I would think that going into the DTI space would make this worse since
the voxels are bigger (?). But if that is what you want to do, use
mri_label2vol to map the aparc+aseg.mgz into the DTI space, then spec
that aparc+aseg in the mri_segstats cmd
doug
On 4/15/15 2:13 AM, Thomas Potrusil wrote:
Hi doug!
you´re right, it´s working without --inv flag. But I have problems
with partial volume effects within subcortical areas close to the
ventricle. ADC values are falsified for some regions when using
mri_segstats (especially caudate and putamen). I want to overcome this
problem by resampling the anat to funct space... Visual inspection of
data showed that registration is very good but scrolling through adc
map with aseg-overlay revealed these PVEs...
Thanks, Tom
*Gesendet:* Mittwoch, 15. April 2015 um 00:19 Uhr
*Von:* "Douglas Greve" <[email protected]>
*An:* [email protected]
*Betreff:* Re: [Freesurfer] dimension mismatch
Don't use the --inv flag on vol2vol
doug
On 4/14/15 10:03 AM, Thomas Potrusil wrote:
Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o
$outdir_dtirecon
I resampled the anatomical into the functional space using (I´m
interested in ADC-values)
mri_vol2vol --mov $dti_vol --reg $outdir_dtirecon/register.dat
--fstarg --inv --o $vol2vol
which worked again very well.
for extracting ADC-values I used
mri_segstats --seg $subj/mri/aparc.a2009s+aseg.mgz --ctab $FSCLUT
--seg-erode 1 --i $outdir_dtirecon/adc.anat.mgh --mul 1000 --sum
$outdir_stat/adc_aparc.stats
Running this command delivers the following error:
ERROR: dimension mismatch between input volume and seg
input 256 256 47
seg 256 256 256
Do you have any idea avoiding this?!
Thanks a lot, Tom
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