Hello Freesurfer Team,
I attended the conference last week in Boston and really enjoyed all I learned! But while trying to run through the Tracula tutorial with my own data, I am having an error with my configuration file:
ERROR: must specify as many DWI dicoms as subjects.
My files are in nifti format, could this possibly be the cause of this error? I have attached my configuration file for reference.
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Kernel info: Darwin 14.5.0 x86_64
Thanks so much!
Jasmin
Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu
Hi Jasmin -
In your dmrirc file , the dcmlist refers to the dicom list. You have put the BVEC/BVAL files there. That is not correct. You need to place the actual pathway to your niftis in this position.
set subjlist = (40 39 36)
# Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified # set dcmroot = Users/jasminalves/Desktop/data/DTI set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec DTI.bval 36/DTI.nii.gz DTI.bvec DTI.bval) *<- Pathway to NIFTIS HERE*
Hope this helps,
best,
Alan
freesurfer@nmr.mgh.harvard.edu
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Alan Francis -
Jasmin Alves