Re: [Freesurfer] Pixelated DTI mask from Tracula

Hi Alessia - So it's the FA map. Yes, this doesn't look like a correct FA map, there's no contrast between the white matter and everything else. The calculation of the FA has nothing to do with the freesurfer or tracula algorithms. It just uses your DWI data set, the gradient directions and the b-values, so these 3 things must be in disagreement if the FA doesn't come out right. I'd look into whether the subjects that have this problem were scanned with a different protocol or if the gradient directions and b-values were not extracted properly for them.

Hope this helps, a.y

On Wed, 21 Nov 2012, Alessia Sarica wrote:

Hi Anastasia,thanks for your fast reply.

I mean the file named dtifit_FA.nii

I've re-run twice recon-all and tracula both, but it doesn't change the result.

Best regards, Alessia.

2012/11/21 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu

  Hi Alessia - I'm not sure what you're referring to as "the dti mask". Can you give me the file
  name of the image that you're displaying in the screehshot? It does look like noise.

  Thanks,
  a.y

  On Wed, 21 Nov 2012, Alessia Sarica wrote:

        Dear Freesurfer Users,I'm a Ph.D. Student and I'm working on tractography using
        Tracula, 
        with the aim of conducting statistical analysis on the FA values.

        I have a cohort of 18 Amyotrophic Lateral Sclerosis Patients, and i'm doing all the
        process phases,
        starting from recon-all, ending to trac-all path.

        I've attached a text file with info about DTI DICOM extracted by ImageJ.

        Now, my problem is about the dti mask, as you can see on the attached image, a
        pixelated one is obtained,
        even if
        the left and right cst tracts seem good. This problem only occurs in few patients,
        not in all of them, even
        if the script
        is the same for all.

        This is the script i'm using:

              #Patient_name
              setenv SUBJECTS_DIR $TUTORIAL_DATA/Patient_recons
              set dtroot = $TUTORIAL_DATA/Patient_tracula
              set subjlist = (Patient_name)
              set runlist = (1)
              set dcmroot = $TUTORIAL_DATA/Patient_tracula
              set dcmlist = (Patient_name/orig/MR000000)
              set bvalfile =
        $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bval
              set bvecfile =
        $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bvec
              set nb0 = 1
              set dob0 = 0
              set doeddy = 1
              set dorotbvecs = 1
              set usemaskanat = 0
              set thrbet = 0.3
              set doregflt = 1
              set doregbbr = 0
              set doregmni = 1
              set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
              set pathlist = (lh.cst_AS rh.cst_AS \
              lh.ilf_AS rh.ilf_AS \
                               lh.unc_AS rh.unc_AS \
              fmajor_PP fminor_PP \
              lh.atr_PP rh.atr_PP \
              lh.cab_PP rh.cab_PP \
              lh.ccg_PP rh.ccg_PP \
              lh.slfp_PP rh.slfp_PP \
              lh.slft_PP rh.slft_PP)
               
              set ncpts = 5
              set nburnin = 200
              set usetrunc = 1
              set nkeep = 5
              set nsample = 5000


        I want to highlight that bval and bvec files are obtained from the tool dicom2nift,
        because Tracula is not
        able to extract them from DICOM header.
        I will really appreciate your help.

        Best regards,
        Alessia.


        --
        Alessia Sarica
        Ph.D. Student Biomedical and Informatics Engineering,
        Bioinformatics Laboratory, Department of Surgical and Medical Sciences,
        University "Magna Græcia" of Catanzaro,
        Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY.
        Phone: +3909613694193

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-- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193