help > Using preprocessed files from SPM
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Jan 14, 2020 04:01 PM | Jasmine Cakmak
Using preprocessed files from SPM
Hello,
I have some past rs-fmri data which has been given to me which has previously been preprocessed in SPM8. The functional images have been normalized to MNI space and are slice-time corrected. The structural images have been normalized and have output files (seg_inv_sn.mat and seg_sn.mat) which I am not sure what to do with in CONN. How would I continue preprocessing with these files -- is there a way to import them? I see that I can import SPM files using the import tool, but it does not seem to work for .mat files.
Thanks,
Jasmine
I have some past rs-fmri data which has been given to me which has previously been preprocessed in SPM8. The functional images have been normalized to MNI space and are slice-time corrected. The structural images have been normalized and have output files (seg_inv_sn.mat and seg_sn.mat) which I am not sure what to do with in CONN. How would I continue preprocessing with these files -- is there a way to import them? I see that I can import SPM files using the import tool, but it does not seem to work for .mat files.
Thanks,
Jasmine
Jan 14, 2020 05:01 PM | Alfonso Nieto-Castanon - Boston University
RE: Using preprocessed files from SPM
Hi Jasmine,
You don't need those seg_*.mat files. If SPM8 has created for you already the tissue class files wc1*.img, wc2*.img and wc3*.img as part of SPM8 "combined normalization and segmentation" procedure then you can simply enter those in Setup.ROIs (as grey/white/csf ROIs, respectively). If does files do not exist (e.g. because you run the standard "normalization" procedure in SPM8), then simply apply segmentation to your already-normalized structural image (e.g. in Setup.structural, select the "structural tools" menu and "apply individual preprocesing step" and then select the step named "structural segmentation (grey/white/csf tissue estimation)" and that will add the resulting grey/white/CSF ROIs to your project.
Hope this helps
Alfonso
Originally posted by Jasmine Cakmak:
You don't need those seg_*.mat files. If SPM8 has created for you already the tissue class files wc1*.img, wc2*.img and wc3*.img as part of SPM8 "combined normalization and segmentation" procedure then you can simply enter those in Setup.ROIs (as grey/white/csf ROIs, respectively). If does files do not exist (e.g. because you run the standard "normalization" procedure in SPM8), then simply apply segmentation to your already-normalized structural image (e.g. in Setup.structural, select the "structural tools" menu and "apply individual preprocesing step" and then select the step named "structural segmentation (grey/white/csf tissue estimation)" and that will add the resulting grey/white/CSF ROIs to your project.
Hope this helps
Alfonso
Originally posted by Jasmine Cakmak:
Hello,
I have some past rs-fmri data which has been given to me which has previously been preprocessed in SPM8. The functional images have been normalized to MNI space and are slice-time corrected. The structural images have been normalized and have output files (seg_inv_sn.mat and seg_sn.mat) which I am not sure what to do with in CONN. How would I continue preprocessing with these files -- is there a way to import them? I see that I can import SPM files using the import tool, but it does not seem to work for .mat files.
Thanks,
Jasmine
I have some past rs-fmri data which has been given to me which has previously been preprocessed in SPM8. The functional images have been normalized to MNI space and are slice-time corrected. The structural images have been normalized and have output files (seg_inv_sn.mat and seg_sn.mat) which I am not sure what to do with in CONN. How would I continue preprocessing with these files -- is there a way to import them? I see that I can import SPM files using the import tool, but it does not seem to work for .mat files.
Thanks,
Jasmine