AFNI version info (afni -ver): 23.3.09
Hi SUMA users:
I’m having problems running: @SUMA_Make_Spec_FS -NIFTI -fspath /users/akannan/a1 -sid a1 and
I am running AFNI in a computing cluster environment where AFNI and freesurfer are installed.
When I run the above command, it creates SUMA folder and start adding files in the folder. But there are numerous warnings and the program does not seem to perform any function because the stats that are being computed are 0's and there are multiple "file not found" errors. I have attached some parts of the output of @SUMA_Make_Spec_FS here:
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writing to /users/akannan/ppa_data/a1/./SUMA/aparc+aseg.nii...
++ 3drefit: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file /users/akannan/ppa_data/a1/SUMA/aparc+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc+aseg.nii
+ setting labeltable
+ loading and re-writing dataset aparc+aseg.nii (/users/akannan/ppa_data/a1/SUMA/aparc+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
**lll: Subscript out of range.**
mri_convert -ot nii mri/aparc.a2009s+aseg.mgz /users/akannan/ppa_data/a1/./SUMA/aparc.a2009s+aseg.nii
reading from mri/aparc.a2009s+aseg.mgz...
TR=8.02, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 0)
j_ras = (7.45058e-09, 2.98023e-08, -1)
k_ras = (-3.72529e-09, 1, 0)
writing to /users/akannan/ppa_data/a1/./SUMA/aparc.a2009s+aseg.nii...
++ 3drefit: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file /users/akannan/ppa_data/a1/SUMA/aparc.a2009s+aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aparc.a2009s+aseg.nii
+ setting labeltable
+ loading and re-writing dataset aparc.a2009s+aseg.nii (/users/akannan/ppa_data/a1/SUMA/aparc.a2009s+aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
lll: Subscript out of range.
Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg.
mri_convert -ot nii mri/aseg.auto.mgz /users/akannan/ppa_data/a1/./SUMA/aseg.auto.nii
reading from mri/aseg.auto.mgz...
TR=8.02, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 0)
j_ras = (7.45058e-09, 2.98023e-08, -1)
k_ras = (-3.72529e-09, 1, 0)
writing to /users/akannan/ppa_data/a1/./SUMA/aseg.auto.nii...
mri_convert -ot nii mri/aseg.mgz /users/akannan/ppa_data/a1/./SUMA/aseg.nii
reading from mri/aseg.mgz...
TR=8.02, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -3.72529e-09, 0)
j_ras = (7.45058e-09, 2.98023e-08, -1)
k_ras = (-3.72529e-09, 1, 0)
writing to /users/akannan/ppa_data/a1/./SUMA/aseg.nii...
++ 3drefit: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=8 (INT32) in file /users/akannan/ppa_data/a1/SUMA/aseg.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Processing AFNI dataset aseg.nii
+ setting labeltable
+ loading and re-writing dataset aseg.nii (/users/akannan/ppa_data/a1/SUMA/aseg.nii in NIFTI storage)
++ 3drefit processed 1 datasets
lll: Subscript out of range.
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.
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++ Running checks now.
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_070.nii.gz
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_071.nii.gz
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__zarglefizz_072.nii.gz
++ Attaching labeltable to: aparc+aseg_REN_all.nii.gz
lll: Subscript out of range.
**-dset aparc+aseg_REN_all.nii.gz not found**
++ Attaching labeltable to: aparc+aseg_REN_gm.nii.gz
lll: Subscript out of range.
**-dset aparc+aseg_REN_gm.nii.gz not found**
++ Attaching labeltable to: aparc+aseg_REN_gmrois.nii.gz
lll: Subscript out of range.
**-dset aparc+aseg_REN_gmrois.nii.gz not found**
++ Attaching labeltable to: aparc+aseg_REN_wmat.nii.gz
lll: Subscript out of range.
**-dset aparc+aseg_REN_wmat.nii.gz not found**
++ Attaching labeltable to: aparc+aseg_REN_csf.nii.gz
lll: Subscript out of range.
