help > Denoised Data files
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Sep 26, 2016  02:09 AM | Sascha Froelich
Denoised Data files
Dear all,

According to what I've read in this forum (e.g. here http://www.nitrc.org/forum/message.php?m...), CONN should create nifti-files of the denoised data. However, in the folder conn*/results/preprocessing, I do not find any nifti-files. The folder conn*/data doesn't contain any nifti-files, either. But I do have mat-files. However, those mat-files do not seem to contain the voxel timecourses (which I'm interested in). The structs of these mat-files look like this when I load them into MATLAB:

    fname: '/Path_to_conn_project/results/preprocessing/cachetmp_DATA_Subject001_Condition001.mat'
    issurface: 0
    matdim: [1x1 struct]
    size: [1x1 struct]
    voxels: [262958x1 double]
    GM: [ ]
    gm: [ ]
    scale: 1
    voxelsinv: [91x109x91 double]
    overwritesoftlink: 1
    conditionsweights: {[300x1 double] [300x1 double] [300x1 double] [300x1 double] [300x1 double]}
    crop: 0
    softlink: 'cachetmp_DATA_Subject001_Condition000.matc'


What can I do to obtain the denoised data in nifti-files? Or alternatively as a mat-file containing the complete voxel timecourses.

Best,
Sascha
Sep 26, 2016  04:09 AM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Denoised Data files
Hi Sascha,

If you are looking for the denoised nifti file, go to "Options" in the "Setup" tab and select "Create confound-corrected time-series", The niftiDATA_Subjectxxx_Condition_xxx.nii file would then be in the results/preprocessing folder.

Is that what you are looking for?


Best
Pravesh

 
Originally posted by Sascha Froelich:
Dear all,

According to what I've read in this forum (e.g. here http://www.nitrc.org/forum/message.php?m...), CONN should create nifti-files of the denoised data. However, in the folder conn*/results/preprocessing, I do not find any nifti-files. The folder conn*/data doesn't contain any nifti-files, either. But I do have mat-files. However, those mat-files do not seem to contain the voxel timecourses (which I'm interested in). The structs of these mat-files look like this when I load them into MATLAB:

    fname: '/Path_to_conn_project/results/preprocessing/cachetmp_DATA_Subject001_Condition001.mat'
    issurface: 0
    matdim: [1x1 struct]
    size: [1x1 struct]
    voxels: [262958x1 double]
    GM: [ ]
    gm: [ ]
    scale: 1
    voxelsinv: [91x109x91 double]
    overwritesoftlink: 1
    conditionsweights: {[300x1 double] [300x1 double] [300x1 double] [300x1 double] [300x1 double]}
    crop: 0
    softlink: 'cachetmp_DATA_Subject001_Condition000.matc'


What can I do to obtain the denoised data in nifti-files? Or alternatively as a mat-file containing the complete voxel timecourses.

Best,
Sascha
Sep 26, 2016  06:09 AM | Sascha Froelich
RE: Denoised Data files
Dear Pravesh,

thanks, this is basically what I am looking for. I went back to the "Setup" menu and checked the box "Create confound-corrected time-series" and hit "Done". Then I selected "Do not overwrite" as I don't think it is necessary to redo the whole preprocessing procedure (it takes about a day). Afterwards, however, I did not find any new files in the folder results/preprocessing.

Do I have to select "overwrite existing"? If not, what else could be the problem?

Best,
Sascha
Sep 26, 2016  06:09 AM | Pravesh Parekh - National Institute of Mental Health and Neurosciences
RE: Denoised Data files
Hi Sascha,

I think you might have to overwrite the data (you need not do the preprpocessing again). Just click done, allow Conn to import the data, and then re-run the denoising step after overwriting files as necessary. I think that if you do not select the overwrite option, Conn would skip all processing and would not create the files.


Best
Pravesh
Sep 26, 2016  08:09 AM | Sascha Froelich
RE: Denoised Data files
That was it! Thanks a lot!

Cheers,
Sascha