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/FsFastFunctionalConnectivityWalkthrough
> 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

_______________________________________________
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.