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 re
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 Anast
Hi Bahram - The anatomical-to-diffusion registration matrix is all zeros,
so something went wrong there. I'll need to see all the output files to
investigate. Can you please zip up this subject's tracula output
directories (dmri, dmri.bedpostX, dpath, dlabel, scripts) and upload
everything fo
Hi Anastasia,
please find the files in attachment.
Best regards
Bahram
2015-08-19 21:55 GMT+02:00 Anastasia Yendiki :
>
> 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/anat2d
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 :
>
> 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 hav
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
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 foll
Hi Viviana - Does it die at that point or does it keep running? If it's
the latter it doesn't look wrong. For your first problem you should make
sure that your path includes the bin/ directory under the FSL
distribution.
a.y
On Wed, 25 Apr 2012, Viviana Siless wrote:
Hi Anastasia,
I ran:
Hi Anastasia,
I ran:
- bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri
and got the following output:
subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
But before it to
Hi Viviana - I cannot replicate this on our systems but I think I know
what your system may be fussy about and I'll amend it. For now, if you
don't get any outputs can you please try running bedpostx directly on
/media/vivi/images/freesurfer/00112288Proc/dmri and see if that works?
Thank
Hello Anastasia,
It fixed the bug. Thank you so much!
Now Im running trac-all -bedp -c
But it's been running for already 3 days, and it just printed that:
> trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is
Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI
template brain, and our atlas was built using the 1mm one. From your
dmrirc file:
# MNI template (the only option for inter-subject registration in this
version)
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii
Hi Anastasia,
My mistake with the expiration date.
Please try with this link:
https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testData.tar.gz
Thanks!
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
On Tue, Apr 17,
Hi Anastasia,
Here is the data:
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet
me know if you have any trouble.
I changed to the other track-all, and the error is the same.
Please let me know if I'm doing anything wrong!
Thank you!
Viviana Siless
--
Parieta
Hi Viviana - If you upload this data set I'm happy to look at it.
Also, I strongly recommend getting the updated version of trac-all from
the wiki (I'm guessing from the log file that you're probably not using
that?) See 2012/01/09 update here:
http://surfer.nmr.mgh.harvard.edu/fswiki
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