[Freesurfer] Two timepoints - same subject, correlation matrix

2011-06-17 Thread Sudhin A. Shah 
Hi,

Can somebody please help me figure out how to correct this issue?

1 subject - 2 functional scans

1) run recon-all on subject anatomical.

2) process functional series (using AFNI/FSL) - each individually.

3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html)
@ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually)

This works (I don't know why since I am not doing anything to register them to 
a common space).

4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 
112 in 2nd timepoint.

I would like to get the exact same number so I can compare them! Of course I 
can manually adjust the rows/columns later, but I am not sure this is the 
smartest way to do this.

Can I do all the steps in Freesurfer?

Thank you,
S


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Re: [Freesurfer] Two timepoints - same subject, correlation matrix

2011-06-21 Thread Sudhin A. Shah 




On Jun 17, 2011, at 6:25 PM, "Sudhin A. Shah"  wrote:

> Hi,
> 
> Can somebody please help me figure out how to correct this issue?
> 
> 1 subject - 2 functional scans
> 
> 1) run recon-all on subject anatomical.
> 
> 2) process functional series (using AFNI/FSL) - each individually.
> 
> 3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html)
> @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each individually)
> 
> This works (I don't know why since I am not doing anything to register them 
> to a common space).
> 
> 4) I get a square matrix of 109 (n x n correlation matrix) in 1 timepoint and 
> 112 in 2nd timepoint.
> 
> I would like to get the exact same number so I can compare them! Of course I 
> can manually adjust the rows/columns later, but I am not sure this is the 
> smartest way to do this.
> 
> Can I do all the steps in Freesurfer?
> 
> Thank you,
> S
> ___
> 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.
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Re: [Freesurfer] Two timepoints - same subject, correlation matrix

2011-06-21 Thread Douglas N Greve 
Hi Sudhin, this looks like an AFNI question. Have you tried posting to 
the AFNI list?
doug

Sudhin A. Shah wrote:
>
>
>
>
> On Jun 17, 2011, at 6:25 PM, "Sudhin A. Shah"  > wrote:
>
>> Hi,
>>
>> Can somebody please help me figure out how to correct this issue?
>>
>> 1 subject - 2 functional scans
>>
>> 1) run recon-all on subject anatomical.
>>
>> 2) process functional series (using AFNI/FSL) - each individually.
>>
>> 3) use 
>> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html)
>> @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each 
>> individually)
>>
>> This works (I don't know why since I am not doing anything to 
>> register them to a common space).
>>
>> 4) I get a square matrix of 109 (n x n correlation matrix) in 1 
>> timepoint and 112 in 2nd timepoint.
>>
>> I would like to get the /exact same number /so I can compare them! Of 
>> course I can manually adjust the rows/columns later, but I am not 
>> sure this is the smartest way to do this.
>>
>> Can I do all the steps in Freesurfer?
>>
>> Thank you,
>> S
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to 
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and 
>> the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to 
>> you in error
>> but does not contain patient information, please contact the sender 
>> and properly
>> dispose of the e-mail.
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Two timepoints - same subject, correlation matrix

2011-06-22 Thread Sudhin A. Shah 
Hi,

So I think I found the solution - 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical)

reg-feat2anat 
aseg2feat or aparc2feat

New question:
Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical 
and cortical segmentations registered to functional space?

