general-discussion > Errors trying to segment T1w images.
Apr 15, 2011  09:04 AM | U P
Errors trying to segment T1w images.


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

TitleAuthorDate
Errors trying to segment T1w images.
U P Apr 15, 2011
U P Apr 21, 2011
U P Apr 18, 2011
Pierre Bellec Apr 15, 2011