0.9422074 0.7957742 0.1950272 -0.5733304 0.8041493 0.5924478 -0.0484727 -0.1867079 -0.9528833 0.2390659 0.3898569 -0.1063898 0.9147088 0.1341999 -0.6614532 0.7378819 0.3382555 0.8823941 0.3270553 -0.7688307 -0.3139264 -0.5570900 -0.4086013 0.6653325 0.6248017 -0.2933309 0.7581020 -0.5824408 0.7689370 -0.4282441 0.4747016 0.1800972 0.5296402 0.8288835 0.7680658 0.3158178 0.5570763 -0.2214999 0.9744585 0.0370050 -0.4175692 -0.8418782 -0.3418731 -0.1784475 -0.4817282 -0.8579599 0.3361637 0.8554551 -0.3939400 0.7858656 -0.5091907 -0.3509137 0.4194232 -0.2589429 -0.8700761 -0.7760561 0.3511497 -0.5238622 0.9987836 -0.0413076 0.0269219 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello,
I generate the files in Linux (using gedit) and they look normal (I have compared them to the files in the tutorial).
So far I have tried ending both with and without .txt, transposing the files, changing to equal number of decimals and adding 'setenv LC_ALL en_US' to the .tchsrc file.
The inputs I am using are dicoms, and even though I specify a path to the b-value files and gradient tables I make (I originally didn't specify these, and got the same error message), new bvecs and bvals are generated in the trac-all -prep process, leading to the error.
Thank you, Joy-Loi
On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Joy - How were your bvecs and bvals files generated? In the past some people have had problems with files exported from Excel b/c it generates text files with Windows-specific end-of-line characters that cannot be read properly on Linux. Do the files look normal when you run "more" on them on the system where you ran trac-all?
a.y
On Wed, 26 Sep 2012, Loi wrote:
Dear FreeSurfers,
I am trying to run trac-all -prep on a single subject, and get the following error:
dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs -b /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals -o /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit Error: bvecs and bvals don't have the same number of entries
I have searched the message thread, and cannot seem to find a solution applicable to my situation: it seems that the trac-all process generates transposed bvec and bval files. Therefore, I tried transposing these manually and specifying the location to these files (as explained in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but attempting to run trac-all again still leads to the same result: new bval and bvec files are generated, and I receive the same error message.
Does anyone know how I can solve this problem?
Thank you, Joy-Loi
My configuration file:
setenv SUBJECTS_DIR /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
set dtroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
set subjlist = id101 set runlist = 1
set dcmroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set dcmlist = id101/orig/1.dcm
set bvalfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
set bvecfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
set nb0 = 10
set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
#set trainfile =
/usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP)
set ncpts = 5
set usetrunc = 1
My bvals:
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000
My bvecs:
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.9998760 0.0011040 0.0157340 -0.7705615 0.6320276 0.0823114 -0.2461791 0.0273479 0.9688392 -0.7953558 0.1076421 0.5965091 0.4620816 -0.8755928 0.1407778 0.2261090 -0.8553081 -0.4661796 0.2601186 0.4095102 -0.8744363 -0.7969547 -0.5877791 0.1392076 -0.5028073 -0.5104712 0.6975709 -0.3073035 0.1334521 -0.9422074 0.7957742 0.1950272 -0.5733304 0.8041493 0.5924478 -0.0484727 -0.1867079 -0.9528833 0.2390659 0.3898569 -0.1063898 0.9147088 0.1341999 -0.6614532 0.7378819 0.3382555 0.8823941 0.3270553 -0.7688307 -0.3139264 -0.5570900 -0.4086013 0.6653325 0.6248017 -0.2933309 0.7581020 -0.5824408 0.7689370 -0.4282441 0.4747016 0.1800972 0.5296402 0.8288835 0.7680658 0.3158178 0.5570763 -0.2214999 0.9744585 0.0370050 -0.4175692 -0.8418782 -0.3418731 -0.1784475 -0.4817282 -0.8579599 0.3361637 0.8554551 -0.3939400 0.7858656 -0.5091907 -0.3509137 0.4194232 -0.2589429 -0.8700761 -0.7760561 0.3511497 -0.5238622 0.9987836 -0.0413076 0.0269219 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Can you please send the original bvals and bvecs files (the ones that you specify in the configuration file), and the configuration file itself? Thanks!
a.y
On Thu, 27 Sep 2012, Loi wrote:
Hello,
I generate the files in Linux (using gedit) and they look normal (I have compared them to the files in the tutorial).
So far I have tried ending both with and without .txt, transposing the files, changing to equal number of decimals and adding 'setenv LC_ALL en_US' to the .tchsrc file.
The inputs I am using are dicoms, and even though I specify a path to the b-value files and gradient tables I make (I originally didn't specify these, and got the same error message), new bvecs and bvals are generated in the trac-all -prep process, leading to the error.
Thank you, Joy-Loi
On Thu, Sep 27, 2012 at 7:30 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Joy - How were your bvecs and bvals files generated? In the past some people have had problems with files exported from Excel b/c it generates text files with Windows-specific end-of-line characters that cannot be read properly on Linux. Do the files look normal when you run "more" on them on the system where you ran trac-all?
a.y
On Wed, 26 Sep 2012, Loi wrote:
Dear FreeSurfers,
I am trying to run trac-all -prep on a single subject, and get the following error:
dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs -b /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals -o /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit Error: bvecs and bvals don't have the same number of entries
I have searched the message thread, and cannot seem to find a solution applicable to my situation: it seems that the trac-all process generates transposed bvec and bval files. Therefore, I tried transposing these manually and specifying the location to these files (as explained in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but attempting to run trac-all again still leads to the same result: new bval and bvec files are generated, and I receive the same error message.
Does anyone know how I can solve this problem?
Thank you, Joy-Loi
My configuration file:
setenv SUBJECTS_DIR /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons
set dtroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data
set subjlist = id101 set runlist = 1
set dcmroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set dcmlist = id101/orig/1.dcm
set bvalfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt
set bvecfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt
set nb0 = 10
set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz
#set trainfile =
/usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt
set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP)
set ncpts = 5
set usetrunc = 1
My bvals:
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000
My bvecs:
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 -0.9998760 0.0011040 0.0157340 -0.7705615 0.6320276 0.0823114 -0.2461791 0.0273479 0.9688392 -0.7953558 0.1076421 0.5965091 0.4620816 -0.8755928 0.1407778 0.2261090 -0.8553081 -0.4661796 0.2601186 0.4095102 -0.8744363 -0.7969547 -0.5877791 0.1392076 -0.5028073 -0.5104712 0.6975709 -0.3073035 0.1334521 -0.9422074 0.7957742 0.1950272 -0.5733304 0.8041493 0.5924478 -0.0484727 -0.1867079 -0.9528833 0.2390659 0.3898569 -0.1063898 0.9147088 0.1341999 -0.6614532 0.7378819 0.3382555 0.8823941 0.3270553 -0.7688307 -0.3139264 -0.5570900 -0.4086013 0.6653325 0.6248017 -0.2933309 0.7581020 -0.5824408 0.7689370 -0.4282441 0.4747016 0.1800972 0.5296402 0.8288835 0.7680658 0.3158178 0.5570763 -0.2214999 0.9744585 0.0370050 -0.4175692 -0.8418782 -0.3418731 -0.1784475 -0.4817282 -0.8579599 0.3361637 0.8554551 -0.3939400 0.7858656 -0.5091907 -0.3509137 0.4194232 -0.2589429 -0.8700761 -0.7760561 0.3511497 -0.5238622 0.9987836 -0.0413076 0.0269219 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu