Thank you , both of these responses were helpful.

My jobs began
running properly once I changed the directories to bic directories, but
now many of my jobs have failed, and when I check the status using
qstat, I only see jobs waiting in an error state (eqw).  This began with
the failing of my "anat" analysis of subject 1.


In my
checks of the errors in the log file (below), I confirm that there is no
"emma" directory, however the surfstat toolbox is present (though I
receive a message saying that the new location is
"/export01/local/matlab7a/toolbox").  My raw files are in ".mnc.gz"
format, is there some other format they should be in?


Here is is the log from the anat analysis:


 
Warning: Name is nonexistent or not a directory: /usr/local/matlab7a/toolbox/emma.
> In path at 110
  In matlabrc at 279
Warning: Name is nonexistent or not a directory: /usr/local/matlab7a/toolbox/surfstat.
> In path at 110
  In matlabrc at 281
Warning: Name is nonexistent or not a directory: /usr/local/matlab7a/toolbox/surfstat.
> In path at 34

******************************
Log of the (matlab) job : anat_subject1
Started on 20-Nov-2013 11:09:55
User: ddawson
host : valhalla
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/kuwook/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_256933926_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_256933926_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_256933926_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!

************************************************
20-Nov-2013 11:18:57 : The job has FAILED
Total time used to process the job : 541.45 sec.
************************************************
'