-dset aparc+aseg_REN_csf.nii.gz not found
++ Attaching labeltable to: aparc+aseg_REN_vent.nii.gz
lll: Subscript out of range.
-dset aparc+aseg_REN_vent.nii.gz not found
++ Attaching labeltable to: aparc+aseg_REN_othr.nii.gz
lll: Subscript out of range.
-dset aparc+aseg_REN_othr.nii.gz not found
++ Attaching labeltable to: aparc+aseg_REN_unkn.nii.gz
lll: Subscript out of range.
-dset aparc+aseg_REN_unkn.nii.gz not found
[details="Summary"]
This text will be hidden
[/details]
.......
------------------- end of optionizing -------------------
-- trying to start Xvfb :27
[1] 1074636
_XSERVTransmkdir: ERROR: euid != 0,directory /tmp/.X11-unix will not be created.
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86AudioPreset
> Warning: Could not resolve keysym XF86Keyboard
> Warning: Could not resolve keysym XF86MonBrightnessCycle
> Warning: Could not resolve keysym XF86BrightnessAuto
> Warning: Could not resolve keysym XF86DisplayOff
> Warning: Could not resolve keysym XF86WWAN
> Warning: Could not resolve keysym XF86RFKill
> Warning: Could not resolve keysym XF86Info
....
Errors from xkbcomp are not fatal to the X server
+++ Command Echo:
afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=6x1:31:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=6x1:32:0:black crop=0:0,0:0 -com SET_PBAR_ALL +2 2=red 1=red .00066=none -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 89.000000 -com SET_FUNC_RANGE 3 -com SET_THRESHNEW 1.0001 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ 8.63221 6.50386 -17.01018 -com SAVE_PNG axialimage ./qc_00_fs_brainmask_abk_a1.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_00_fs_brainmask_abk_a1.sag blowup=2 -com SAVE_PNG coronalimage ./qc_00_fs_brainmask_abk_a1.cor blowup=2 -com QUITT ./__tmp_chauf_iiAyv3GVpCU
+/users/akannan/ppa_data/a1/SUMA/__workdir_fs_qc_lKRC2ORhd23/__tmp_chauf_iiAyv3GVpCU
AFNI QUITTs!
+* Removing temporary image directory './__tmp_chauf_iiAyv3GVpCU'.
[1] + Done Xvfb :27 -screen 0 1024x768x24
++ DONE (good exit)
see: ./qc_00_fs_brainmask_abk_a1*
.............
++ ------------- Process afni_fs_aparc+aseg_2000.txt ---------------
# Nvox FR_BR_MASK FR_PARC_MASK FR_ALL_ROI # SEG__TYPE FILE_NAME
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_all.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_7it4i-pzOeI9PZ6nBDJxFg argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
2984801 1.000000 2.534583 2.864410 # br_mask brainmask.nii
1177630 0.394542 1.000000 1.130131 # parc_mask fs_parc_wb_mask.nii.gz
1042030 0.349112 0.884853 1.000000 # all aparc+aseg_REN_all.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_gm.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_RDl-9_d4glqonviQoB63eg argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
505964 0.169513 0.429646 0.485556 # gm aparc+aseg_REN_gm.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_gmrois.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_xxOSYII9DLRBqU_OmOpqYg argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
505964 0.169513 0.429646 0.485556 # gmrois aparc+aseg_REN_gmrois.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_wmat.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_ZuL3tS0U-2QzLwxljqjQDg argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
485056 0.162509 0.411892 0.465491 # wmat aparc+aseg_REN_wmat.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_vent.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_fd_VazcWL8Ax51KXqdhsug argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
49271 0.016507 0.041839 0.047284 # vent aparc+aseg_REN_vent.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_csf.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_S5AHR5ljmoYtDQgAnJQTVg argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
1494 0.000501 0.001269 0.001434 # csf aparc+aseg_REN_csf.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_othr.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_MGrJGZdZtSAjK5giO-NTBA argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
245 0.000082 0.000208 0.000235 # othr aparc+aseg_REN_othr.nii.gz
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_unkn.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_qPlIWckVvU7F1nblqjXrxQ argv[9]=-verbose
++ 3dcalc: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Computing output statistics
0 0.000000 0.000000 0.000000 # unkn aparc+aseg_REN_unkn.nii.gz
++ Start counting the ROIs.
