Sorry, one more thing. Add --regheader to the command lien
On 5/12/2022 5:12 PM, James Hengenius wrote:
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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
<dgr...@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 Caution
Hello 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.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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