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help > RE: Preprocessing and differing number of slices
Mar 20, 2013 05:03 AM | Alfonso Nieto-Castanon - Boston University
RE: Preprocessing and differing number of slices
Dear Daniel,
Regarding question (1), sorry this was a bug in the code I had not seen before, please change line 110 in conn_setup_wizard from:
tempvol=spm_vol(OPTIONS.XFUNCTIONAL_FILES{nsub}{1}{1});
to:
tempvol=spm_vol(OPTIONS.XFUNCTIONAL_FILES{nsubject}{1}{1});
and I believe that should fix this issue (after this change, the wizard should prompt you again for the slice order when the preprocessing steps encounter a subject with different number of acquisitions).
Regarding question (2), you can store more than one set of analyses in the same conn project. Typically if you only want to add a different set of analyses to an existing project (e.g. keeping the same preprocessing, but changing something in the first-level analysis step), you can simply go to the top-right corner in the 'first-level analysis' tab where it reads 'ANALYSIS_01', select 'new' to define a new set of analyses, and then define the new analysis options there. In the 'first-level analyses' tab as well as in the 'second-level results' tab you will then be able to switch between the two sets of analyses using the same drop-down list in the top right corner.
If, on the other hand, your different analyses involve different 'preprocessing' options (e.g. different frequency filtering, or different possible BOLD signal confounds), even if they involve the same 'spatial preprocesing' options (e.g. realignment, normalization, segmentation, etc.), then you are right you may want to create a different conn project for this. In this case, simply click on the 'New' button in the 'setup' tab to start a new project, answer 'no' to the 'spatially preprocess your data now' question, and then enter the the swra* files as functional files, the normalized anatomical volumes (typically wm*.nii files) as structurals, the motion realignment parameters (rp_*.txt files) as first-level covariates, and the normalized segmentation masks (typically wc1* to wc3* files) for grey/white/csf ROIs. Another, perhaps simpler, option would be to simply click on 'save as' to create a new project using your current project as template. The new project will already have all the appropriate files in the setup option defined, so you can simply go on an continue from there to the preprocessing tab and make the necessary changes there.
Let me know if this helps
Best regards
Alfonso
Originally posted by Daniel Fitzgerald:
Regarding question (1), sorry this was a bug in the code I had not seen before, please change line 110 in conn_setup_wizard from:
tempvol=spm_vol(OPTIONS.XFUNCTIONAL_FILES{nsub}{1}{1});
to:
tempvol=spm_vol(OPTIONS.XFUNCTIONAL_FILES{nsubject}{1}{1});
and I believe that should fix this issue (after this change, the wizard should prompt you again for the slice order when the preprocessing steps encounter a subject with different number of acquisitions).
Regarding question (2), you can store more than one set of analyses in the same conn project. Typically if you only want to add a different set of analyses to an existing project (e.g. keeping the same preprocessing, but changing something in the first-level analysis step), you can simply go to the top-right corner in the 'first-level analysis' tab where it reads 'ANALYSIS_01', select 'new' to define a new set of analyses, and then define the new analysis options there. In the 'first-level analyses' tab as well as in the 'second-level results' tab you will then be able to switch between the two sets of analyses using the same drop-down list in the top right corner.
If, on the other hand, your different analyses involve different 'preprocessing' options (e.g. different frequency filtering, or different possible BOLD signal confounds), even if they involve the same 'spatial preprocesing' options (e.g. realignment, normalization, segmentation, etc.), then you are right you may want to create a different conn project for this. In this case, simply click on the 'New' button in the 'setup' tab to start a new project, answer 'no' to the 'spatially preprocess your data now' question, and then enter the the swra* files as functional files, the normalized anatomical volumes (typically wm*.nii files) as structurals, the motion realignment parameters (rp_*.txt files) as first-level covariates, and the normalized segmentation masks (typically wc1* to wc3* files) for grey/white/csf ROIs. Another, perhaps simpler, option would be to simply click on 'save as' to create a new project using your current project as template. The new project will already have all the appropriate files in the setup option defined, so you can simply go on an continue from there to the preprocessing tab and make the necessary changes there.
Let me know if this helps
Best regards
Alfonso
Originally posted by Daniel Fitzgerald:
Dear Conn forum,
We've been using the (excellent) conn toolbox to look at resting state fMRI data, but have run into a couple of issues:
1) We have some data where a few subjects have a different number of slices (40 instead of 43 for the rest of the group). When we try to do the setup from the wizard, it comes back asking for the order of only 40 slices and then only passes through one subject to the next step. How can we fully process data that varies in slice number with the wizard?
2) Quite often we have already looked at a number of subjects and want to set up a different analysis without redoing the preprocessing (within CONN) from scratch. In this case, should we be using the basic setup screen and entering swra* files? Does this still properly grab motion parameters? Also, which structural image should be chosen when entering already preprocessed data?
Thank you and keep up the great work with this toolbox.
Daniel Fitzgerald - danfitz@uic.edu
University of Illinois at Chicago, Department of Psychiatry
Mood and Anxiety Disorders Research Program
We've been using the (excellent) conn toolbox to look at resting state fMRI data, but have run into a couple of issues:
1) We have some data where a few subjects have a different number of slices (40 instead of 43 for the rest of the group). When we try to do the setup from the wizard, it comes back asking for the order of only 40 slices and then only passes through one subject to the next step. How can we fully process data that varies in slice number with the wizard?
2) Quite often we have already looked at a number of subjects and want to set up a different analysis without redoing the preprocessing (within CONN) from scratch. In this case, should we be using the basic setup screen and entering swra* files? Does this still properly grab motion parameters? Also, which structural image should be chosen when entering already preprocessed data?
Thank you and keep up the great work with this toolbox.
Daniel Fitzgerald - danfitz@uic.edu
University of Illinois at Chicago, Department of Psychiatry
Mood and Anxiety Disorders Research Program
Threaded View
| Title | Author | Date |
|---|---|---|
| Daniel Fitzgerald | Mar 18, 2013 | |
| Alfonso Nieto-Castanon | Mar 20, 2013 | |
| Daniel Fitzgerald | Apr 22, 2014 | |
| Alfonso Nieto-Castanon | Apr 22, 2014 | |
| Daniel Fitzgerald | Apr 16, 2013 | |
| Alfonso Nieto-Castanon | May 24, 2013 | |