problems with @SUMA_Make_Spec_FS

AFNI Message Board
1

Hi,

I am having a problem with @SUMA_Make_Spec_FS that I hope you can help me with.

I have noticed that after running the command (from the base of the relevant FreeSurfer output directory):


@SUMA_Make_Spec_FS -sid p1032

that some of the files in the SUMA directory that is created (e.g., “T1.nii”) are out of alignment with the “p1032_SurfVol+orig” file in that directory (when viewed in AFNI).

There are some (non-fatal) errors that are logged during the execution of @SUMA_Make_Spec_FS that are likely to be related - for example:


mri_convert -ot nii mri/T1.mgz /sci/anat/db_ver1/p1032/./SUMA/T1.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mri/T1.mgz...
TR=2730.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -9.18154e-14, 0)
j_ras = (0, 0, -1)
k_ras = (-2.18714e-14, 1, 0)
writing to /sci/anat/db_ver1/p1032/./SUMA/T1.nii...
Error: base brick /p1032_SurfVol+orig not found.

It all works fine when using the “-NIFTI” flag to “@SUMA_Make_Spec_FS”.

This is with:


Precompiled binary linux_openmp_64: May 29 2021 (Version AFNI_21.1.09 'Domitian')

Thanks for any help!

2

Hi-

Yes, noted in the help file the “-NIFTI” option is “really useful”—and it should probably always be used:


@SUMA_Make_Spec_FS [options] -sid SUBJECT_ID

examples ('-NIFTI' is really useful-- see below!):

      @SUMA_Make_Spec_FS -help
      @SUMA_Make_Spec_FS -NIFTI -sid subject1
      @SUMA_Make_Spec_FS -NIFTI -fspath subject1/surface_stuff -sid subject1
      @SUMA_Make_Spec_FS -NIFTI -sid 3.14159265 -debug 1

It sounds like when using it, which should be done, there is no problem—is that correct?

–pt

3

Hi,

It sounds like when using it, which should be
done, there is no problem—is that correct?

Yes, that’s right - it works when using the “-NIFTI” option. I haven’t been using the “-NIFTI” option in the past (which used to work fine), so I have a set of participants with SUMA directories that don’t contain that form of output (and code that uses those files). But I can move those over if not using “-NIFTI” is no longer supported.

Thanks,

Damien.

4

Hi, Damien-

The “-NIFTI” is the way to go, yes.

We are considering making that functionality the default, in fact.

–pt