I would use step 3 for the wmparc instead of vol2vol.

you need both --seg and --seg-erode

--seg-erode 1 --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz

doug

On 03/20/2014 04:43 AM, Rotem Saar wrote:

Hi Doug,

Thanks you for directing me to my mistake in step 3 (see below new cmd line in step 3). What I did is the following -

1. dt_recon --i

/usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec

2. mri_vol2vol --mov

/usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii --targ /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --no-save-reg

3. mri_label2vol --seg

/usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --temp /usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o /usr/local/freesurfer/subjects/Anatomy0981/mri/forMD.bshort

it created many *.bshort files

My qs:

1. Should I repeat step 3 with the wmparc.mgz or is it not necessary ?
2. How do I plot all MD values like I did before for FA values ?

trying to use -

mri_segstats --seg-erode 1 /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked

always end with the same message - it wants a segmentation volume but nothing works ("unknown")... I used aseg.mgz for example and other options - nada. However, If I omit the "-erode 1" it reports the table, but for FA values. What do I need to change in step 3 and how can I fix the last step ?

Thank you for your help

Rotem

2014-03-17 8:42 GMT+02:00 Rotem Saar <saar.rotem@gmail.com mailto:saar.rotem@gmail.com>:

Dear Doug,

I'm now working with freesurfer 5.3, for this example, subject is
"Anatomy0981". A while ago I wrote to the list trying to extract
the MD values for each ROI as in the diffusion analysis that ends
with the FA value for each ROI (for each subject).
I wrote my FA script, and asked u to advise on how to convert it
to my needs (MD instead of FA), u wrote -

> Use mri_label2vol to transfer the wmparc.mgz into the DTI space,
then
> use mri_segstats with --seg-erode 1 to compute summaries of the
MD in
> each region

(steps below for FA values ended fine) - this is what I did -

1)  dt_recon --i /usr/local/freesurfer/
  subjects/Anatomy0981/DTI/I160.dcm
--s Anatomy0981 --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
/usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval
/usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec

2) mri_vol2vol --mov
/usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \
             --targ
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz \
             --inv --interp nearest --o
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz \
             --reg
/usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat
--no-save-reg

3) mri_label2vol --mov
/usr/local/freesurfer/subjects/Anatomy0981/DTI/lowb.nii \
             --targ
/usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg.mgz \
             --inv --interp nearest --o
/usr/local/freesurfer/subjects/Anatomy0981/mri/aparc+aseg2diff.mgz \
             --reg
/usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat
--no-save-reg

4) mri_segstats --seg-erode 1
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i
/usr/local/freesurfer/subjects/Anatomy0981/DTI/fa-masked.mgz --sum
/usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked

error after step 3: ERROR: Option --mov unknown
Trying to use vol2vol instead of label2vol ended successfully, but
then when trying to perform step 4, it failed again -
ERROR: Option
/usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc2diff.mgz unknown

Can u advise on what am I doing wrong ?

Thanks !!




Rotem Saar-Ashkenazy
Department of Brain and Cognitive Science
Ben Gurion University of the Negev
Beer-Sheva 84105
Israel

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