On Fri, Sep 12, 2014 at 11:08 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

You need to have your ROI as a segmentation in the anatomical
(conformed) space. If it is a label on the surface, you can use
mri_label2vol to turn it into a volume (make sure to use --proj frac 0 1
.1 to fill the ribbon). When you run funcroi-config specify -seg
yourseg.mgz 1 where yourseg.mgz is the output of mri_label2vol and "1"
refers to the fact that the output volume is a binary mask where your
ROI is 1 and everything else is 0

doug

On 09/12/2014 09:05 AM, Jiahe Zhang wrote:
> Hi Doug,
>
> I was able to get the surface connectivity analysis to run
> successfully for the L.Cingulate example that you posted online
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
> For my own analysis, I'm hoping to use my own functionally defined
> ROIs instead of freesurfer segmented regions. For that, do I pass a
> vol2surf command on my spherical ROIs and then run the same analysis?
> I saw that to prepare a ROI for this kind of analysis, I need to
> create a configuration file using funcroi-config, but this command
> seems to use anatomical ROIs based on freesurfer segmentation again.
>
> Could you advise how to proceed?
>
> Thanks,
> Jiahe
>
>
> On Mon, Aug 11, 2014 at 5:18 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> How did you look at fmcpr.up.sm6.fsaverage.lh.nii.gz? If you did
> not do
> this, try it
>
> tksurfer fsaverage lh inflated -ov fmcpr.up.sm6.fsaverage.lh.nii.gz -t
> fmcpr.up.sm6.fsaverage.lh.nii.gz
>
> This will bring up an overlay as well as a time course
>
>
> On 08/11/2014 05:05 PM, Jiahe Zhang wrote:
> > Both looked fine. First value in .mincost is .45
> >
> >
> > On Mon, Aug 11, 2014 at 4:51 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > two ways:
> >
> > 1. run tkregister-sess to visually check them
> > 2. look at the first value in register.dof6.dat.mincost. It
> is hard to
> > say what a threshold is for a good registration, but typical
> > values are
> > about .5 or so. If it is .8 or more, it is probably a
> problem (and
> > probably the initialization is not good)
> >
> >
> > On 08/11/2014 04:35 PM, Jiahe Zhang wrote:
> > > I'm not sure how to check the registration. I see a
> > register.dof6.dat
> > > being produced for each run but I can't tell if it
> contains the
> > > correct parameters. How can I tell if the registration was
> accurate?
> > >
> > >
> > > On Mon, Aug 11, 2014 at 4:01 PM, Douglas N Greve
> > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>

> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> > >
> > > did you check the registration?
> > >
> > > On 08/11/2014 03:53 PM, Jiahe Zhang wrote:
> > > > There's nothing even when the threshold is set to 0.
> > > >
> > > > I just checked the preprocessing outputs. I can see
> > normal-looking
> > > > volumes
> > > > fmcpr.nii.gz
> > > > fmcpr.up.nii.gz
> > > > fmcpr.up.sm6.mni305.2mm.nii.gz
> > > >
> > > > But there is nothing when I open
> > fmcpr.up.sm6.fsaverage.lh.nii.gz or
> > > > fmcpr.up.sm6.fsaverage.rh.nii.gz
> > > >
> > > >
> > > >
> > > >
> > > > On Wed, Aug 6, 2014 at 6:40 PM, Douglas N Greve
> > > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:
> > > >
> > > >
> > > > When you say that they are "empty" what do you
> mean? That
> > > there is
> > > > nothing above threshold or that there is nothing
> > regardless
> > > of how low
> > > > the threshold is? See if you get something if
> you set the
> > > thresh close
> > > > to 0. Does this happen in the volume and the
> surface? Have
> > > you checked
> > > > the registration to assure that it is accurate?
> > > >
> > > > On 08/06/2014 06:33 PM, Jiahe Zhang wrote:
> > > > > Hi Doug,
> > > > >
> > > > > I was trying to run functional connectivity
> analysis
> > following
> > > > > instructions on the FreeSurferWiki
> > > > >
> > > >
> > >
> >
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough).
> > > > > I was able to successfully run the following
> > commands (nothing
> > > > errored
> > > > > as far as I can tell) but the resulting partial
> > > correlation and
> > > > > significance maps turned out to be empty.
> Could you
> > take a
> > > look
> > > > at the
> > > > > commands and let me know if anything can be
> improved?
> > > > >
> > > > > 1. PREPROC
> > > > > preproc-sess -s subject_001 -fwhm 6 -surface
> > fsaverage lhrh
> > > > > -mni305-2mm -fsd bold -per-run -stc up
> > > > >
> > > > > 2. SEED CONFIG
> > > > > fcseed-config -segid 1010 -fcname
> > L_Posteriorcingulate.dat
> > > -fsd bold
> > > > > -mean -cfg mean.L_Posteriorcingulate.config
> > > > >
> > > > > 3. SEED TIMECOURSE
> > > > > fcseed-sess -s subject_001 -cfg
> > > mean.L_Posteriorcingulate.config
> > > > >
> > > > > (wm.dat and vcsf.dat were similarly created)
> > > > >
> > > > > 4. ANALYSIS CONFIG
> > > > > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf
> > -surface
> > > fsaverage
> > > > > lh -fwhm 6 -notask -taskreg
> L_Posteriorcingulate.dat 1
> > > -nuisreg
> > > > > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5
> > -nskip 4
> > > -fsd bold
> > > > > -TR 5 -per-run -lpf .1
> > > > >
> > > > > 5. ANALYSIS
> > > > > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s
> > subject_001
> > > > >
> > > > > Thanks,
> > > > > Jiahe
> > > > >
> > > > >
> > > > > --
> > > > > Jiahe Zhang
> > > > > Ph.D. Student
> > > > > Department of Psychology
> > > > > Northeastern University
> > > > > 617-373-4789
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > Freesurfer mailing list
> > > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>
> > > > Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>>>
> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358>

> > <tel:617-724-2358 <tel:617-724-2358>>>>
> > > > Fax: 617-726-7422 <tel:617-726-7422>
> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
> <tel:617-726-7422>
> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422

> <tel:617-726-7422>
> > > <tel:617-726-7422 <tel:617-726-7422>>>
> > > >
> > > > Bugs:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > > >
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > >
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > > >
> > <http://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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>

> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu

> <mailto: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.
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jiahe Zhang
> > > > Ph.D. Student
> > > > Department of Psychology
> > > > Northeastern University
> > > > 617-373-4789 <tel:617-373-4789> <tel:617-373-4789
> > <tel:617-373-4789>>
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>

> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > Phone Number: 617-724-2358 <tel:617-724-2358>
> > <tel:617-724-2358 <tel:617-724-2358>>
> > > Fax: 617-726-7422 <tel:617-726-7422>
> > >
> > > Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > >
> <http://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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >
> > >
> > > --
> > > Jiahe Zhang
> > > Ph.D. Student
> > > Department of Psychology
> > > Northeastern University
> > > 617-373-4789
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358

> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> >
> > --
> > Jiahe Zhang
> > Ph.D. Student
> > Department of Psychology
> > Northeastern University
> > 617-373-4789
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto: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 <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> --
> Jiahe Zhang
> Ph.D. Student
> Department of Psychology
> Northeastern University
> 617-373-4789
>
>
> _______________________________________________
> 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

Jiahe Zhang

Ph.D. Student

Department of Psychology

Northeastern University

617-373-4789