Re: [Freesurfer] adc brainstem-subs
thanks a lot, works great :-) Thomas Gesendet: Donnerstag, 10. März 2016 um 09:31 Uhr Von: "Eugenio Iglesias" <e.igles...@bcbl.eu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 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" <am-dam-...@gmx.at> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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" <am-dam-...@gmx.at> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
