can't access intermediate files

[johnscot]

Hi,

Congratulations on your method and associated publications. I installed and tested msseg. I wish to assess wm lesions in brains. I wish to access the intermediate file. I adjusted the options.debug to 1, but no intermediate files were saved. I have included my working from matlab below. Can you advise as to why the intermediate files are not visible? After running the workflow below, I only have the output file: t1_msseg_seg.nii.gz.

Many Thanks John

/home/tempie/myo_dys

t1_path='/home/tempie/myo_dys/msseg/crf_dmn_004a_1_mr/t1'

t1_path =

/home/tempie/myo_dys/msseg/crf_dmn_004a_1_mr/t1

flair_path='/home/tempie/myo_dys/msseg/crf_dmn_004a_1_mr/flair_op'

flair_path =

/home/tempie/myo_dys/msseg/crf_dmn_004a_1_mr/flair_op

brainmask_path='/home/tempie/myo_dys/msseg/crf_dmn_004a_1_mr/fmask'

brainmask_path =

/home/tempie/myo_dys/msseg/crf_dmn_004a_1_mr/fmask

options.debug = 1;

[segmentation, seg_pve] = msseg(t1_path, brainmask_path, flair_path, options); MSSEG: Using FLAIR image to remove outliers [NiftyReg WARNING]: No filename extension provided - the Nifti library is used by default [NiftyReg WARNING]: No filename extension provided - the Nifti library is used by default [NiftyReg WARNING]: No filename extension provided - the Nifti library is used by default MSSEG: registering priors (360.3353 secs.) MSSEG: estimate tissue (821.1287 secs.) MSSEG: find lesion candidates (5.4802 secs.) MSSEG: Re-estimate tissue (521.6009 secs.)

[sergivalverde]

Hi @johnscot.

This was not specified in the README file. Intermediate files are conserved in the save image folder, inside the .run hidden folder.

Hope you can find it now.

[johnscot]

Dear Sergi,

I have found them now. Many thanks for the quick reply.

Best wishes John

On Mon, Dec 12, 2016 at 5:55 PM, Sergi Valverde notifications@github.com wrote:

Hi @johnscot https://github.com/johnscot.

This was not specified in the README file. Intermediate files are conserved in the save image folder, inside the .run hidden folder.

Hope you can find it now.

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