# Nvox FR_BR_MASK FR_PARC_MASK FR_ALL_ROI # VAL TISS__TYPE STRING_LABEL
0 0.000000 0.000000 0.000000 # 0 tiss__unkn Unknown
0 0.000000 0.000000 0.000000 # 1 tiss__wmat Left-Cerebral-White-Matter
0 0.000000 0.000000 0.000000 # 2 tiss__gm Left-Cerebral-Cortex
0 0.000000 0.000000 0.000000 # 3 tiss__vent Left-Lateral-Ventricle
0 0.000000 0.000000 0.000000 # 4 tiss__vent Left-Inf-Lat-Vent
0 0.000000 0.000000 0.000000 # 5 tiss__wmat Left-Cerebellum-White-Matter
0 0.000000 0.000000 0.000000 # 6 tiss__gm Left-Cerebellum-Cortex
0 0.000000 0.000000 0.000000 # 7 tiss__gm Left-Thalamus-Proper
0 0.000000 0.000000 0.000000 # 8 tiss__gm Left-Caudate
0 0.000000 0.000000 0.000000 # 9 tiss__gm Left-Putamen
0 0.000000 0.000000 0.000000 # 10 tiss__gm Left-Pallidum
23427 0.007849 0.019893 0.022482 # 11 tiss__vent 3rd-Ventricle
683 0.000229 0.000580 0.000655 # 12 tiss__vent 4th-Ventricle
0 0.000000 0.000000 0.000000 # 13 tiss__gm Brain-Stem
0 0.000000 0.000000 0.000000 # 14 tiss__gm Left-Hippocampus
0 0.000000 0.000000 0.000000 # 15 tiss__gm Left-Amygdala
0 0.000000 0.000000 0.000000 # 16 tiss__csf CSF
0 0.000000 0.000000 0.000000 # 17 tiss__gm Left-Accumbens-area
0 0.000000 0.000000 0.000000 # 18 tiss__gm Left-VentralDC
0 0.000000 0.000000 0.000000 # 19 tiss__othr Left-vessel
0 0.000000 0.000000 0.000000 # 20 tiss__vent Left-choroid-plexus
0 0.000000 0.000000 0.000000 # 21 tiss__wmat Right-Cerebral-White-Matter
0 0.000000 0.000000 0.000000 # 22 tiss__gm Right-Cerebral-Cortex
0 0.000000 0.000000 0.000000 # 23 tiss__vent Right-Lateral-Ventricle
0 0.000000 0.000000 0.000000 # 24 tiss__vent Right-Inf-Lat-Vent
0 0.000000 0.000000 0.000000 # 25 tiss__wmat Right-Cerebellum-White-Matter
0 0.000000 0.000000 0.000000 # 26 tiss__gm Right-Cerebellum-Cortex
0 0.000000 0.000000 0.000000 # 27 tiss__gm Right-Thalamus-Proper
0 0.000000 0.000000 0.000000 # 28 tiss__gm Right-Caudate
0 0.000000 0.000000 0.000000 # 29 tiss__gm Right-Putamen
0 0.000000 0.000000 0.000000 # 30 tiss__gm Right-Pallidum
0 0.000000 0.000000 0.000000 # 31 tiss__gm Right-Hippocampus
0 0.000000 0.000000 0.000000 # 32 tiss__gm Right-Amygdala
0 0.000000 0.000000 0.000000 # 33 tiss__gm Right-Accumbens-area
0 0.000000 0.000000 0.000000 # 34 tiss__gm Right-VentralDC
0 0.000000 0.000000 0.000000 # 35 tiss__othr Right-vessel
0 0.000000 0.000000 0.000000 # 36 tiss__vent Right-choroid-plexus
13200 0.004422 0.011209 0.012667 # 37 tiss__vent 5th-Ventricle
0 0.000000 0.000000 0.000000 # 38 tiss__wmat WM-hypointensities
0 0.000000 0.000000 0.000000 # 39 tiss__othr non-WM-hypointensities
