Re: [Freesurfer] mri_segstats dimension mistach

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That worked, thank you so much!

Regards,

Fahad ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Wednesday, July 5, 2023 9:53 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats dimension mistach

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Hi Fahad,

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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

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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