Hi Marie,

Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and after correcting for total intraranial volume, and for LGI, it just removed the significance of the association.

Thanks again, Panos

Hi Panos,

It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area, and thus LGI, and volume is governed by a power law, which means that if you linearly correct for intracranial volume, some of its effect will remain.

Hope it helps,

Marie

On Jul 10, 2014, at 10:57 AM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi FS Community,

I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume.

Thanks in advance, Panos _______________________________________________ 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.

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Hi Emily,

1. That's fine because the BET-based mask is not used by default in the the tractography. The brain mask from the freesurfer segmentation of the structural scan is used instead.

2. To check the diffusion-to-anatomical registration, you can look at the aparc+aseg registered into diffusion space, i.e., from the dlabel/diff directory, overlaid onto the FA map. It's also important to check that the gradient table is correct by looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines. Assuming the protocol is the same for all subjects, you just need to do this latter check for one of your subjects only.

3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of specific tracts. Information on the anatomical regions that these tracts go through or next to is derived from a set of training subjects. See our paper for more info:

http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstrac...

Hope this helps, a.y

On Thu, 10 Jul 2014, ebelleau@uwm.edu wrote:

Hello,

I have a few questions about Tracula. I am very new to DTI, so I hope you can bare with me.

1.) I have been checking my registration at the prep stage. I am very new to this so it may be that I am not looking at the right files.

I looked at my eddy current corrected diffusion data (which I believe is in data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed that the no_dif_brain_mask does not cover very well for some of my subjects. Should I individually tailor the Fractional Intensity Threshold for BET mask extraction from low-b images at the prep stage?

2.) In general what files should I be checking at each phase (prep, bedpost, path)?

3.)How do you generate the whole-brain ROIS to guide the tractography (is the white matter mask that is generated at the prep phase involved)?

Thanks,

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

Hi Emily - When a mask is used as input to bedpostx, all voxels outside that mask will be zero in all bedpostx output volumes. So it makes sense to use the same mask for any subsequent processing. Is the mask that you're referring to a symbolic link to another volume? You can run ls -l to see what volume it points to.

a.y

On Mon, 14 Jul 2014, ebelleau@uwm.edu wrote:

Hi Anastasia,

Thank you so much, this is really helpful.

I have one other question. So, at the bedpost stage, the no_dif_brain mask is used correct (looking at the fsl webpage), or at this stage the freesurfer segmentation is used as well?

If in addition to using tracula, lets say if I also wanted to look into doing local probablistic tractography in FSL (using probtractx). I know that probtractx uses the output from the fsl bedpost stage. In this case then, would I need to adjust the no_dif_brain mask since it was used in the bedpost stage? I planned on using the output from the bedpost stage in tracula into FSL's probtractx to also try some local probablistic tractography.

Emily

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 14, 2014 4:14:49 AM Subject: Re: [Freesurfer] Tracula

Hi Emily,

1. That's fine because the BET-based mask is not used by default in the

the tractography. The brain mask from the freesurfer segmentation of the structural scan is used instead.

2. To check the diffusion-to-anatomical registration, you can look at the

aparc+aseg registered into diffusion space, i.e., from the dlabel/diff directory, overlaid onto the FA map. It's also important to check that the gradient table is correct by looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines. Assuming the protocol is the same for all subjects, you just need to do this latter check for one of your subjects only.

3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of

specific tracts. Information on the anatomical regions that these tracts go through or next to is derived from a set of training subjects. See our paper for more info:

http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstrac...

Hope this helps, a.y

On Thu, 10 Jul 2014, ebelleau@uwm.edu wrote:

...

Hello,

I have a few questions about Tracula. I am very new to DTI, so I hope you can bare with me.

1.) I have been checking my registration at the prep stage. I am very new to this so it may be that I am not looking at the right files.

I looked at my eddy current corrected diffusion data (which I believe is in data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed that the no_dif_brain_mask does not cover very well for some of my subjects. Should I individually tailor the Fractional Intensity Threshold for BET mask extraction from low-b images at the prep stage?

2.) In general what files should I be checking at each phase (prep, bedpost, path)?

3.)How do you generate the whole-brain ROIS to guide the tractography (is the white matter mask that is generated at the prep phase involved)?

Thanks,

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

---

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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

Hi Emily - Sorry for the confusion. The mask in the bedpostx output directory is a copy of whichever mask was input to bedpostx. By default, tracula uses the anatomical mask for this. If that mask doesn't cover the brain well, I would check for diffusion-to-anatomical miregistration. Probtrackx will use whichever mask you specify as its input.

a.y

On Mon, 14 Jul 2014, ebelleau@uwm.edu wrote:

Hi Anastasia,

So probtractx uses the output from the bedpost stage (which I ran in Tracula). I noticed that the bedpost stage (in the dmri.bedpostx folder) also outputs a no_dif_brain mask. I guess what I am worried about is that if bedpost creates this no_dif_brain mask, that is what will be utilized in probtractx instead of the Freesurfer brain mask.

