PostFreeSurfer related pull request #135
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1/ Changing tabs to spaces, removal of trailing line spaces 2/ Fixing a bug with generation of c_ras.mat. The code to generate c_ras.mat failed in some cases so we replaced it with a more robust version. 3/ When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped: * Adding T2w related images to the spec file
1/ Changing tabs to spaces, removal of trailing line spaces 2/ When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped: * Adding T2w related images to the spec file * `applywarp` to `AtlasSpaceT2wImage`
1/ Changing tabs to spaces, removal of trailing line spaces 2/ Explicit prinrout of parameters 3/ Addition of `--mppversion` parameter and related check / validation code 4/ When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped: * Myelin mapping
1/ Changing tabs to spaces, removal of trailing line spaces 2/ Explicit printout of parameters 3/ Addition of `--mppversion` parameter and related check / validation code 4/ Temporary suppression of colored echo outputs 5/ When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped: * Myelin mapping
glasserm
requested changes
Sep 29, 2019
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Turning off the myelin mapping script is not really what you want to do as multiple other things besides myelin mapping occur in it including:
- Creation of single warp field for final resampling of the T1w image (with masking and bias correction) for both T1w and MNI space
- Creation of the thickness map corrected for folding and creation of its CIFTI files
- Setting a palette on the Jacobian volume for the atlas registration
- Resampling of the bias field to MNI space
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We also need to have no T2w checks for the last few loops in CreateMyelinMaps for #Create CIFTI Files and #Add CIFTI Maps to Spec. |
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Lets also class RegName="FS" into legacy mode as I mentioned in fMRISurface. |
mharms
reviewed
Oct 7, 2019
mharms
reviewed
Oct 7, 2019
mharms
reviewed
Oct 7, 2019
|
It looks good to me now |
glasserm
approved these changes
Oct 7, 2019
mharms
reviewed
Oct 8, 2019
mharms
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Oct 8, 2019
mharms
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Oct 8, 2019
mharms
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Oct 8, 2019
mharms
reviewed
Oct 8, 2019
mharms
reviewed
Oct 8, 2019
mharms
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Oct 8, 2019
mharms
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Oct 8, 2019
mharms
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Oct 8, 2019
mharms
reviewed
Oct 9, 2019
mharms
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Oct 9, 2019
mharms
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mharms
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Oct 9, 2019
coalsont
reviewed
Oct 10, 2019
coalsont
reviewed
Oct 10, 2019
coalsont
reviewed
Oct 10, 2019
coalsont
reviewed
Oct 10, 2019
mharms
reviewed
Oct 10, 2019
coalsont
approved these changes
Oct 11, 2019
glasserm
requested changes
Oct 12, 2019
|
Default set to MSMSulc |
mharms
approved these changes
Oct 12, 2019
glasserm
approved these changes
Oct 12, 2019
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PostFreeSurferPipeline.shrelated changes1/ Cosmetic changes
Changing tabs to spaces, removal of trailing line spaces
2/ Explicit printout of parameters
3/ Addition of
--mppversionparameter and related check / validation code4/ Temporary suppression of colored echo outputs
5/ Enabling run w/o T2w image
When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped:
PostFreeSurferPipeline_1res.shrelated changes1/ Cosmetic changes
Changing tabs to spaces, removal of trailing line spaces
2/ Explicit prinrout of parameters
3/ Addition of
--mppversionparameter and related check / validation code4/ Enabling run w/o T2w image
When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped:
FreeSurfer2CaretConvertAndRegisterNonlinear.shrelated changes1/ Cosmetic changes
Changing tabs to spaces, removal of trailing line spaces
2/ Fixing a bug with generation of c_ras.mat
The code to generate c_ras.mat failed in some cases so we replaced it with a more robust version.
3/ Enabling run w/o T2w image
When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped:
FreeSurfer2CaretConvertAndRegisterNonlinear_1res.shrelated changes1/ Cosmetic changes
Changing tabs to spaces, removal of trailing line spaces
2/ Enabling run w/o T2w image
When T2w image is missing and T2wRestoreImage is set to NONE the following steps are skipped:
applywarptoAtlasSpaceT2wImage