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.ro...@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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