Do you have a reference to the Schwartz atlas? I can't seem to find it.

Thanks in advance.

Best Kasper

2016-05-17 14:30 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

the schwartz atlas is built from 3T data, which has somewhat different contrast properties due to the field-strength dependence of T1

Hopefully somone else can answer b) as I don't remember.

cheers Bruce

On Tue, 17 May 2016, Kasper Jessen wrote:

I would like to know the following:

...

a) what is the differences between the 3T Atlas (schwartz atlas) and the standard atlas? b) what does the 3T-specific NU intensity correction parameters do differently than the standard?

Best Kasper

2016-05-10 8:09 GMT+02:00 Kasper Jessen kasper_j@cnsr.dk: Dear FreeSurfer group, Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment.

However, where can i find the documentation for the above?

Best regards, Kasper

-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Kasper,

On May 17, 2016, at 10:05 , Kasper Jessen kasper_j@cnsr.dk wrote:

I would like to know the following:

a) what is the differences between the 3T Atlas (schwartz atlas) and the standard atlas? b) what does the 3T-specific NU intensity correction parameters do differently than the standard?

If I recall correctly this is based on http://www.sciencedirect.com/science/article/pii/S1053811909006703: Improvement of brain segmentation accuracy by optimizing non-uniformity correction using N3

Type Journal Article Author Weili Zheng Author Michael W. L. Chee Author Vitali Zagorodnov URL http://www.sciencedirect.com/science/article/pii/S1053811909006703 Volume 48 Issue 1 Pages 73-83 Publication NeuroImage ISSN 1053-8119 Date October 15, 2009 Journal Abbr NeuroImage

So most likely it reduces the N# smoothing distance from the default 200 to 50

Here is the relevant part from recon-all (v5.3): if ($DoNuIntensityCor3T) then # params from Zheng, Chee, Zagorodnov 2009 NeuroImage paper # "Improvement of brain segmentation accuracy by optimizing # non-uniformity correction using N3" set NuIterations = 1; set cmd = ($cmd --proto-iters 1000 --distance 50) endif

A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong…

Best Regards Sebastian

Best Kasper

2016-05-10 8:09 GMT+02:00 Kasper Jessen kasper_j@cnsr.dk: Dear FreeSurfer group,

Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment.

However, where can i find the documentation for the above?

Best regards, Kasper

-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Kasper,

On May 17, 2016, at 17:44 , Kasper Jessen kasper_j@cnsr.dk wrote:

Thanks for the answers :-)

Sebastian: What do you mean with "A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong…"

What is it that is probably wrong?

I would be amazed if that rationale was a truthful description of the full physical basis for the changes in inhomogeneities; and to be on the safe side (I never even discussed this with a physicist) I declare that it is incomplete and hence “wrong”. The last thing I want is to spread half-baked information as ground truth…

Best Regards Sebastian

Best regards, Kasper

2016-05-17 14:48 GMT+02:00 Moeller, Sebastian sebastian.moeller1@rwth-aachen.de: Hi Kasper,

...

On May 17, 2016, at 10:05 , Kasper Jessen kasper_j@cnsr.dk wrote:

I would like to know the following:

a) what is the differences between the 3T Atlas (schwartz atlas) and the standard atlas? b) what does the 3T-specific NU intensity correction parameters do differently than the standard?

    If I recall correctly this is based on http://www.sciencedirect.com/science/article/pii/S1053811909006703:

Improvement of brain segmentation accuracy by optimizing non-uniformity correction using N3

Type Journal Article Author Weili Zheng Author Michael W. L. Chee Author Vitali Zagorodnov URL http://www.sciencedirect.com/science/article/pii/S1053811909006703 Volume 48 Issue 1 Pages 73-83 Publication NeuroImage ISSN 1053-8119 Date October 15, 2009 Journal Abbr NeuroImage

So most likely it reduces the N# smoothing distance from the default 200 to 50

Here is the relevant part from recon-all (v5.3): if ($DoNuIntensityCor3T) then # params from Zheng, Chee, Zagorodnov 2009 NeuroImage paper # "Improvement of brain segmentation accuracy by optimizing # non-uniformity correction using N3" set NuIterations = 1; set cmd = ($cmd --proto-iters 1000 --distance 50) endif

A somewhat wrong, but intuitive rationale is with array coils the loops are smaller and hence the coil sensitivity profiles as well and these modulate the intensity inhomogeneity. But again that is probably wrong…

Best Regards Sebastian

...

Best Kasper

2016-05-10 8:09 GMT+02:00 Kasper Jessen kasper_j@cnsr.dk: Dear FreeSurfer group,

Our subject sample has been obtained on a 3 Tesla MR scanner. For this reason we used the -3T flag to enable the 3T-specific NU intensity correction parameters and usage of the special 3T atlas for Talairach alignment.

However, where can i find the documentation for the above?

Best regards, Kasper

-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j@cnsr.dk eller kasper.jessen@regionh.dk _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.