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 -in
>> bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.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.bbr.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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