When bedpost is conducted in Tracula, is the brain mask from the freesurfer segmentation of the structural scan utilized?

I am sorry. I know I am making this confusing!

Thanks,

Emily

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 14, 2014 10:18:11 AM Subject: Re: [Freesurfer] Tracula

Hi Emily - When a mask is used as input to bedpostx, all voxels outside that mask will be zero in all bedpostx output volumes. So it makes sense to use the same mask for any subsequent processing. Is the mask that you're referring to a symbolic link to another volume? You can run ls -l to see what volume it points to.

a.y

On Mon, 14 Jul 2014, ebelleau@uwm.edu wrote:

...

Hi Anastasia,

Thank you so much, this is really helpful.

I have one other question. So, at the bedpost stage, the no_dif_brain mask is used correct (looking at the fsl webpage), or at this stage the freesurfer segmentation is used as well?

If in addition to using tracula, lets say if I also wanted to look into doing local probablistic tractography in FSL (using probtractx). I know that probtractx uses the output from the fsl bedpost stage. In this case then, would I need to adjust the no_dif_brain mask since it was used in the bedpost stage? I planned on using the output from the bedpost stage in tracula into FSL's probtractx to also try some local probablistic tractography.

Emily

----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Monday, July 14, 2014 4:14:49 AM Subject: Re: [Freesurfer] Tracula

Hi Emily,

1. That's fine because the BET-based mask is not used by default in the

the tractography. The brain mask from the freesurfer segmentation of the structural scan is used instead.

2. To check the diffusion-to-anatomical registration, you can look at the

aparc+aseg registered into diffusion space, i.e., from the dlabel/diff directory, overlaid onto the FA map. It's also important to check that the gradient table is correct by looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines. Assuming the protocol is the same for all subjects, you just need to do this latter check for one of your subjects only.

3. TRACULA doesn't do whole-brain tractography. It reconstructs a set of

specific tracts. Information on the anatomical regions that these tracts go through or next to is derived from a set of training subjects. See our paper for more info:

http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstrac...

Hope this helps, a.y

On Thu, 10 Jul 2014, ebelleau@uwm.edu wrote:

...

Hello,

I have a few questions about Tracula. I am very new to DTI, so I hope you can bare with me.

1.) I have been checking my registration at the prep stage. I am very new to this so it may be that I am not looking at the right files.

I looked at my eddy current corrected diffusion data (which I believe is in data.nii.gz in the dmri folder) with the no_dif_brain_mask.nii, and noticed that the no_dif_brain_mask does not cover very well for some of my subjects. Should I individually tailor the Fractional Intensity Threshold for BET mask extraction from low-b images at the prep stage?

2.) In general what files should I be checking at each phase (prep, bedpost, path)?

3.)How do you generate the whole-brain ROIS to guide the tractography (is the white matter mask that is generated at the prep phase involved)?

Thanks,

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

---

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

---

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

For surface area, you should correct with the ICV (note you should use ICV and not something like ICV^(2/3)) doug

On 07/10/2014 04:52 PM, Marie Schaer wrote:

Hi Panos,

Then I would say that it's interesting to understand why the results change depending on the correction. Here is a list of papers that may be relevant, but you'll certainly find many others: http://www.ncbi.nlm.nih.gov/pubmed/8159014 http://pages.jh.edu/~kechen/pnas-brains.pdf http://www.touchophthalmology.com/sites/www.touchoncology.com/files/migrated...

Best,

Marie

On Jul 10, 2014, at 11:50 AM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi Marie,

Thank you for your reply. I wanted to compare the LGI and Surface Area between two cohorts, from which one has a significantly higher intracranial volume than the other. I was wondering about the correction because the results, especially in the case of SA, are the opposite before and after correcting for total intraranial volume, and for LGI, it just removed the significance of the association.

Thanks again, Panos

...

Hi Panos,

It all depends on what your question is: whether the between-group difference in LGI and surface area is an absolute difference (then don't correct), or whether you want to see if it holds after correction. In any case, by geometric definition, the relationship between surface area, and thus LGI, and volume is governed by a power law, which means that if you linearly correct for intracranial volume, some of its effect will remain.

Hope it helps,

Marie

On Jul 10, 2014, at 10:57 AM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi FS Community,

I was wondering whether LGI and Surface Area need to be corrected for total Intracranial Volume.

Thanks in advance, Panos _______________________________________________ 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

---

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

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