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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@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*
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Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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