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It should not be that pixelated. My guess is that slicer is doing some kind of smart interpolation to make it look better. One way around it would be to map your input to the conformed space and run mri_segstats on that

On 7/6/2023 3:57 PM, Fahad Hannan wrote:

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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://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

 

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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


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