Hi Bahram - The gradient table is a text file with 3 columns. You need to
multiply the 3rd column by -1. You can do this in matlab, awk, perl, or
any scripting language that handles text files.
Best,
a.y
On Wed, 26 Aug 2015, B M wrote:
Hi Anastasia,
Thank you very much for your help and recommendations. I will try to fix
These Problems. I would like to ask you one more question. Is there any
command which could help me to invert the gradient vectors for my DWI
scan in the z direction?
Best
Bahram
2015-08-24 17:57 GMT+02:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:
Hi Bahram - I looked at your subject's files. First, the
freesurfer recon failed in the right hemisphere, probably
because of a visible artifact on your T1 (see aseg screenshot).
This affects the aparc+aseg, so you can't run tracula before you
fix it.
Second, the gradient vectors for your DWI scan probably need to
be inverted in the z direction (see other screenshot with the
principal eigenvectors of the tensors shown over the FA map).
The vectors are oriented correctly in the axial view, but not in
the sagittal or coronal view (see for example their orientation
in the cingulum bundle in saggital view, where the cross-hair is
centered, or in the corticospinal tract in coronal view). This
is not causing your error, but you have to fix it for the
tractography to work properly.
Third, your DWI data has very anisotropic resolution (1.8 x 1.8
x 6.5 mm). Your voxels are almost 4 times as big in z than in
x/y. This is not causing your error, but it is not optimal for
diffusion analysis. Anisotropic voxels can bias estimates of
diffusion anisotropy. Also, you only have 12 directions with
b=1000 and the other directions were acquired with a much lower
b-value (b=200). It's unlikely that you'll get reliable fits of
crossing-fiber models like the one used by tracula on this data.
Again, this is not causing the error you're seeing but it will
make it difficult to get usable results from this DWI data.
Best,
a.y
On Thu, 20 Aug 2015, B M wrote:
Hi Anastasia,
please find the files in attachment.
Best regards
Bahram
2015-08-19 21:55 GMT+02:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
Hi Bahram - There are some errors in there
related to registration files. Can you please send
these files?
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat
Thanks,
a.y
On Tue, 18 Aug 2015, B M wrote:
Hi Anastasia,
Please find attached the trac-all.log
file. Thank you very much for your help.
Bahram
2015-08-17 19:31 GMT+02:00 Anastasia
Yendiki <ayend...@nmr.mgh.harvard.edu>:
Hi Bahram - Can you please send us
your entire trac-all.log file? Thanks!
a.y
On Fri, 14 Aug 2015, B M wrote:
Dear experts,
I have the last version of
tTrakula. i did the first step with
trac-all -prep -c
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
This worked properly to the
end as shown below:
trac-preproc finished
without error at Fri Aug 14 17:31:29 CEST 2015
However looking at logfile i
found following errors:
flirt
-inbmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.ni
i.gz
-ref
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz
-out
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bb
r.nii.gz
-applyxfm -init
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
-interp
nearestneighbour
terminate called after
throwing an instance of 'NEWMAT::SingularException'
Abort (core dumped)
OR
Loading brain mask of output
subject from
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_
mask.bbr.nii.gz
niiRead(): error opening
file
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_
mask.bbr.nii.gz
ERROR: Could not read
/home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_
mask.bbr.nii.gz
AND as i tried the next step
i got the following error:
bm@bm-linux:~$ trac-all
-bedp -c
bmdaten/Auswertung/ALS-Review/Trakula/dmrirc
INFO: SUBJECTS_DIR is
bmdaten/Auswertung/ALS-Review/Trakula/
INFO: Diffusion root is
bmdaten/Auswertung/ALS-Review/Trakula/
Actual FREESURFER_HOME
/usr/local/freesurfer
WARN: Running FSL's bedbost
locally - this might take a while
WARN: It is recommended to
run this step on a cluster
bedpostx_mgh -n 2
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax
error: "("
unexpected
Could you please advise me
what to do?
Best
Bahram
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contains patient information, please contact the Partners Compliance
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but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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