NITRC NeuroImaging Analysis Kit (NIAK) Forum: general-discussion

the quality of the nonlinear warp

Kangjoo Lee — Mon, 23 Apr 2018 21:59:53 GMT

Dear Pierre,

I'm reporting some clinical results on fMRI connectivity analyses, and we are handling a small volume in the brain, the hippocampus, across our group of patients with temporal lobe epilepsy. The reason behind this concern is actually that our resampled voxel size was quite large, 4 mm x 4 mm x 4mm isotropic voxels.

So I'm wondering how I can best report the quality of the nonlinear warp performed using NIAK, to compare if the same voxel represents the same area (part of hippocampus) across subjects in our study. Any suggestion?

While my connectivity analyses was based on my own development, I preprocessed my T1 and BOLD images from individual patients using the standard pipeline suggested by NIAK.

Thank you for your help.

Best,
Kangjoo

a functional parcellation

francesca bottino — Mon, 19 Mar 2018 14:49:05 GMT

Hi,
I would to use the functions of this paper that are usefull to reproduce a functional parcellation Bellec's method.
Can you suggest me what I should downloada and refer to?
Thank you.
Francesca Bottino

NIAK FOR ICA physiological noise reduction

Isadora Olive — Fri, 02 Mar 2018 23:13:36 GMT

Hello! I am just discovering NIAK, so I have a very basic question. I saw it indicated in a paper as an alternative toolbox for noise reduction with ICA. Nevertheless, it is not unambiguously stated in the tutorial which option of regression of confounds correspond to the ICA method? Would it be the temporal filtering?

Isadora

NIAK Pipeline : Motion Data for ADHD-200

Amritha Harikumar — Wed, 06 Dec 2017 22:29:07 GMT

Hello,

I am using the ABIDE and ADHD-200 pre-processed NIAK pipeline data for my master's thesis. As such, I would like to match the motion data (e.g. mean FD values) to make sure subjects in both groups are equally grouped on similar mean FD values. However, I am unable to locate this info for the ADHD-200 data. In the ABIDE database, it is listed under a column labeled 'mean FD'. I do not see the same for the ADHD-200. I looked through the motion data files for the NIAK pipeline in ADHD-200, and only located the matlab, .csv and pdf files for each subject. Please help me on locating the mean FD values for the ADHD-200 subjects. Thank you!

Best,
Amritha

RE: psom_run_script- no gb_psom_opt_matlab

Pierre Bellec — Fri, 28 Apr 2017 3:17:07 GMT

Very happy to hear that!

Best,

Pierre

RE: psom_run_script- no gb_psom_opt_matlab

Aki Nikolaidis — Fri, 14 Apr 2017 17:38:20 GMT

Hi Pierre,

Thanks! We were able to convert the docker image to singularity and run it successfully on our local server.

Thanks for the help!

Best,
Aki

RE: psom_run_script- no gb_psom_opt_matlab

Pierre Bellec — Fri, 14 Apr 2017 16:18:58 GMT

Hi Aki,

I believe soon you will be able to pull directly images from docker hub using singularity. In the meantime we are releasing the images on github, as binaries:
https://github.com/SIMEXP/niak/releases

Check the link to niak-boss-0.18.1.img.gz

Best,

Pierre

RE: psom_run_script- no gb_psom_opt_matlab

Aki Nikolaidis — Fri, 24 Mar 2017 19:43:36 GMT

Hi Pierre,

My apologies, I'm a little unclear on what do download and what to do with it. We are running NIAK on Singularity instead of Docker, would there be a Singularity .img file you can point me to for the 0.18.1 release?

best regards,
Aki

RE: psom_run_script- no gb_psom_opt_matlab

Pierre Bellec — Wed, 22 Mar 2017 3:17:03 GMT

Hi Aki,

Sorry for the late answer. Could you please give it a try with the new 0.18.1 release?
https://hub.docker.com/r/simexp/niak-boss/tags/

Best,

Pierre

psom_run_script- no gb_psom_opt_matlab

Aki Nikolaidis — Fri, 17 Mar 2017 20:22:28 GMT

Hello All,

I'm working on setting up NIAK with Singularity on our local Linux server. I am having a problem running niak_pipeline_fmri_preprocess.m

I open the Octave session with Singularity and NIAK loaded using this terminal command: psom_console.sh -p /usr/local/share/singularity/niak-boss-0.17.0.img

When I run the niak_tutorial_fmri_preprocessing command I get the following error message, and this is the same error message I received previously when running niak_pipeline_fmri_preprocess using the files_in and opt arguments just as is done online, but with my own files. Please let me know if you have any ideas for next steps.