0 0.000000 0.000000 0.000000 # 40 tiss__othr Optic-Chiasm
0 0.000000 0.000000 0.000000 # 41 tiss__wmat CC_Posterior
0 0.000000 0.000000 0.000000 # 42 tiss__wmat CC_Mid_Posterior
0 0.000000 0.000000 0.000000 # 43 tiss__wmat CC_Central
0 0.000000 0.000000 0.000000 # 44 tiss__wmat CC_Mid_Anterior
0 0.000000 0.000000 0.000000 # 45 tiss__wmat CC_Anterior
0 0.000000 0.000000 0.000000 # 46 tiss__unkn ctx-lh-unknown
0 0.000000 0.000000 0.000000 # 47 tiss__gm ctx-lh-bankssts
0 0.000000 0.000000 0.000000 # 48 tiss__gm ctx-lh-caudalanteriorcingulate
0 0.000000 0.000000 0.000000 # 49 tiss__gm ctx-lh-caudalmiddlefrontal
0 0.000000 0.000000 0.000000 # 50 tiss__gm ctx-lh-cuneus
0 0.000000 0.000000 0.000000 # 51 tiss__gm ctx-lh-entorhinal
0 0.000000 0.000000 0.000000 # 52 tiss__gm ctx-lh-fusiform
0 0.000000 0.000000 0.000000 # 53 tiss__gm ctx-lh-inferiorparietal
0 0.000000 0.000000 0.000000 # 54 tiss__gm ctx-lh-inferiortemporal
0 0.000000 0.000000 0.000000 # 55 tiss__gm ctx-lh-isthmuscingulate
0 0.000000 0.000000 0.000000 # 56 tiss__gm ctx-lh-lateraloccipital
0 0.000000 0.000000 0.000000 # 57 tiss__gm ctx-lh-lateralorbitofrontal
0 0.000000 0.000000 0.000000 # 58 tiss__gm ctx-lh-lingual
0 0.000000 0.000000 0.000000 # 59 tiss__gm ctx-lh-medialorbitofrontal
0 0.000000 0.000000 0.000000 # 60 tiss__gm ctx-lh-middletemporal
0 0.000000 0.000000 0.000000 # 61 tiss__gm ctx-lh-parahippocampal
0 0.000000 0.000000 0.000000 # 62 tiss__gm ctx-lh-paracentral
0 0.000000 0.000000 0.000000 # 63 tiss__gm ctx-lh-parsopercularis
0 0.000000 0.000000 0.000000 # 64 tiss__gm ctx-lh-parsorbitalis
0 0.000000 0.000000 0.000000 # 65 tiss__gm ctx-lh-parstriangularis
0 0.000000 0.000000 0.000000 # 66 tiss__gm ctx-lh-pericalcarine
0 0.000000 0.000000 0.000000 # 67 tiss__gm ctx-lh-postcentral
0 0.000000 0.000000 0.000000 # 68 tiss__gm ctx-lh-posteriorcingulate
0 0.000000 0.000000 0.000000 # 69 tiss__gm ctx-lh-precentral
0 0.000000 0.000000 0.000000 # 70 tiss__gm ctx-lh-precuneus
0 0.000000 0.000000 0.000000 # 71 tiss__gm ctx-lh-rostralanteriorcingulate
0 0.000000 0.000000 0.000000 # 72 tiss__gm ctx-lh-rostralmiddlefrontal
0 0.000000 0.000000 0.000000 # 73 tiss__gm ctx-lh-superiorfrontal
0 0.000000 0.000000 0.000000 # 74 tiss__gm ctx-lh-superiorparietal
0 0.000000 0.000000 0.000000 # 75 tiss__gm ctx-lh-superiortemporal
0 0.000000 0.000000 0.000000 # 76 tiss__gm ctx-lh-supramarginal
0 0.000000 0.000000 0.000000 # 77 tiss__gm ctx-lh-frontalpole
0 0.000000 0.000000 0.000000 # 78 tiss__gm ctx-lh-temporalpole
0 0.000000 0.000000 0.000000 # 79 tiss__gm ctx-lh-transversetemporal
