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
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/MR00)
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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
--
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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