Hi Fahad,

Here is the wiki page about how to Convert from FreeSurfer Space Back to Native Anatomical Space - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

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