Hi , congratulations on this work and thanks
for sharing it.
I want to segment T1w MR axial images using NIAK. I only write my
input file
and I let the default options for the name of the output and the
structure opt.
The directory I use for the images is bricks/t1_ processing.
I have been trying but I have errors.
Please,
could you help me to solve them?
When I use an example image yours,
[files_in,files_out,opt]
=
niak_brick_mask_brain_t1('func_motor_subject1_a_mc_f_p_res_s.nii')
I have the following
errors:
Deriving a
segmentation of the T1 image using Otsu intensity threshold
... 0.754 sec.
Competitive region
growing starting from dense white matter regions ...
Building a spatial
density
map ... 28.03 secs.
Extracting connected
clusters in dense voxels ... 35.20 secs. 3322 dense core clusters
were found.
Propagation of cluster
labels, number of iterations :
??? Error using
==> or
Inputs must have
the same size.
Error in ==>
niak_clustering_space_density at 184
mask_todo =
mask_todo|mask_extra;
Error in ==>
niak_mask_brain_t1 at 206
mask_brain =
niak_clustering_space_density(mask_conf,mask_head,opt.region_growing);
Error in ==>
niak_brick_mask_brain_t1 at 239
mask =
niak_mask_brain_t1(anat,opt_mask)
And then with my
image .img:
Deriving a
segmentation of the T1 image using Otsu intensity threshold
... 3.839 sec.
Competitive region
growing starting from dense white matter regions ...
Building a spatial
density
map ... 32.65 secs.
Extracting connected
clusters in dense voxels ... 26.33 secs. 30 dense core clusters
were found.
Propagation of cluster
labels, number of iterations :
??? Error using
==> save
Unable to write
file \tmp\niak_tmp_814723686_vol.mnc: No such file or
directory.
(But I have created
a folder called tmp)
Error in ==>
niak_file_tmp at 63
save(file_name,'flag_tmp')
Error in ==>
niak_morph at 88
file_tmp =
niak_file_tmp('_vol.mnc');
Error in ==>
niak_clustering_space_density at 192
mask_border_new =
niak_morph(mask_border,['-successive D' arg_m]); % dilate the
border
Error in ==>
niak_mask_brain_t1 at 206
mask_brain =
niak_clustering_space_density(mask_conf,mask_head,opt.region_growing);
Error in ==>
niak_brick_mask_brain_t1 at 239
mask =
niak_mask_brain_t1(anat,opt_mask)
Thanks very
much,
Regards
Threaded View
Title | Author | Date |
---|---|---|
U P | Apr 15, 2011 | |
U P | Apr 21, 2011 | |
U P | Apr 18, 2011 | |
Pierre Bellec | Apr 15, 2011 | |