External Email - Use Caution
Hi Fahad,
Here is the wiki page about how to Convert from FreeSurfer Space Back to Native Anatomical Space - https://secure-web.cisco.com/1SH-F86njclC8pQKcB6nkwsqK8lnEDnPON_A24-6CmCwRHC...
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fahad Hannan Sent: Monday, July 3, 2023 3:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_segstats dimension mistach
External Email - Use Caution Hello,
I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use the following command:
"mri_segstats --seg $SUBJECTS_DIR/P6V1/mri/wmparc.mgz --sum $SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm --in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt"
I get a dimension mismatch error:
ERROR: dimension mismatch between input volume and seg input 112 112 80 seg 256 256 256
Seems like during the recon-all process, freesurfer changed the dimensions of the segmentation file to 256 256 256. Is there a way I can resample the segmentation file to the input files dimensions, I know I can resample the input to the norm.mgz file but I do not want to tamper with the input file.
Thanks, Fahad