On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail <IKOUBIYR@BWH.HARVARD.EDU> wrote:
It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames …
Ismail
On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:
I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up?
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,_______________________________________________
This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason.
Also why the DICOMs wouldn’t work at the beginning ?
Thanks,
Ismail
On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ismail - You can see from the log file that the command that causes the error is this:
mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz
It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out.
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,_______________________________________________
Here it is.
But how could the problem be related to the nifti volume since I have errors
when using the DICOMs too ?
Thanks again,
Ismail
On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki<ayendiki@nmr.mgh.harvard.edu> wrote:
the bvecs/bvals. Can you send the log file from scripts/trac-all.log?
Hi Ismail - It sounds like the error has to do with the nifti volume, not
:
Thanks,
a.y
On Mon, 4 Jul 2016, Koubiyr, Ismail wrote:
Hi Anastasia,
Thank you for getting back to me.
Here are more details about my problem, I think it should help you
understand more.
I run trac-all -prep -c on some DICOM files but I had the following error
0043WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368
space,.6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII
header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I also tried to de-mosiac the DICOMs, it gave me the same error.
Then I converted the DICOMs into NIFTI, which allowed me not to get the
previous error but something else weird happened. Now I get :
ERROR: fMRIframe: frame >= nframes
I checked the bvecs and bvals files, they seem normal, no additional
willbut when the new bvecs and bvals are created, they seem messed up. I
attach you all the bvecs and bvals I used and the ones I get too._______________________________________________
Ideally, the DICOMs should work fine but I have no idea why I get these
errors.
The bvecs and bvals are obtained from dcm2nii and then corrected to avoid
any additional space.
Thank you in advance for your help.
Best,
Ismail
P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used.
On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:
Hi Ismail - Are you passing the nifti volume as input to trac-all?
It's
hard to tell without looking at your configuration file.
Best,
a.y
On Tue, 28 Jun 2016, Koubiyr, Ismail wrote:
Hi everyone,
I have some problems trying to run TRACULA on some DWI
data. It is a mosaic Siemens DWI. I first converted the
DICOM files with dcm2nii to get the bvec and bval files.
Then I run the trac-all -prep -c command and I get the
following error :
WARNING: file /My/path/to/dicom does not contain a Siemens
ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header
I tried to unpack the mosaics with gdcmtar, but I got the
same error.
Thank you in advance for your help,
Ismail
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