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April 28, 2022 07:29AM
Howdy-

I ran:
@SUMA_AlignToExperiment \
    -exp_anat FT_anat+orig. \
    -surf_anat ~/REF_TEMPLATES/MNI_avg152T1+tlrc. \
    -wd \
    -align_centers
... and got "MNI_avg152T1_Alnd_Exp.A2E.1D" (-> which is the mat_MNI_to_anat).

And I ran:
align_epi_anat.py \
    -dset1 short_epi+orig. \
    -dset2 FT_anat+orig. \
    -dset1to2 \
    -partial_axial \
    -dset1_strip None \
    -dset2_strip None \
    -edge \
    -cost lpa
... getting "short_epi_al_mat.aff12.1D" (-> mat_EPI_to_anat). Note that in this step, the whole EPI time series was selected---is that really what you want? Normally we use 3dvolreg for across-EPI motion correction, and just select a single volume from the EPI time series to align to the anatomical. (It will take a much longer time to have the whole EPI aligned in the way currently coded here; in your case, it sounds like you should already have a processed/motion-corrected EPI time series, anyways?)

I can then run:
cat_matvec \
    -ONELINE \
    MNI_avg152T1_Alnd_Exp.A2E.1D \
    short_epi_al_mat.aff12.1D -I \
    > mat_MNI_to_EPI.aff12.1D
... with no error. (Note the use of ">" to redirect the output---that was missing from your command, above, and would create a "missing" file error, but it would be a different filename than what you had input.)

Note that I don't think I would use @SUMA_AlignToExperiment in this way, if I were wanting to bring a volumetric ROI dataset from one space to another. It should be OK, but I would probably use 3dAllineate if I only wanted affine, and (as noted above) a nonlinear program for closer alignment.

--pt
Subject Author Posted

3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 27, 2022 03:58PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

rick reynolds April 27, 2022 04:14PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley Attachments

philippn April 27, 2022 05:14PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

rick reynolds April 27, 2022 05:21PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 27, 2022 05:24PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 27, 2022 06:26PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 28, 2022 07:29AM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 28, 2022 11:35AM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 28, 2022 12:31PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 28, 2022 07:17PM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

ptaylor April 29, 2022 08:52AM

Re: 3dNwarpApply error: Warp dataset 'nwarp native_al_mat.aff12.1D' name is too much like a matrix text file moody smiley

philippn April 29, 2022 04:04PM



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