Hi all,
We've run into an issue where lta_convert is failing if the filename line in a volume geometry is of a specific length. We've identified the source of the problem, and made a pull request on GitHub that at least partially fixes the issue (https://github.com/freesurfer/freesurfer/pull/180). Doug's requested that all bugs be posted to the mailing list, so I excerpt the pull request below.
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It is currently possible to create a valid VolGeom string that will break readVolGeom, by setting the length of the line beginning "filename = " to be 255 characters (+ `'\n'`).
The filename is defined to be a 1024 byte string, and so up to 1023 characters:
https://github.com/freesurfer/freesurfer/blob/9b79bf0eef76710a70a5b73142a8f6...
So, in writeVolGeom, a line may be written that is up to 1035 characters long (`"filename = "` + 1023 + `'\n'`):
https://github.com/freesurfer/freesurfer/blob/9b79bf0eef76710a70a5b73142a8f6...
If the line is exactly 255 characters long (excluding newline), then the `fgets` call will retrieve the entire contents of the line (256 characters - terminating `'\NUL'`) without retrieving a newline. The next call to `fgets` will then get a line of length 0, resulting in a premature termination of the loop.
To observe an effect of this issue, consider the following LTA file:
type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 1.0000 1 4 4 2.327464342117310e+00 4.245608299970627e-02 3.455499932169914e-02 -1.319661331176758e+01 -7.824462652206421e-02 3.904805898666382e+00 2.233271896839142e-01 -5.291442871093750e-01 -4.939173907041550e-02 -1.728723645210266e-01 4.818737983703613e+00 7.657078552246094e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = /scratch/03763/oesteban/fmriprep-phase1/work/ds000110/fmriprep_wf/single_subject_07_wf/func_preproc_task_IncidentalencodingtaskusingPosnercueingparadigmwithobjectvgreeblejudgment_run_05_wf/bold_reg_wf/bbreg_wf/bbregister/ants_susceptibility_War volume = 64 64 30 voxelsize = 3.437500000000000e+00 3.437500000000000e+00 4.000000000000000e+00 xras = 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 yras = 0.000000000000000e+00 9.979115724563599e-01 -6.459446996450424e-02 zras = 0.000000000000000e+00 6.459447741508484e-02 9.979115724563599e-01 cras = 3.437500000000000e+00 8.357086181640625e-01 4.582891845703125e+01 dst volume info valid = 1 # volume info valid filename = /scratch/03763/oesteban/fmriprep-phase1/work/ds000110/fmriprep_wf/single_subject_07_wf/anat_preproc_wf/t1_merge/sub-07_T1w_ras_template.nii.gz volume = 124 256 256 voxelsize = 1.500000000000000e+00 8.593999743461609e-01 8.593999743461609e-01 xras = 9.998608827590942e-01 1.065783575177193e-02 -1.283265277743340e-02 yras = -9.511843323707581e-03 9.962262511253357e-01 8.627174794673920e-02 zras = 1.370369549840689e-02 -8.613768219947815e-02 9.961889982223511e-01 cras = -3.533935546875000e-01 5.862289428710938e+00 -1.128549194335938e+01 subject sub-07 fscale 0.100000
If you save this as `test.lta`, the following command fails in an unexpected way:
$ lta_convert --inlta truncated.lta --outlta out.lta $Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $
--inlta: truncated.lta input LTA transform. --outlta: out.lta output LTA. LTAchangeType: dst geometry must be valid
The offending line is:
filename = /scratch/03763/oesteban/fmriprep-phase1/work/ds000110/fmriprep_wf/single_subject_07_wf/func_preproc_task_IncidentalencodingtaskusingPosnercueingparadigmwithobjectvgreeblejudgment_run_05_wf/bold_reg_wf/bbreg_wf/bbregister/ants_susceptibility_War
Add or remove a character and the command proceeds without error. However, supposing you add a character (and, critically, convert between `RAS_TO_RAS` and `VOX_TO_VOX`):
$ lta_convert --inlta extended.lta --outlta out1.lta $Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $
--inlta: extended.lta input LTA transform. --outlta: out1.lta output LTA. LTA read, type : 1 1.01550 0.01035 0.02607 -3.12509; -0.00760 0.97176 -0.10423 6.51772; -0.02702 0.10772 1.03053 -46.97261; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file out1.lta... lta_convert successful. $ lta_convert --inlta out1.lta --outlta out2.lta --ltavox2vox $Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $
--inlta: out1.lta input LTA transform. --outlta: out2.lta output LTA. --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.01550 0.01035 0.02607 -3.12509; -0.00760 0.97176 -0.10423 6.51772; -0.02702 0.10772 1.03053 -46.97261; 0.00000 0.00000 0.00000 1.00000; LTAchangeType: dst geometry must be valid
This is a result of the truncation that occurs during the read.
Thanks for your time, -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University