Thanks,
S

On 06/21/11, Douglas N Greve   wrote:
> 
> Hi Sudhin, this looks like an AFNI question. Have you tried posting to 
> the AFNI list?
> doug
> 
> Sudhin A. Shah wrote:
> >
> >
> >
> >
> > On Jun 17, 2011, at 6:25 PM, "Sudhin A. Shah"  > > wrote:
> >
> >> Hi,
> >>
> >> Can somebody please help me figure out how to correct this issue?
> >>
> >> 1 subject - 2 functional scans
> >>
> >> 1) run recon-all on subject anatomical.
> >>
> >> 2) process functional series (using AFNI/FSL) - each individually.
> >>
> >> 3) use 
> >> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) 
> >> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29)
> >> @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each 
> >> individually)
> >>
> >> This works (I don't know why since I am not doing anything to 
> >> register them to a common space).
> >>
> >> 4) I get a square matrix of 109 (n x n correlation matrix) in 1 
> >> timepoint and 112 in 2nd timepoint.
> >>
> >> I would like to get the /exact same number /so I can compare them! Of 
> >> course I can manually adjust the rows/columns later, but I am not 
> >> sure this is the smartest way to do this.
> >>
> >> Can I do all the steps in Freesurfer?
> >>
> >> Thank you,
> >> S
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu  >> >
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> >> (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 
> >> (http://www.partners.org/complianceline) . If the e-mail was sent to 
> >> you in error
> >> but does not contain patient information, please contact the sender 
> >> and properly
> >> dispose of the e-mail.
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> 

-- 
Sudhin A. Shah
Postdoctoral Fellow
Laboratory of Cognitive Neuromodulation
Weill Cornell Medical College, NY,NY
(212) 746-4514


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Re: [Freesurfer] Two timepoints - same subject, correlation matrix

2011-06-22 Thread Sudhin A. Shah 
Got it :
aseg2feat --feat featdir --seg aparc+aseg


On 06/22/11, "Sudhin A. Shah"   wrote:
> 
> 
> Hi,
> 
> So I think I found the solution - 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical)
> 
> reg-feat2anat 
> aseg2feat or aparc2feat
> 
> New question:
> Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical 
> and cortical segmentations registered to functional space?
> 
> Thanks,
> S
> 
> On 06/21/11, Douglas N Greve   wrote:
> > 
> > Hi Sudhin, this looks like an AFNI question. Have you tried posting to 
> > the AFNI list?
> > doug
> > 
> > Sudhin A. Shah wrote:
> > >
> > >
> > >
> > >
> > > On Jun 17, 2011, at 6:25 PM, "Sudhin A. Shah"  > > > wrote:
> > >
> > >> Hi,
> > >>
> > >> Can somebody please help me figure out how to correct this issue?
> > >>
> > >> 1 subject - 2 functional scans
> > >>
> > >> 1) run recon-all on subject anatomical.
> > >>
> > >> 2) process functional series (using AFNI/FSL) - each individually.
> > >>
> > >> 3) use 
> > >> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html) 
> > >> (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html%29)
> > >> @ROI_Corr_Mat -ts proc_func1 -roi aparc+aseg -prefix all (each 
> > >> individually)
> > >>
> > >> This works (I don't know why since I am not doing anything to 
> > >> register them to a common space).
> > >>
> > >> 4) I get a square matrix of 109 (n x n correlation matrix) in 1 
> > >> timepoint and 112 in 2nd timepoint.
> > >>
> > >> I would like to get the /exact same number /so I can compare them! Of 
> > >> course I can manually adjust the rows/columns later, but I am not 
> > >> sure this is the smartest way to do this.
> > >>
> > >> Can I do all the steps in Freesurfer?
> > >>
> > >> Thank you,
> > >> S
> > >> ___
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu  > >> >
> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > >> (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 
> > >> (http://www.partners.org/complianceline) . If the e-mail was sent to 
> > >> you in error
> > >> but does not contain patient information, please contact the sender 
> > >> and properly
> > >> dispose of the e-mail.
> > > 
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> > 
> > -- 
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422
> > 
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> > (https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)
> > 
> 
> -- 
> Sudhin A. Shah
> Postdoctoral Fellow
> Laboratory of Cognitive Neuromodulation
> Weill Cornell Medical College, NY,NY
> (212) 746-4514
> 

-- 
Sudhin A. Shah
Postdoctoral Fellow
Laboratory of Cognitive Neuromodulation
Weill Cornell Medical College, NY,NY
(212) 746-4514


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