Thanks a ton Martin,

can you possibly clue me into where I could find study_average?

best, jon On Nov 6, 2013, at 2:16 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Jon,

passing the --qdec-long flag to mris_preproc will automatically generate the right names (e.g. the .long. directories) and take the data from there. You can pass the study_average vie the --target flag. The default is to use fsaverage which is distributed with FreeSurfer.

So mris_preproc maps the thickness maps to the subject average, while the mris_surf2surf command is for smoothing the stack of thickness maps and generates the …_sm10.mgh file.

Best, Martin

On Nov 6, 2013, at 2:07 PM, Jonathan Holt whatsdac@umich.edu wrote:

...

FS experts,

I have two questions, when running mris_preproc and mri_surf2surf should I be passing these any of the .long directories created with recon-all -long? As I read through the tutorial I’m missing their significance in the analysis section of the longitudinal stream. It seems like fsaverage is being used (I’m not sure when that was even generated)

Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m wondering where, in your tutorial examples lh.thickness_sm10.mgh comes from/is located. Found in

mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape

best,

jon

---

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---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

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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.

OH,

I see, then how would I generate my own study average, if I wanted to do so?

On Nov 6, 2013, at 2:48 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Jon,

that is just a placeholder, indicating that this can be your own average in a real study. You can simply use 'fsaverage' for it, now.

Best, Martin

On Nov 6, 2013, at 2:22 PM, Jonathan Holt whatsdac@umich.edu wrote:

...

Thanks a ton Martin,

can you possibly clue me into where I could find study_average?

best, jon On Nov 6, 2013, at 2:16 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

...

Hi Jon,

passing the --qdec-long flag to mris_preproc will automatically generate the right names (e.g. the .long. directories) and take the data from there. You can pass the study_average vie the --target flag. The default is to use fsaverage which is distributed with FreeSurfer.

So mris_preproc maps the thickness maps to the subject average, while the mris_surf2surf command is for smoothing the stack of thickness maps and generates the …_sm10.mgh file.

Best, Martin

On Nov 6, 2013, at 2:07 PM, Jonathan Holt whatsdac@umich.edu wrote:

...

FS experts,

I have two questions, when running mris_preproc and mri_surf2surf should I be passing these any of the .long directories created with recon-all -long? As I read through the tutorial I’m missing their significance in the analysis section of the longitudinal stream. It seems like fsaverage is being used (I’m not sure when that was even generated)

Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m wondering where, in your tutorial examples lh.thickness_sm10.mgh comes from/is located. Found in

mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape

best,

jon

---

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

---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

---

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.

---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

Thank you Martin,

This is more than enough.

Jon On Nov 6, 2013, at 3:42 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

Hi Jon,

Usually you would select a specific subject to be the target, sometimes that subject is in the mid age range, etc. Also sometimes people remove that subject from the study to not introduce a bias.

In most cases, however, people simply use fsaverage unless they have a reason to switch.

I don't know how you create your own 'average' surface. Maybe someone else can answer that.

Best, Martin

On 11/06/2013 02:57 PM, Jonathan Holt wrote:

...

OH,

I see, then how would I generate my own study average, if I wanted to do so?

On Nov 6, 2013, at 2:48 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

...

Hi Jon,

that is just a placeholder, indicating that this can be your own average in a real study. You can simply use 'fsaverage' for it, now.

Best, Martin

On Nov 6, 2013, at 2:22 PM, Jonathan Holt whatsdac@umich.edu wrote:

...

Thanks a ton Martin,

can you possibly clue me into where I could find study_average?

best, jon On Nov 6, 2013, at 2:16 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:

...

Hi Jon,

passing the --qdec-long flag to mris_preproc will automatically generate the right names (e.g. the .long. directories) and take the data from there. You can pass the study_average vie the --target flag. The default is to use fsaverage which is distributed with FreeSurfer.

So mris_preproc maps the thickness maps to the subject average, while the mris_surf2surf command is for smoothing the stack of thickness maps and generates the …_sm10.mgh file.

Best, Martin

On Nov 6, 2013, at 2:07 PM, Jonathan Holt whatsdac@umich.edu wrote:

...

FS experts,

I have two questions, when running mris_preproc and mri_surf2surf should I be passing these any of the .long directories created with recon-all -long? As I read through the tutorial I’m missing their significance in the analysis section of the longitudinal stream. It seems like fsaverage is being used (I’m not sure when that was even generated)

Secondly, I see that mris_preproc outputs a thickness.mgh file, but I’m wondering where, in your tutorial examples lh.thickness_sm10.mgh comes from/is located. Found in

mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex —noreshape

best,

jon

---

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

---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

---

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.

---

Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu _______________________________________________ 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.