0 0.000000 0.000000 0.000000 # 80 tiss__gm ctx-lh-insula
0 0.000000 0.000000 0.000000 # 81 tiss__unkn ctx-rh-unknown
0 0.000000 0.000000 0.000000 # 82 tiss__gm ctx-rh-bankssts
0 0.000000 0.000000 0.000000 # 83 tiss__gm ctx-rh-caudalanteriorcingulate
0 0.000000 0.000000 0.000000 # 84 tiss__gm ctx-rh-caudalmiddlefrontal
0 0.000000 0.000000 0.000000 # 85 tiss__gm ctx-rh-cuneus
0 0.000000 0.000000 0.000000 # 86 tiss__gm ctx-rh-entorhinal
0 0.000000 0.000000 0.000000 # 87 tiss__gm ctx-rh-fusiform
0 0.000000 0.000000 0.000000 # 88 tiss__gm ctx-rh-inferiorparietal
0 0.000000 0.000000 0.000000 # 89 tiss__gm ctx-rh-inferiortemporal
0 0.000000 0.000000 0.000000 # 90 tiss__gm ctx-rh-isthmuscingulate
0 0.000000 0.000000 0.000000 # 91 tiss__gm ctx-rh-lateraloccipital
0 0.000000 0.000000 0.000000 # 92 tiss__gm ctx-rh-lateralorbitofrontal
0 0.000000 0.000000 0.000000 # 93 tiss__gm ctx-rh-lingual
0 0.000000 0.000000 0.000000 # 94 tiss__gm ctx-rh-medialorbitofrontal
0 0.000000 0.000000 0.000000 # 95 tiss__gm ctx-rh-middletemporal
0 0.000000 0.000000 0.000000 # 96 tiss__gm ctx-rh-parahippocampal
0 0.000000 0.000000 0.000000 # 97 tiss__gm ctx-rh-paracentral
0 0.000000 0.000000 0.000000 # 98 tiss__gm ctx-rh-parsopercularis
0 0.000000 0.000000 0.000000 # 99 tiss__gm ctx-rh-parsorbitalis
0 0.000000 0.000000 0.000000 # 100 tiss__gm ctx-rh-parstriangularis
0 0.000000 0.000000 0.000000 # 101 tiss__gm ctx-rh-pericalcarine
0 0.000000 0.000000 0.000000 # 102 tiss__gm ctx-rh-postcentral
0 0.000000 0.000000 0.000000 # 103 tiss__gm ctx-rh-posteriorcingulate
0 0.000000 0.000000 0.000000 # 104 tiss__gm ctx-rh-precentral
0 0.000000 0.000000 0.000000 # 105 tiss__gm ctx-rh-precuneus
0 0.000000 0.000000 0.000000 # 106 tiss__gm ctx-rh-rostralanteriorcingulate
0 0.000000 0.000000 0.000000 # 107 tiss__gm ctx-rh-rostralmiddlefrontal
0 0.000000 0.000000 0.000000 # 108 tiss__gm ctx-rh-superiorfrontal
0 0.000000 0.000000 0.000000 # 109 tiss__gm ctx-rh-superiorparietal
0 0.000000 0.000000 0.000000 # 110 tiss__gm ctx-rh-superiortemporal
0 0.000000 0.000000 0.000000 # 111 tiss__gm ctx-rh-supramarginal
0 0.000000 0.000000 0.000000 # 112 tiss__gm ctx-rh-frontalpole
0 0.000000 0.000000 0.000000 # 113 tiss__gm ctx-rh-temporalpole
0 0.000000 0.000000 0.000000 # 114 tiss__gm ctx-rh-transversetemporal
0 0.000000 0.000000 0.000000 # 115 tiss__gm ctx-rh-insula
0 0.000000 0.000000 0.000000 # 220 tiss__unkn Left-undetermined
0 0.000000 0.000000 0.000000 # 221 tiss__unkn Right-undetermined
++ Done making: stats_fs_rois_2000_abk_a1.1D
...
