Demo does not support this data type (solution: use niimath)

[Thinking-leaf]

Hello, I met a problem when using nii2mesh.
./nii2mesh $SUBJECTS_DIR/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz -p 1 -l 0 -s 100 $SUBJECTS_DIR/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala.p1l0s100.stl
Demo does not support this data type (solution: use niimath)

I don't know why this error rises even when the input format is NIFTI. And after this, I tried to solve this by installing niimath but nothing changed.
So what's wrong?

[neurolabusc]

What datatype is your image? You use niimath to detect the data type:

$ niimath $SUBJECTS_DIR/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz
<nifti_image
  nifti_type = 'NIFTI-1+'
  header_filename = 'sag_int_36sl_21.nii'
  image_filename = 'sag_int_36sl_21.nii'
  image_offset = '352'
  ndim = '4'
  nx = '64'
  ny = '64'
  nz = '36'
  nt = '2'
  dx = '3.25'
  dy = '3.25'
  dz = '3.6'
  dt = '3'
  datatype = '4'
  datatype_name = 'INT16'

nii2mesh only supports the most popular data types (DT_UINT8 DT_UINT16 DT_INT16 DT_FLOAT32). Since niimath exports to float32 by default, you could try:

niimath $SUBJECTS_DIR/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz -add 0 flt32

[Thinking-leaf]

Thanks for your comment. As you can see below, the datatype of this nifti file is 'INT32'
$ niimath $SUBJECTS_DIR/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz
<nifti_image
nifti_type = 'NIFTI-1+'
header_filename = '/Applications/freesurfer/7.2.0/trial2/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz'
image_filename = '/Applications/freesurfer/7.2.0/trial2/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz'
image_offset = '352'
ndim = '3'
nx = '176'
ny = '256'
nz = '256'
dx = '0.999998'
dy = '1'
dz = '1'
datatype = '8'
datatype_name = 'INT32'
nvox = '11534336'
nbyper = '4'
byteorder = 'LSB_FIRST'
xyz_units = '2'
xyz_units_name = 'mm'
time_units = '8'
time_units_name = 's'
descrip = 'FreeSurfer Jul 13 2021'
qform_code = '1'
qform_code_name = 'Scanner Anat'
qto_xyz_matrix = '0.996803 -0.013412 0.0787298 -89.019 0.00732101 0.996993 0.0771508 -108.054 -0.0795276 -0.076328 0.993906 -146.884 0 0 0 1'
qto_ijk_matrix = '0.996808 0.00732104 -0.0795279 77.8446 -0.013412 0.996993 -0.076328 95.3233 0.0787298 0.0771508 0.993906 161.334 0 0 0 1'
quatern_b = '-0.0384288'
quatern_c = '0.0396253'
quatern_d = '0.00519125'
qoffset_x = '-89.019'
qoffset_y = '-108.054'
qoffset_z = '-146.884'
qfac = '1'
qform_i_orientation = 'Left-to-Right'
qform_j_orientation = 'Posterior-to-Anterior'
qform_k_orientation = 'Inferior-to-Superior'
sform_code = '1'
sform_code_name = 'Scanner Anat'
sto_xyz_matrix = '0.996803 -0.013412 0.0787298 -89.019 0.00732101 0.996993 0.0771508 -108.054 -0.0795276 -0.076328 0.993906 -146.884 0 0 0 1'
sto_ijk matrix = '0.996808 0.00732104 -0.0795279 77.8446 -0.013412 0.996993 -0.076328 95.3233 0.0787298 0.0771508 0.993906 161.334 0 0 0 1'
sform_i_orientation = 'Left-to-Right'
sform_j_orientation = 'Posterior-to-Anterior'
sform_k_orientation = 'Inferior-to-Superior'
num_ext = '0'
/>
However, after running the code
niimath $SUBJECTS_DIR/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz -add 0 flt32
I recheck its datatype, nothing changed.
<nifti_image
nifti_type = 'NIFTI-1+'
header_filename = '/Applications/freesurfer/7.2.0/trial2/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz'
image_filename = '/Applications/freesurfer/7.2.0/trial2/sub-OAS30001_ses-d0129_T1w/mri/lh.amygdala_mask-in-rawavg.nii.gz'
image_offset = '352'
ndim = '3'
nx = '176'
ny = '256'
nz = '256'
dx = '0.999998'
dy = '1'
dz = '1'
datatype = '8'
datatype_name = 'INT32'
nvox = '11534336'
nbyper = '4'
byteorder = 'LSB_FIRST'
xyz_units = '2'
xyz_units_name = 'mm'
time_units = '8'
time_units_name = 's'
descrip = 'FreeSurfer Jul 13 2021'
qform_code = '1'
qform_code_name = 'Scanner Anat'
qto_xyz_matrix = '0.996803 -0.013412 0.0787298 -89.019 0.00732101 0.996993 0.0771508 -108.054 -0.0795276 -0.076328 0.993906 -146.884 0 0 0 1'
qto_ijk_matrix = '0.996808 0.00732104 -0.0795279 77.8446 -0.013412 0.996993 -0.076328 95.3233 0.0787298 0.0771508 0.993906 161.334 0 0 0 1'
quatern_b = '-0.0384288'
quatern_c = '0.0396253'
quatern_d = '0.00519125'
qoffset_x = '-89.019'
qoffset_y = '-108.054'
qoffset_z = '-146.884'
qfac = '1'
qform_i_orientation = 'Left-to-Right'
qform_j_orientation = 'Posterior-to-Anterior'
qform_k_orientation = 'Inferior-to-Superior'
sform_code = '1'
sform_code_name = 'Scanner Anat'
sto_xyz_matrix = '0.996803 -0.013412 0.0787298 -89.019 0.00732101 0.996993 0.0771508 -108.054 -0.0795276 -0.076328 0.993906 -146.884 0 0 0 1'
sto_ijk matrix = '0.996808 0.00732104 -0.0795279 77.8446 -0.013412 0.996993 -0.076328 95.3233 0.0787298 0.0771508 0.993906 161.334 0 0 0 1'
sform_i_orientation = 'Left-to-Right'
sform_j_orientation = 'Posterior-to-Anterior'
sform_k_orientation = 'Inferior-to-Superior'
num_ext = '0'
/>
lh.amygdala_mask-in-rawavg.nii.gz

