hello pt
I pushed a little bit my analysis
1. I confirm that the remaining differences of brain orientations using 3dCM (between anat and bold) create misalignment when using afni_proc.py in a second time.
2. I tried to not deboblique the anat and to just use 3dCM prior to @animal_warper. This was a huge fail since I realize that 3dCM and @Align_Centers are actually doing deboblique by default...
3. I am still currently trying to align the bold_deob and anat_deob but without success
I am still confused about how the information of deoblique angle (or/and center?) is lost in the process.
Any other thoughts on what is my best option for this analysis?
trying align_epi_anat.py? but it is already by default in afni_proc.py...
Is there absolutely no way to have to anat_deob match bold_deob other than aligning masks?
A way to calculate the differences/error of oblique/center between anat_deob and bold_deob?
for info: the command afni_proc.py that I am trying to run
afni_proc.py -subj_id Unity2021_03_18 -script \
Unity2021_03_18/proc.Unity2021_03_18 \
-scr_overwrite -out_dir \
Unity2021_03_18/Unity2021_03_18.results \
-blocks tshift align tlrc volreg blur mask regress -dsets \
Unity2021_03_18/BOLD_restingstate_deob.nii.gz \
-copy_anat \
Unity2021_03_18/anatT1_deob.nii.gz \
-anat_has_skull no -align_opts_aea -cost lpc+zz -check_flip -giant_move \
-epi_strip 3dAutomask -align_epi_strip_method 3dAutomask -mask_dilate 1 \
-volreg_align_to MIN_OUTLIER -volreg_tlrc_warp -mask_epi_anat yes \
-tlrc_base \
Unity2021_03_18/anatT1_deob_in_stdy_template.nii.gz \
-tlrc_NL_warp -tlrc_NL_warped_dsets \
Unity2021_03_18/anatT1_deob_in_stdy_template.nii.gz \
Unity2021_03_18/1Dconcat.1D \
Unity2021_03_18/concate_WARP.nii.gz \
-regress_motion_per_run -regress_apply_mot_types demean deriv \
-blur_size 3 -mask_import WMa \
atlas_to_study_template/WM2mm.nii.gz \
-regress_make_corr_vols WMa -regress_anaticor_fast \
-regress_run_clustsim yes -regress_est_blur_errts -html_review_style \
pythonic -execute -tcat_remove_first_trs 5
Sorry about that,
Clem
PS:
My apologize to Daniel, the command is working fine
3drefit -atrcopy IJK_TO_DICOM_REAL original_dset modified_dset
except that it seems that atrcopy is requiring something like that
3drefit -atrcopy original_dset IJK_TO_DICOM_REAL original_dset modified_dset
my viewer (ITKsnape) was doing some crap in addition to that... that is why I was thinking that it was not working
