Dear all,
I am trying to run @afni_refacer_run and running into some issues. It gives me three warnings, starting with "No output dataset will be calculated". I think the other two are cause by the first one. There are also errors about "Xvfb -- not found in path", but as I understand this is to show some QA images, hence not relevant to processing?
The full output is below:
$ @afni_refacer_run -input dzne_MPRAGE_1iso_PAT2_s03.nii.gz -mode_reface -prefix reface.dzne.de
++ Found input file: dzne_MPRAGE_1iso_PAT2_s03.nii.gz
++ AFNI refacer, version = 2.31
++ AFNI MNI template dataset = /share/apps/abin/MNI152_2009_template_SSW.nii.gz
++ AFNI refacer shell dataset = /share/apps/abin/afni_refacer_shell_sym_1.0.nii.gz
++ Mode for running = reface
++ 3dcopy: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ 3dUnifize: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
+ Pre-processing: ADV...........UW[s138538]Gm
++ Output dataset ./tmp.01.uni.nii
++ ===== Elapsed = 24.7 sec
++ 3dAllineate: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: Zhark the Registrator
++ Option '-cmass' enables center-of-mass code = 7 = +xyz
++ Source dataset: /storage/users/username/peoples/silke/ISME/deface_test/niiMPRAGE/7197dd9cd-17_05_01/scans/__work_refacer.reface.dzne.de.Nag2GmbG7cc/tmp.01.uni.nii
++ Base dataset: /share/apps/abin/MNI152_2009_template_SSW.nii.gz
++ Loading datasets into memory
++ Local correlation: blok type = 'TOHD(5.17699)'
*+ WARNING: No output dataset will be calculated
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Abs =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= -4.2532 y-shift= 4.3677 z-shift=-19.4002 ... enorm= 20.3355 mm
z-angle= 2.6489 x-angle= 17.5828 y-angle= 1.7674 ... total= 17.9067 deg
x-scale= 0.9060 y-scale= 0.9566 z-scale= 0.8948 ... vol3D= 0.7755=(0.9188)^3 [base bigger than source]
++ Wrote -1Dmatrix_save tmp.02.mat_a2t.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 247.8
++ ###########################################################
++ 3dAllineate: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /share/apps/abin/afni_refacer_shell_sym_1.0.nii.gz
++ Base dataset: (not given)
++ Loading datasets into memory
*+ WARNING: -1D*_apply 'tmp.03.mat_t2a.1D': 1 isn't enough rows for source dataset -- last row will repeat
+ -cmass x y z shifts = 0.042 -4.482 -8.437
+ shift search range is +/- = 61.632 121.338 116.202
++ OpenMP thread count = 15
++ ========== Applying transformation to 2 sub-bricks ==========
volume 0..1
*+ WARNING: Re-using final row of -1D*_apply 'tmp.03.mat_t2a.1D' for sub-brick #1
++ Output dataset ./tmp.04.sh_t2a.nii
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 5.1
++ ###########################################################
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
+ removed 41 isolas from volume 0
+ removed 12 isolas from volume 1
++ Output dataset ./tmp.05.sh_t2a_thr.nii
++ 3drefit: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset tmp.05.sh_t2a_thr.nii
+ loading and re-writing dataset tmp.05.sh_t2a_thr.nii (/storage/users/username/peoples/silke/ISME/deface_test/niiMPRAGE/7197dd9cd-17_05_01/scans/__work_refacer.reface.dzne.de.Nag2GmbG7cc/tmp.05.sh_t2a_thr.nii in NIFTI storage)
++ 3drefit processed 1 datasets
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=tmp.05.sh_t2a_thr.nii argv[3]=-b argv[4]=tmp.00.INPUT.nii argv[5]=-expr argv[6]=step(a-99)*b argv[7]=-session argv[8]=/tmp argv[9]=-prefix argv[10]=3dcalc_AFN_YOOiryrFHXSquoJOfMnDNQ argv[11]=-verbose
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing sub-brick 1
++ Computing output statistics
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=tmp.05.sh_t2a_thr.nii argv[3]=-expr argv[4]=step(a-99)*a argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_PIz9OIajxhXoXn5C6O5mpQ argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing sub-brick 1
++ Computing output statistics
+++ Proc for reface
with subbrick 1 and list index 2
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
+ removed 76995 isolas from volume 0
++ Output dataset ./tmp.06.reface.orig_mskd.nii
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./tmp.07.reface.sh_t2a_thr_mskd.nii
++ 3dBlurInMask: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: RW Cox
++ Removed 3 isolas from mask dataset
++ Number of voxels in mask = 846823
++ forcing output to be stored in float format
++ mri_blur3D: #iter=9 fx=0.03560 fy=0.03560 fz=0.03560
++ Output dataset ./tmp.99.result.reface.nii
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./tmp.99.result.reface.nii
++ Output final dsets
+++ Command Echo:
3dcopy tmp.99.result.reface.nii ../reface.dzne.de
++ 3dcopy: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ My command:
@chauffeur_afni -ulay tmp.00.INPUT.nii -ulay_range 2% 98% -olay tmp.99.result.reface.nii -func_range_perc_nz 95 -cbar Plasma -pbar_posonly -opacity 9 -prefix ../reface.dzne.de_QC/reface.dzne.de -montx 5 -monty 3 -montgap 3 -set_xhairs OFF -label_mode 1 -label_size 4
++ Using AFNI ver : AFNI_22.1.02
++ chauffeur ver : 6.31
** ERROR: Xvfb -- not found in path -- program fails
++ DONE (bad exit): check for errors
++ 3dcalc: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../reface.dzne.de.face.nii.gz
++ My command:
@chauffeur_afni -ulay tmp.00.INPUT.nii -ulay_range 2% 98% -olay ../reface.dzne.de.face.nii.gz -func_range_perc_nz 95 -cbar Reds_and_Blues_Inv -opacity 5 -prefix ../reface.dzne.de_QC/reface.dzne.de.face -montx 5 -monty 3 -montgap 3 -set_xhairs OFF -label_mode 1 -label_size 4
++ Using AFNI ver : AFNI_22.1.02
++ chauffeur ver : 6.31
** ERROR: Xvfb -- not found in path -- program fails
++ DONE (bad exit): check for errors
++ Done.
After that, there are three files generated - reface.dzne.de.face.nii.gz, reface.dzne.de+orig.BRIK and reface.dzne.de+orig.HEAD.
Any suggestion what is going on? If it is indeed cause by no Xvfb, then is it possible to circumvent that? We dont want to mess with it, since apparently it can cause conflicts with xrdp.
Thank you!
Best wishes,
Renat.
