general-discussion
general-discussion > RE: Sica stage failing in twins
Aug 28, 2012 03:08 AM | Pierre Bellec
RE: Sica stage failing in twins
Hi Kevin,
First of all, sorry for the late answer.
I'm running into an error in the NIAK pipeline which is quite possibly due to me trying to use it incorrectly. The design of my fMRI protocol is to test monozygotic twins on a task. I've previously run the pipeline without issue on the twins considering each as their own subject with their own anatomical scan. However, as the twins really are very similar, I'm trying to preprocess their data as run1 and run2 of one "subject" (actually a twin pair). My hope is that considering them as runs within a subject will minimize the inter-twin error, which is more important than the between twin error to our analysis.
That's an interesting idea. I am not sure this is going to work
optimally though. You'll only run a rigid-body coregistration
between the twins. Even though they have similar brains, this may
not be enough to cover up the differences. Also that means that you
will use only one of the T1 scan to run the coregistration in
stereotaxic space. A better solution would be to have a
hierarchical scheme, where twins T1 scans are first (non-linearly)
coregistered on each other, before a single transformation to
stereotaxic space is estimated. This will however highly bias the
data of twin pairs, which will be way better coregistered than
between-twins data. This may or may not be a problem (it will be if
you are testing some kind of heritability). This may not be easy to
work around in any case because the twins's brains are more similar
than unrelated brains in the first place. Tough one. Needless to
say, no twins coregistration strategy was implemented in NIAK.
Could be a neat idea for a summer student though.
I don't relly get where that error could come from. It says it doesn't find the randperm function which doesn't make sense (that's a standard command). There must be something going on with the configuration of the machine that's running the job. I'd try to restart the pipeline a couple of times before giving up and looking for a bug. Let me know if that error is reproducible.
I hope this helps. Best,
Pierre
Thanks!
Kevin
>> logs.sica_subject10_run2
ans =
******************************
Log of the (matlab) job : sica_subject10_run2
Started on 01-Aug-2012 18:39:03
User: kevin
host : dumain
system : unix
******************************
command =
niak_brick_sica(files_in,files_out,opt);
files_in =
fmri: [1x116 char]
mask: [1x91 char]
files_out =
space: [1x127 char]
time: [1x126 char]
files_clean =
{}
opt =
nb_comp: 50
folder_out: [1x76 char]
flag_test: 0
norm: 'mean'
algo: 'Infomax'
flag_verbose: 1
********************
The job starts now !
********************
**************************************
Spatial independent component analysis
**************************************
Reading data /5htgrip/5htgrip1/kevin/melissa_niak/niak/intermediate/subject10/time_filter/fmri_subject10_session1_run2_a_mc_f.mnc ...
Reading brain mask /5htgrip/5htgrip1/kevin/melissa_niak/niak/anat/subject10/func_subject10_mask_nativefunc.mnc ...
Correction of the mean of time series ...
Performing spatial independent component analysis with 50 components, this might take a while ...
Reducing the data to 50 principal dimensions...
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Undefined function or method 'randperm' for input arguments of type 'double'.
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/commands/sica/niak_sica.m at line 1015
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/commands/sica/niak_sica.m at line 176
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/bricks/sica/niak_brick_sica.m at line 227
File /data/aces/aces1/pbellec/public/psom-dev/psom_run_job.m at line 110
File /data/aces/aces1/pbellec/public/psom-dev/psom_pipeline_process.m at line 614
File /data/aces/aces1/pbellec/public/psom-dev/psom_run_pipeline.m at line 351
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/pipeline/niak_pipeline_fmri_preprocess.m at line 570
****************
Checking outputs
****************
The output file or directory /5htgrip/5htgrip1/kevin/melissa_niak/niak/quality_control/subject10/corsica/fmri_subject10_session1_run2_a_mc_f_sica_space.mnc has not been generated!
The output file or directory /5htgrip/5htgrip1/kevin/melissa_niak/niak/quality_control/subject10/corsica/fmri_subject10_session1_run2_a_mc_f_sica_time.mat has not been generated!
