general-discussion > anat subject 1 failing
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Nov 29, 2013 04:11 PM | 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.
************************************************
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.
************************************************