thanks a lot, works great :-)
Thomas
Gesendet: Donnerstag, 10. März 2016 um 09:31 Uhr
Von: "Eugenio Iglesias"
An: "Freesurfer support list"
Betreff: Re: [Freesurfer] adc brainstem-subs
Dear Thomas,
I am assuming that your ADC volume is defined in the voxel space of the other images in your subject directory (and that's why its dimensions are 256x256x256).
In that case, you have two options:
1. Instead of using brainstemSsLabels.v10.mgz, you can use brainstemSsLabels.v10.1mm.mgz, which is defined in the same voxel space as the rest of your data. This is the easiest alternative.
2. If you want to work at higher resolution, you can also upsample your ADC data to the space of the brainstem segmentation. You can do this with:
mri_convert [ADCvolume] [ADCvolumeResampled] -rl brainstemSsLabels.v10.mgz -odt float
and then work with [ADCvolumeResampled] and brainstemSsLabels.v10.mgz
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
From: "Thomas Potrusil"
To: "Freesurfer support list"
Sent: Thursday, March 10, 2016 9:17:19 AM
Subject: [Freesurfer] adc brainstem-subs
Dear FreeSurfers,
I wan´t to extract adc values from newly segmented brainstem substructures by using
mri_segstats --seg $brainstem_subs --ctab $FSCLUT --id 173 174 175 178 --seg-erode 1 --i $outdir_dtirecon/adc_anat.mgh --mul 1000 --sum $outdir_stat/adc_brainstem_subs.stats
However, based on the fact that the seg volume is much smaller (173x221x140) than my input adc-file (256x256x256) I get an ERROR: dimension mismatch between input volume and seg !!
Do you have any suggestions to overcome this problem?
Thanks in advance,
TomP
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