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
Von: "Douglas Greve" <[email protected]>
An: [email protected]
Betreff: Re: [Freesurfer] dimension mismatch
Don't use the --inv flag on vol2vol
doug
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doug
On 4/14/15 10:03 AM, Thomas Potrusil wrote:
Dear FreeSurfers!After successful registration usingdt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o $outdir_dtireconI 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 $vol2volwhich worked again very well.for extracting ADC-values I usedmri_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.statsRunning this command delivers the following error:ERROR: dimension mismatch between input volume and seg
input 256 256 47
seg 256 256 256Do you have any idea avoiding this?!Thanks a lot, Tom_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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