Hi Dr. Greve,

This works for me if I define seeds into subject-wise anatomical space.

Now, location of seed regions across subjects might differ because these are defined in subject-wise anatomical space. Hence subject-wise connectivity maps are generated from subject-wise seeds but these can be displayed only on fsaverage space, not on subject-wise space. That means connectivity maps are normalized here and we can do 2nd level analysis (keeping subject-wise seeds as subject-wise (not normalized)).

(a). If above points are correct, then it's fine to calculate 2nd level maps but I am not sure how seeds can be overlaid on 2nd level maps or 1st level maps because seeds are not normalized but both 1st and 2nd level connectivity maps are. Is there any way I can make sure that self connectivity is giving correlation coefficient ~1. (b). If above points are incorrect i.e. if subject-wise connectivity maps are not normalized and are in subject-wise space then (i) why can't we overlay those on subject-wise connectivity maps on subject-wise surfaces and (ii) how second level maps can be calculated from un-normalized 1st-level level maps?

For second level analysis, I am using isxconcat-sess and mri_glmfit.

Could you please clarify this for me?

Thanks, Sahil

On Tue, May 10, 2016 at 10:44 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu

wrote:

You should map the ROI into the individual subject's anatomical space, the specify the ROI when you configure the seed (eg, fcseed-config -seg ROI.mgz -segid 1 ...)

On 05/10/2016 10:37 AM, Sahil Bajaj wrote:

...

Hello all,

I am interested in importing some seed regions which are in MNI space in order to calculate functional connectivity maps. Looks like command preproc-sess doesn't normalize the BOLD data and only the regions generated by FreeSurfer LookUp table which have 'segid', can be used to calculate functional connectivity maps.

I was wondering how can I normalize the BOLD and T1w data so that I can use

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...

...

instructions to calculate functional connectivity from MNI seed regions.

Thanks, Sahil

--

Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com mailto:E-mail%3Asahil.phy@gmail.com

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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.

I already used this argument during preprocessing. According to the explanation here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr... in step-3, time-series data are sampled onto fsaverage then I am not sure why 2nd-level analysis is showing me significant self connectivity little far from the seed regions which are in subject-wise anatomical space.

On Wed, May 11, 2016 at 3:08 PM, Martin Juneja mj70481@gmail.com wrote:

I would suggest you to check if preproc is done using the argument -mni-305-2mm.

On Wed, May 11, 2016 at 12:48 PM, Sahil Bajaj sahil.brain@gmail.com wrote:

...

Hi Dr. Greve,

This works for me if I define seeds into subject-wise anatomical space.

Now, location of seed regions across subjects might differ because these are defined in subject-wise anatomical space. Hence subject-wise connectivity maps are generated from subject-wise seeds but these can be displayed only on fsaverage space, not on subject-wise space. That means connectivity maps are normalized here and we can do 2nd level analysis (keeping subject-wise seeds as subject-wise (not normalized)).

(a). If above points are correct, then it's fine to calculate 2nd level maps but I am not sure how seeds can be overlaid on 2nd level maps or 1st level maps because seeds are not normalized but both 1st and 2nd level connectivity maps are. Is there any way I can make sure that self connectivity is giving correlation coefficient ~1. (b). If above points are incorrect i.e. if subject-wise connectivity maps are not normalized and are in subject-wise space then (i) why can't we overlay those on subject-wise connectivity maps on subject-wise surfaces and (ii) how second level maps can be calculated from un-normalized 1st-level level maps?

For second level analysis, I am using isxconcat-sess and mri_glmfit.

Could you please clarify this for me?

Thanks, Sahil

On Tue, May 10, 2016 at 10:44 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:

...

You should map the ROI into the individual subject's anatomical space, the specify the ROI when you configure the seed (eg, fcseed-config -seg ROI.mgz -segid 1 ...)

On 05/10/2016 10:37 AM, Sahil Bajaj wrote:

...

Hello all,

I am interested in importing some seed regions which are in MNI space in order to calculate functional connectivity maps. Looks like command preproc-sess doesn't normalize the BOLD data and only the regions generated by FreeSurfer LookUp table which have 'segid', can be used to calculate functional connectivity maps.

I was wondering how can I normalize the BOLD and T1w data so that I can use

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...

...

instructions to calculate functional connectivity from MNI seed

regions.

...

Thanks, Sahil

--

Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com mailto:E-mail%3Asahil.phy@gmail.com

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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.

--

---

Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com E-mail%3Asahil.phy@gmail.com

---

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

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.