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November 29, 2021 11:31AM
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
Subject Author Posted

3drefit -deoblique

Doughboys November 12, 2021 01:12PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 02:45PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 02:54PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 03:24PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 03:50PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 04:53PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 05:18PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 05:25PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 05:36PM

Re: 3drefit -deoblique

Doughboys November 22, 2021 04:09PM

Re: 3drefit -deoblique

Daniel Glen November 22, 2021 04:23PM

Re: 3drefit -deoblique

Doughboys November 24, 2021 01:27PM

Re: 3drefit -deoblique

ptaylor November 24, 2021 04:14PM

Re: 3drefit -deoblique

Doughboys November 24, 2021 04:35PM

Re: 3drefit -deoblique

ptaylor November 24, 2021 05:19PM

Re: 3drefit -deoblique

ptaylor November 24, 2021 09:22PM

Re: 3drefit -deoblique

Doughboys November 25, 2021 11:44AM

Re: 3drefit -deoblique

ptaylor November 26, 2021 09:42AM

Re: 3drefit -deoblique

Doughboys November 26, 2021 02:00PM

Re: 3drefit -deoblique

Doughboys November 29, 2021 11:31AM

Re: 3drefit -deoblique

Doughboys November 29, 2021 03:14PM

Re: 3drefit -deoblique

Doughboys November 29, 2021 04:11PM



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