Complete boiler plate methods section of the README #17
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Remi-Gau
added
documentation 📄
marcobarilari
approved these changes
Oct 2, 2019
Collaborator
marcobarilari
left a comment
marcobarilari
left a comment
There was a problem hiding this comment.
Not an expert but sounds complete regarding the steps implemented in the pipeline. It would be nice to have (in the future) an automated generated text retrieving the details from the scripts (e.g. getOptions/spmMyDefaults etc)
|
|
||
| The fMRI data were pre-processed and analyzed using statistical parametric mapping (SPM12 – v7487; Wellcome Center for Neuroimaging, London, UK; www.fil.ion.ucl.ac.uk/spm) running on {octave 4.{??} / matlab 20{XX} (Mathworks)}. | ||
|
|
||
| The preprocessing of the functional images was performed in the following order: removing of dummy scans, {slice timing correction}, realignment, normalization to MNI, smoothing. |
Collaborator
There was a problem hiding this comment.
(I might be wrong) on the last meeting (1st oct) we discussed about how to deal with the dummies removal/onset time and @mohmdrezk proposed to remove them before BIDS conversion (and therefore not mention them?). Is it correct?
Contributor
Author
There was a problem hiding this comment.
True. I agree with what @mohmdrezk said below.
Collaborator
|
@marco : It will be in the pipeline during the BIDS preparation (not before), and in the last step, the dummies will be removed before copying the files to “RAW”.
We can mention it in the end of the dicom2BIDS.
… On 2 Oct 2019, at 14:44, marcobarilari ***@***.***> wrote:
@marcobarilari approved this pull request.
Not an expert but sounds complete regarding the steps implemented in the pipeline. It would be nice to have (in the future) an automated generated text retrieving the details from the scripts (e.g. getOptions/spmMyDefaults etc)
In README.md <#17 (comment)>:
> @@ -120,20 +132,42 @@ _There's no way to avoid all the error (short of doing a four-dimensional realig
## Boiler plate methods section
-Work in progress...
+### Preprocessing
+
+The fMRI data were pre-processed and analyzed using statistical parametric mapping (SPM12 – v7487; Wellcome Center for Neuroimaging, London, UK; www.fil.ion.ucl.ac.uk/spm) running on {octave 4.{??} / matlab 20{XX} (Mathworks)}.
+
+The preprocessing of the functional images was performed in the following order: removing of dummy scans, {slice timing correction}, realignment, normalization to MNI, smoothing.
(I might be wrong) on the last meeting (1st oct) we discussed about how to deal with the dummies removal/onset time and @mohmdrezk <https://github.com/mohmdrezk> proposed to remove them before BIDS conversion (and therefore not mention them?). Is it correct?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub <#17>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACJHG54DH4RRLTKYWFRARH3QMSJR3ANCNFSM4I4L6TVA>.
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Just a first step to make it easier in the future to write the methods section.