If you pass it dicom, it will try to extract the bvalues, which is where it is failing. doug
Antonella Kis wrote:
Dear Doug,
Sorry but I still have a question about this error: I understood that dt_recon it takes original dicom images as input and it generates multiple NIFTI volumes that will be used in later steps.So why I need to use the NIFTI as input?
Thnak you. AK
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com *Cc:* "fischl@nmr.mgh.harvard.edu" fischl@nmr.mgh.harvard.edu; "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, August 30, 2011 3:51 PM *Subject:* Re: [Freesurfer] Fw: Error with dt_recon
It's looking for the values in the dicom file (which apparently does not have them). Convert the dicom to nifit, then use the nifti as input, then pass files with bvals and bvects on the command line. doug
Antonella Kis wrote:
Dear Bruce:
I am running the dt_recon: # setenv FREESURFER_HOME /usr/local/freesurfer # setenv
SUBJECTS_DIR $FREESURFER_HOME
# cd /usr/local/freesurfer/NPI001 # dt_recon --i
/usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti
and I am getting the following error:
ERROR: cannot extract sDiffusion.alBValue[1] from
/usr/local/freesurfer/NPI001/dti/dwi-infodump.dat
Can you please give me a hint?
Thank you. AK
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