Best Regards,
Aki

---Error message for tutorial---
--2017-03-17 18:32:01-- http://www.nitrc.org/frs/download.php/7241/data_test_niak_mnc1.zip
Resolving www.nitrc.org (www.nitrc.org)... 132.239.16.23
Connecting to www.nitrc.org (www.nitrc.org)|132.239.16.23|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 2726269 (2.6M) [application/force-download]
Saving to: '/home/anikolai/SampleData/data_test_niak_mnc1/data_test_niak_mnc1.zip'

100%[===============================================================================================================>] 2,726,269 1.31M/s in 2.0s
2017-03-17 18:32:04 (1.31 MB/s) - '/home/anikolai/SampleData/data_test_niak_mnc1/data_test_niak_mnc1.zip' saved [2726269/2726269]
Deleting file '/home/anikolai/SampleData/data_test_niak_mnc1/data_test_niak_mnc1.zip'
ans = 0
Generating pipeline for individual fMRI preprocessing :
Adding subject1 ; 0.33 sec
Adding subject2 ; 0.33 sec
Adding group-level quality control of coregistration in anatomical space (linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in anatomical space (non-linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in functional space ; 0.01 sec
Adding group-level quality control of motion correction (motion parameters) ; 0.01 sec
Adding group-level quality control of scrubbing time frames with excessive motion ; 0.00 sec
Adding the report on fMRI preprocessing ; 0.40 sec
Logs will be stored in /home/anikolai/SampleData/fmri_preprocess/logs/
Generating dependencies ...
Percentage completed : 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100- 0.12 sec
Setting up the to-do list ...
I found 75 job(s) to do.
stopped in /usr/local/niak/extensions/psom/psom_run_pipeline.m at line 505
505: [flag_failed,msg] = psom_run_script(cmd_deamon,script_deamon,opt_script,opt_logs);
debug> dbcont
stopped in /usr/local/niak/extensions/psom/psom_run_script.m at line 239
239: if ~isempty(cmd)
debug> dbcont
error: 'gb_psom_opt_matlab' undefined near line 240 column 67
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5
niak_tutorial_fmri_preprocessing at line 75 column 1
error: evaluating argument list element number 3
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5
niak_tutorial_fmri_preprocessing at line 75 column 1
>>

---Error Message on My Files---
pipeline = niak_pipeline_fmri_preprocess(files_in,opt)
warning: The following field(s) were ignored in the structure opt: corsica
warning: called from
psom_struct_defaults at line 112 column 5
niak_pipeline_fmri_preprocess at line 454 column 5
Generating pipeline for individual fMRI preprocessing :
Adding subject1 ; 0.41 sec
Adding subject2 ; 0.39 sec
Adding subject3 ; 0.42 sec
Adding subject4 ; 0.42 sec
Adding group-level quality control of coregistration in anatomical space (linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in anatomical space (non-linear stereotaxic space) ; 0.01 sec
Adding group-level quality control of coregistration in functional space ; 0.01 sec
Adding group-level quality control of motion correction (motion parameters) ; 0.01 sec
Adding group-level quality control of scrubbing time frames with excessive motion ; 0.00 sec
Adding the report on fMRI preprocessing ; 0.54 sec

Logs will be stored in /home/anikolai/demo_niak/fmri_preprocess/logs/
Generating dependencies ...
Percentage completed : 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100- 0.31 sec
Setting up the to-do list ...
I found 189 job(s) to do.
error: 'gb_psom_opt_matlab' undefined near line 240 column 67
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5
error: evaluating argument list element number 3
error: called from
psom_run_script at line 240 column 15
psom_run_pipeline at line 505 column 18
niak_pipeline_fmri_preprocess at line 749 column 5