BUG: Downstream FreeSurfer surface I/O broken

[larsoner]

A newline appears to have been removed from MRISwriteTriangularSurface at some point, and this breaks downstream readers when generating things with latest FreeSurfer.

For example, the output of this command:

$ mri_watershed -useSRAS -surf ./fsaverage \
    ~/applications/freesurfer-6/subjects/fsaverage/mri/T1.mgz ws.mgz

On Freesurfer 6 produces a file fsaverage_brain that starts with:

ÿÿþcreated by larsoner on Tue Aug 20 13:55:57 2019

^@^@(^B^@^@P^@À^K^[SÁ<89>8:Bªñ»A<98>ü<98>...

And on latest Freesurfer dev starts with:

ÿÿþcreated by larsoner on Tue Aug 20 13:59:19 2019
^@^@(^B^@^@P^@À^DìðÁ<8c>ËúB¨<93><A<9a>;˾¾^TB^ZÓnB<85>äÄÁ<9a>^VRB^X·WA<9c>...

There is a newline missing, which is problematic because downstream readers such as nibabel assume the procedure for reading should be the following:

1. Read magic
2. Read stamp
3. dump the next line
4. Read dimensionality
5. Read data

Because of the missing newline, on latest freesurfer the fobj.readline() dump-the-next-line step must be removed in order for the file to be read properly. This behavior should probably be reverted (?) so that downstream readers don't suffer from this problem.

I assume this change is buried somewhere in the history of MRISwriteTriangularSurface, but don't actually know:

https://github.com/freesurfer/freesurfer/blame/5e5b72f4871bfffe0246aed964a588b97ace65fc/utils/mrisurf_io.cpp#L5837-L5840

My best guess is that in the old code (about a year ago when it was in mrisurf.c?), the current_date_time() maybe had a newline on it?

  time_str = current_date_time();
  ...
  fwrite3(TRIANGLE_FILE_MAGIC_NUMBER, fp);
  fprintf(fp, "created by %s on %s\n", user, time_str);

This would have caused two newlines to be written before the data. But this is just speculation on my part!

[ahoopes]

You're right - the extra newline was accidentally removed as a result of the c++ refactor, and this change only got caught by external surface readers. The newline has been re-added as of 2aae19d, and any previously "broken" surface files can be correctly resaved with an updated mris_convert (or one from a previous stable release).