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Hi Douglas,
Thanks for the suggestion! However, using mri_vol2vol generates the error message:
ERROR: SUBJECTS_DIR undefined.
If I set SUBJECTS_DIR to the study directory, I get the following error:
movvol ICBM152_2009c_AtlasWhite.nii.gz
targvol T1w_MNI.nii.gz outvol AtlasWhite_resampled.nii.gz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1653169738 ERROR: no registration (R) is specified
Invalid argument
mri_vol2vol --targ T1w_MNI.nii.gz --interp nearest --mov ICBM152_2009c_AtlasWhite.nii.gz --o AtlasWhite_resampled.nii.gz : Signal 124
Note that our participant directories aren't in the standard Freesurfer subject directory structure, if that matters. Is mri_vol2vol looking for a Freesurfer generated registration somewhere in the subject directory?
Thanks!
Jim H
On Thu, May 12, 2022 at 3:43 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
try this mri_vol2vol --targ T1w_MNI.nii.gz --interp nearest --mov ICBM152_2009c_AtlasWhite.nii.gz --o WhiteAtlas_resampled.nii.gz
On 5/9/2022 11:58 AM, James Hengenius wrote:
External Email - Use CautionHello FS experts,
I'm trying to reslice a third-party atlas into the same resolution as my data in MNI space. I am using the following command:
mri_convert --like T1w_MNI.nii.gz --resample_type nearest ICBM152_2009c_AtlasWhite.nii.gz WhiteAtlas_resampled.nii.gz
Output is:
mri_convert --like T1w_MNI.nii.gz --resample_type nearest ICBM152_2009c_AtlasWhite.nii.gz WhiteAtlas_resampled.nii.gz reading from ICBM152_2009c_AtlasWhite.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: transform src into the like-volume: T1w_MNI.nii.gz writing to WhiteAtlas_resampled.nii.gz...
In the resulting resampled atlas, the boundaries of the ROIs appear to use an interpolation and not nearest neighbor (i.e., they take values other than the ROI values in the atlas). Not sure if I can embed images - if so, see the attached for an example:
[image: image.png]
The output is the same whether I include the --resample_type nearest flag or leave it out, making me think that mri_convert is ignoring the flag and using the default interp option.
This can be replicated in the relatively current version "freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b" as well as the older "$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $" (which we keep around for old pipeline compatibility).
Any ideas on how to fix this so the ROI interfaces take appropriate (nearest neighbor) values rather than interpolated values?
Thanks all!
Jim H.
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