++ Done making: stats_fs_rois_2009_abk_a1.1D
++ Compressing all remaining .nii files, except for SurfVol.
@SUMA_Make_Spec_FS ... finished
Also, I have attached the output of “afni_system_check.py -check_all” here:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 5.14.0-284.11.1.el9_2.x86_64
version: #1 SMP PREEMPT_DYNAMIC Tue May 9 17:09:15 UTC 2023
distribution: Rocky Linux 9.2 (Blue Onyx)
number of CPUs: 2
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /jhpce/shared/jhpce/core/afni/23.3.09/afni
afni version : Precompiled binary linux_rocky_8: Nov 22 2023
: AFNI_23.3.09 'Septimius Severus'
AFNI_version.txt : AFNI_23.3.09, linux_rocky_8, Nov 22 2023, official
which python : /jhpce/shared/community/core/conda_R/4.3/bin/python
python version : 3.11.4
which R : /jhpce/shared/community/core/conda_R/4.3/R/bin/R
R version : R version 4.3.1 Patched (x86_64-conda-linux-gnu)
instances of various programs found in PATH:
afni : 1 (/jhpce/shared/jhpce/core/afni/23.3.09/afni)
R : 1 (/jhpce/shared/community/core/conda_R/4.3/R/bin/R)
python : 3
/jhpce/shared/community/core/conda_R/4.3/bin/python3.11
/jhpce/shared/jhpce/core/conda/miniconda3-23.3.1/bin/python3.10
/usr/bin/python3.9
python2 : 0
python3 : 3
/jhpce/shared/community/core/conda_R/4.3/bin/python3.11
/jhpce/shared/jhpce/core/conda/miniconda3-23.3.1/bin/python3.10
/usr/bin/python3.9
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : success
R RHOME : /jhpce/shared/community/core/conda_R/4.3/R/lib64/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /users/akannan/.local/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.8.2
-------------------------------- env vars --------------------------------
PATH = /jhpce/shared/jhpce/core/freesurfer/7.4.1/fsfast/bin:/jhpce/shared/jhpce/core/freesurfer/7.4.1/tktools:/jhpce/shared/jhpce/core/freesurfer/7.4.1/mni/bin:/jhpce/shared/jhpce/core/freesurfer/7.4.1/bin:/jhpce/shared/community/core/conda_R/4.3/bin:/jhpce/shared/community/core/conda_R/4.3/texlive/bin/x86_64-linux:/jhpce/shared/community/core/conda_R/4.3/R/bin:/jhpce/shared/jhpce/core/conda/miniconda3-23.3.1/condabin:/jhpce/shared/jhpce/core/conda/miniconda3-23.3.1/bin:/jhpce/shared/jhpce/core/afni/23.3.09:/jhpce/shared/jhpce/core/JHPCE_tools/3.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/users/akannan/bin
PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /jhpce/shared/community/core/conda_R/4.3/lib:/jhpce/shared/jhpce/core/JHPCE_tools/3.0/lib:/jhpce/shared/community/core/conda_R/4.3/R/lib64/R/lib:/users/akannan/lib
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- no .tcshrc, will create one as a follower of .cshrc
-- considered operations: path, apsearch
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 4 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 1 0 1 0
.tcshrc 0 0 0 1
.bashrc 1 0 1 0
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /jhpce/shared/jhpce/core/afni/23.3.09
------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.14.0
which yum : /usr/bin/yum
yum version : 4.14.0
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* dot file test : want 4 modifications across 3 files:
* insufficient data for AFNI bootcamp
(see "Prepare for Bootcamp" on install pages)
I tried to look for the error in the AFNI support but couldn't find any answers to it. It would be great if anyone could provide insights on this issue. Thank you for your help!
Sincerely,
Arun