resting state proc.py fatal error

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1

Dear AFNI experts,

I faced the below error message while running resting-state proc py (example 11).

*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 15.855433 degrees from plumb.
++ opened source dataset ‘vr_base_min_outlier+orig’
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./final_epi_vr_base_min_outlier+tlrc.BRIK
++ total CPU time = 27.1 sec Elapsed = 14.7
3dcopy 6002236_anat_ns+tlrc anat_final.6002236
++ WARNING: file /Users/lab/.afni.log is now 287270347 (287 million) bytes long!
++ 3dcopy: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.6002236+tlrc
tee out.allcostX.txt
++ WARNING: file /Users/lab/.afni.log is now 287270421 (287 million) bytes long!
++ 3dAllineate: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./anat_final.6002236+tlrc.HEAD
++ Base dataset: ./final_epi_vr_base_min_outlier+tlrc.HEAD
++ Loading datasets into memory
++ Local correlation: blok type = ‘TOHD(10.354)’
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be large
*+ WARNING: - at least one is more than 20% of search range

  •    -cmass x y z shifts =    4.298   -7.429  -17.998
  • shift search range is +/- = 78.966 90.522 73.188
  •                              5.4%     8.2%    24.6%

*+ WARNING: No output dataset will be calculated
++ OpenMP thread count = 12

  • initial Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
    ++ allcost output: init #0
    ls = 0.471159
    sp = 0.418892
    mi = 4.41839
    crM = 0.280962
    nmi = 0.929895
    je = 4.41839
    hel = -0.0625828
    crA = 0.531186
    crU = 0.496604
    lss = 0.528841
    lpc = 0.0154796
    lpa = 0.98452
    lpc+ = 0.332198
    lpa+ = 1.30124
    ++ 3dAllineate: total CPU time = 5.8 sec Elapsed = 11.0
    ++ ###########################################################

++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed :frowning:

  •       Please check your results - PLEASE PLEASE PLEASE

++ ***********************************************************
3dmask_tool -input copy_af_FSvent+orig -dilate_input -1 -prefix copy_af_FSvent_erode
++ WARNING: file /Users/lab/.afni.log is now 287270542 (287 million) bytes long!
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2…
++ padding all datasets by 0 (for dilations)
** FATAL ERROR: failed to open mask dataset ‘copy_af_FSvent+orig’
** Program compile date = Sep 1 2021

I checked the copy_af_FSvent+orig and it looked fine (please see attached) and only this subject’s data showed an error message. Could you please let me know what could be an issue here?

Best,
JW

FS_vent.png
FS_vent.png824×380 30.9 KB

2

Hi, Jim-

This is a tangential note—there are those messages about the long log file:


++ WARNING: file /Users/lab/.afni.log is now 287270347 (287 million) bytes long!

Well, it is unnecessary to use the log file—it gets giant over time, and in practice we never really refer to it. By default, now we turn the use of that off with an environment variable.

Unless you really want to keep it around, I would recommend deleting that log file and turning off the writing of it. To do those steps, you can run this to turn off its creation:


@AfniEnv -set AFNI_DONT_LOGFILE  YES

… and this to remove the one that is there:


\rm /Users/lab/.afni.log

To address your afni_proc.py (AP) error, could you please post your AP command?

–pt

3

What does “3dinfo -av_space” say about your original ventricle dataset? Is it +tlrc for some reason?

  • rick