So demo still doesn't support the data type (solution:use niimath)
how to use niimath to solve this problem? I attached the sample nifti file here so that you can have a try on it. Thanks for your help!

[neurolabusc]

Your call to niimath created a new image named flt32.nii.gz that will be in float 32 format. The idea was to create a copy of your input image.

[Thinking-leaf]

Oh, sorry for my being unfamiliar with this toolbox. Brilliant idea! It saves my work!
But I have multiple works and how can I define the name and path of the output images?

[neurolabusc]

You can use Python, Matlab or bash scripts to automate this. FSL has a lot of helper bash functions to automate tasks. The inner loopo of your bash script would look like:

niimath ${inname} -dehaze 5 temp
nii2mesh temp -dehaze 5 ${inname}

[Thinking-leaf]

Thanks again! Here is my final code
#!/bin/tcsh
foreach subject (sub*)
niimath $SUBJECTS_DIR/{$subject}/mri/rh.amygdala_mask-in-rawavg.nii.gz -add 0 $SUBJECTS_DIR/{$subject}/mri/rh.amygdala_mask-in-rawavg.(flt32).nii.gz
./nii2mesh $SUBJECTS_DIR/{$subject}/mri/rh.amygdala_mask-in-rawavg.(flt32).nii.gz -q 2 -p 1 -l 0 $SUBJECTS_DIR/{$subject}/mri/lh.amygdala_q2p1l0.gz
end