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Hi,
Just to follow up, is there a way to retain the segmentation quality? It becomes pixelated when returning to native space. Is there a method similar to how I can load the wmparc.mgz + my volume into 3DSlicer and they overlap perfectly despite the wmparc being in freesurfer space. I'm trying to find a better way to get segmentation based stats without the use of 3Dslicer which can be tedious. I've attached images showing the difference.
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,
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://secure-web.cisco.com/1KPsNCHMEXNGgU3B_g0aRawlnTSIfd9p4ELLuirD2g6gBVf...https://secure-web.cisco.com/1SH-F86njclC8pQKcB6nkwsqK8lnEDnPON_A24-6CmCwRHC_v0s6AwvY_foOYGXPrbz_PgXgmdPkQnHYy_AMudJENZoBcBNcrqdJGYd-N6ZKQjjSH-gzCI5Dq5ZHU2wFNKxRh944qf6UZNgqhb4s_XDC669KdGDt4GGk_mpnPRMKrIRyGvLfJb8vKw02AHSq1SM528T730feGzUsjm9FM5CgiF3QW5mg-UlGeOlPUDGd9xvS0cKt60Wny7zkFNwJMyH553-KKUKzzeyOvA09Wnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-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
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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
