Hi Doug,
I was trying to run functional connectivity analysis following instructions on the FreeSurferWiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...). 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
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/FsFastFunctionalConnectivityWalkthr...). 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?
- PREPROC
preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up
- SEED CONFIG
fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config
- SEED TIMECOURSE
fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
(wm.dat and vcsf.dat were similarly created)
- 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
- 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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/FsFastFunctionalConnectivityWalkthr... ).
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?
- PREPROC
preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh -mni305-2mm -fsd bold -per-run -stc up
- SEED CONFIG
fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config
- SEED TIMECOURSE
fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config
(wm.dat and vcsf.dat were similarly created)
- 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
- 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 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.
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> 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> > 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 <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> 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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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> 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 howlow
the threshold is? See if you get something if you set the threshclose
to 0. Does this happen in the volume and the surface? Have youchecked
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/FsFastFunctionalConnectivityWalkthr... ).
> 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 -fsdbold
> -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 -surfacefsaverage
> lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsdbold
> -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> > 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 <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> 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 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
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
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> 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>>> 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>> > > 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 <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>> > > 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 > > > 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> > > > _______________________________________________ > 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 <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> 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
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 wrote:
two ways:
- run tkregister-sess to visually check them
- 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> 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.gzor
> 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>>> 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 analysisfollowing
> > instructions on the FreeSurferWiki > > > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr... ).
> > 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 -ssubject_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>> > > 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 <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>> > > 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 > > > 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> > > > _______________________________________________ > 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 <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> 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
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> 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>>> 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>>>> 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>>> > > > 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>> > <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>>> > > > > 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 > > > > > > 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>> > > 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 <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> > 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
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/FsFastFunctionalConnectivityWalkthr... ). 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 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> wrote:
two ways: 1. run tkregister-sess to visually check them 2. look at the first value in register.dof6.dat.mincost. It is hardto
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 wasaccurate?
> > > 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>>> 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>>>> 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/FsFastFunctionalConnectivityWalkthr... ).
> > > 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>>> > > > 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>> > <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>>> > > > > 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 > > > > > > 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>> > > 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 <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> > 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
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/FsFastFunctionalConnectivityWalkthr...). 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
Hi Doug,
My issue is I am not intending to use a labeled segmented ROI. My main goal is to calculate the connectivity strength between two binarized ROIs that are functionally defined. Can fcseed-config accept non Freesurfer segmented ROIs?
Thanks, JIahe
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/FsFastFunctionalConnectivityWalkthr... ).
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/FsFastFunctionalConnectivityWalkthr... ).
> > > > 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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Jiahe Zhang