**********************************************
01-Aug-2012 18:39:06 : The job has FAILED
Total time used to process the job : 2.79 sec.
**********************************************
First of all, sorry for the late answer.
I'm running into an error in the NIAK pipeline which is quite possibly due to me trying to use it incorrectly. The design of my fMRI protocol is to test monozygotic twins on a task. I've previously run the pipeline without issue on the twins considering each as their own subject with their own anatomical scan. However, as the twins really are very similar, I'm trying to preprocess their data as run1 and run2 of one "subject" (actually a twin pair). My hope is that considering them as runs within a subject will minimize the inter-twin error, which is more important than the between twin error to our analysis.
I ran the pipeline first for one half of the
twins, and those jobs are complete. Now I've restarted it with the
second run information included. It runs OK up to the sica step,
where it produces errors (below). I'm wondering if this error has
to do with the differences between the twins' data, or some
configuration on my part? Also, I'd appreciate any thoughts on
using this design, is it a fool's errand to consider twins as
runs?
I don't relly get where that error could come from. It says it doesn't find the randperm function which doesn't make sense (that's a standard command). There must be something going on with the configuration of the machine that's running the job. I'd try to restart the pipeline a couple of times before giving up and looking for a bug. Let me know if that error is reproducible.
I hope this helps. Best,
Pierre
Thanks!
Kevin
>> logs.sica_subject10_run2
ans =
******************************
Log of the (matlab) job : sica_subject10_run2
Started on 01-Aug-2012 18:39:03
User: kevin
host : dumain
system : unix
******************************
command =
niak_brick_sica(files_in,files_out,opt);
files_in =
fmri: [1x116 char]
mask: [1x91 char]
files_out =
space: [1x127 char]
time: [1x126 char]
files_clean =
{}
opt =
nb_comp: 50
folder_out: [1x76 char]
flag_test: 0
norm: 'mean'
algo: 'Infomax'
flag_verbose: 1
********************
The job starts now !
********************
**************************************
Spatial independent component analysis
**************************************
Reading data /5htgrip/5htgrip1/kevin/melissa_niak/niak/intermediate/subject10/time_filter/fmri_subject10_session1_run2_a_mc_f.mnc ...
Reading brain mask /5htgrip/5htgrip1/kevin/melissa_niak/niak/anat/subject10/func_subject10_mask_nativefunc.mnc ...
Correction of the mean of time series ...
Performing spatial independent component analysis with 50 components, this might take a while ...
Reducing the data to 50 principal dimensions...
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Undefined function or method 'randperm' for input arguments of type 'double'.
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/commands/sica/niak_sica.m at line 1015
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/commands/sica/niak_sica.m at line 176
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/bricks/sica/niak_brick_sica.m at line 227
File /data/aces/aces1/pbellec/public/psom-dev/psom_run_job.m at line 110
File /data/aces/aces1/pbellec/public/psom-dev/psom_pipeline_process.m at line 614
File /data/aces/aces1/pbellec/public/psom-dev/psom_run_pipeline.m at line 351
File /data/aces/aces1/pbellec/public/niak-0.6.4.1/pipeline/niak_pipeline_fmri_preprocess.m at line 570
****************
Checking outputs
****************
The output file or directory /5htgrip/5htgrip1/kevin/melissa_niak/niak/quality_control/subject10/corsica/fmri_subject10_session1_run2_a_mc_f_sica_space.mnc has not been generated!
The output file or directory /5htgrip/5htgrip1/kevin/melissa_niak/niak/quality_control/subject10/corsica/fmri_subject10_session1_run2_a_mc_f_sica_time.mat has not been generated!
**********************************************
01-Aug-2012 18:39:06 : The job has FAILED
Total time used to process the job : 2.79 sec.
**********************************************
Threaded View
| Title | Author | Date |
|---|---|---|
| Kevin Casey | Aug 22, 2012 | |
| Pierre Bellec | Aug 28, 2012 | |
| Kevin Casey | Aug 28, 2012 | |