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Nov 29, 2013  08:11 AM | Debra Dawson
anat subject 1 failing
Hello, 

I am running the fmri_preprocessing pipeline on a bic terminal, and all of my attempts fail at the anatomy stage.  I am using the following niak installation : /data/aces/aces1/pbellec/public/niak-0.6.3; and the following matlab installation:  /usr/local/matlab7a  (which does not have the emma toolbox installed, but I have no permission to install it).  Any help with this would be much appreciated, I have been stuck for a week with no progress!  (username ddawson)

Below is the error log:



Warning: Unable to open display , MATLAB is starting without a display.
  You will not be able to display graphics on the screen.

                              < M A T L A B >
                  Copyright 1984-2007 The MathWorks, Inc.
                         Version 7.4.0.287 (R2007a)
                              January 29, 2007

 
  To get started, type one of these: helpwin, helpdesk, or demo.
  For product information, visit http://www.mathworks.com.
 
Warning: Name is nonexistent or not a directory: /usr/local/matlab7a/toolbox/emma.
> In path at 110
  In matlabrc at 279

******************************
Log of the (matlab) job : anat_subject1
Started on 29-Nov-2013 10:43:25
User: ddawson
host : node20
system : unix
******************************

command =

niak_brick_civet(files_in,files_out,opt)


files_in =

     anat: [1x128 char]
    civet: 'gb_niak_omitted'


files_out =

        transformation_lin: [1x124 char]
         transformation_nl: [1x124 char]
    transformation_nl_grid: [1x129 char]
                  anat_nuc: [1x109 char]
       anat_nuc_stereo_lin: [1x110 char]
        anat_nuc_stereo_nl: [1x109 char]
                      mask: [1x114 char]
               mask_stereo: [1x115 char]
                  classify: [1x119 char]
                    pve_wm: [1x117 char]
                    pve_gm: [1x117 char]
                   pve_csf: [1x118 char]
                    verify: [1x107 char]


opt =

      n3_distance: 25
       folder_out: [1x82 char]
        flag_test: 0
    civet_command: ''
     flag_verbose: 1
            civet: 'gb_niak_omitted'


********************
The job starts now !
********************
Running CIVET on volume /data/shmuel/shmuel1/debbie/HumanRest_2/raw//beaulne_anne_marie_20100719_093834//beaulne_anne_marie_20100719_093834_2_mri.mnc.gz. This is going to take a while ! (roughly one hour)

succ =

     0


msg =




Copying /tmp/niak_tmp_anat_subject1_751251883_civet/coco/transforms/linear/anat_coco_t1_tal.xfm to /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013//subject1//anat/subject1//transf_subject1_nativet1_to_stereolin.xfm
Warning:
cp: cannot stat `/tmp/niak_tmp_anat_subject1_751251883_civet/coco/transforms/linear/anat_coco_t1_tal.xfm': No such file or directory

> In niak_brick_civet at 429
  In psom_run_job at 118
Copying /tmp/niak_tmp_anat_subject1_751251883_civet/coco/transforms/nonlinear/anat_coco_nlfit_It.xfm to /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013//subject1//anat/subject1//transf_subject1_stereolin_to_stereonl.xfm


********************
Something went bad ... the job has FAILED !
The last error message occured was :
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
File /data/aces/aces1/pbellec/public/niak-0.6.3/bricks/fmri_preprocess/niak_brick_civet.m at line 437
File /data/aces/aces1/pbellec/public/niak-0.6.3/extensions/psom/psom_run_job.m at line 118

****************
Checking outputs
****************
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/transf_subject1_nativet1_to_stereolin.xfm has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/transf_subject1_stereolin_to_stereonl.xfm was successfully generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/transf_subject1_stereolin_to_stereonl_grid.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_nativet1.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_stereolin.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_stereonl.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_mask_nativet1.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_mask_stereolin.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_classify_stereolin.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_pve_wm_stereolin.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_pve_gm_stereolin.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_pve_csf_stereolin.mnc has not been generated!
The output file or directory /data/shmuel/shmuel1/debbie/HumanRest_2/niak_out_Nov2013/subject1/anat/subject1/anat_subject1_verify.png has not been generated!

************************************************
29-Nov-2013 10:52:41 : The job has FAILED
Total time used to process the job : 555.65 sec.
************************************************