Re: [Freesurfer] resting state motion censoring

[Douglas Greve]

I think that will work


On 4/23/18 3:08 PM, Adam Martersteck wrote:



Hi Freesurfer team & Doug,

Thought I would check in again about censoring volumes and using 
fcseedcor.


I was thinking about if it hasn't been incorporated yet -- could I 
create my own first level covariate .dat file and run fcseedcor on a 
per subject basis and pass the new .dat to xreg? I assume the .dat 
file would be difference than the one we use for selxavg3 (currently 
just passing a .dat file with just a single column of a list of 
volumes that violate criteria).


The new xreg file would have to be /m/ rows long (where /m/ is the 
number of TRs).
And if frame 119, 120, and 121 where to be excluded: then it would be 
a /m/ by 3 matrix with column 1, row 119 set to 1; row 120 column 2 
set to 1; row 121 column 3 set to 1.


Is that all correct?

Thanks,
Adam

On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck > wrote:


Hi Freesurfer team & Doug,

Just thought I'd check back in as you had asked! Any thoughts on
censoring resting state volumes for fcseedcorr?

Thanks,
Adam

On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve
> wrote:

Currently there is no way to do this. But it might not be hard
to add.
If I don't get back in a couple of weeks, send me a reminder.


On 02/14/2018 12:13 PM, Adam Martersteck wrote:
> Just a quick follow-up question,
> For FD/DVARS or other "censoring" criteria -- using -tpexclusion
> worked great for surface based analysis with mkanalsysis and
selxavg3.
> Is there a way to do this for seed-to-seed analysis (fcseedcor)?
>
> Thanks!
>
> On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve
> 
>> wrote:
>
>     Yes,you need a time point exclusion file (-tpexclude
filename
>     option to
>     mkanalysis-sess). Run mkanalysis with -help to get more
info on how to
>     create it.
>
>     On 01/25/2018 04:43 PM, Adam Martersteck wrote:
>     > Hi Freesurer experts,
>     >
>     > I’m looking to censor (drop volumes) from my resting
state fMRI time
>     > series that violate a predetermined motion and signal
threshold (FD
>     > and DVARS). I've already determined which volumes
violate X and Y
>     > criteria.
>     >
>     > Is there a way to to tell FS to "ignore" these time
points in the
>     > analysis such as in preproc-sess or mkanalysis-sess?
>     >
>     > If there is not and if I were to drop the volumes
directly from
>     the 4D
>     > file before starting any pre-processing and analysis 
– would
>     that be
>     > a problem for finding and regressing the
auto-correlation in the
>     time
>     > series?
>     >
>     > Thanks!
>     > Adam
>     >
>     >
>     > ___
>     > 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: https://gate.nmr.mgh.harvard.edu/filedrop2

>     >
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html

>   
 

Re: [Freesurfer] resting state motion censoring

[Adam Martersteck]

External Email - Use Caution

Hi Freesurfer team & Doug,

Thought I would check in again about censoring volumes and using fcseedcor.

I was thinking about if it hasn't been incorporated yet -- could I create
my own first level covariate .dat file and run fcseedcor on a per subject
basis and pass the new .dat to xreg? I assume the .dat file would be
difference than the one we use for selxavg3 (currently just passing a .dat
file with just a single column of a list of volumes that violate criteria).

The new xreg file would have to be *m* rows long (where *m* is the number
of TRs).
And if frame 119, 120, and 121 where to be excluded: then it would be a *m* by
3 matrix with column 1, row 119 set to 1; row 120 column 2 set to 1; row
121 column 3 set to 1.

Is that all correct?

Thanks,
Adam

On Thu, Mar 15, 2018 at 9:47 AM, Adam Martersteck 
wrote:

> Hi Freesurfer team & Doug,
>
> Just thought I'd check back in as you had asked! Any thoughts on censoring
> resting state volumes for fcseedcorr?
>
> Thanks,
> Adam
>
> On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Currently there is no way to do this. But it might not be hard to add.
>> If I don't get back in a couple of weeks, send me a reminder.
>>
>>
>> On 02/14/2018 12:13 PM, Adam Martersteck wrote:
>> > Just a quick follow-up question,
>> > For FD/DVARS or other "censoring" criteria -- using -tpexclusion
>> > worked great for surface based analysis with mkanalsysis and selxavg3.
>> > Is there a way to do this for seed-to-seed analysis (fcseedcor)?
>> >
>> > Thanks!
>> >
>> > On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve
>> > > wrote:
>> >
>> > Yes,you need a time point exclusion file (-tpexclude filename
>> > option to
>> > mkanalysis-sess). Run mkanalysis with -help to get more info on how
>> to
>> > create it.
>> >
>> > On 01/25/2018 04:43 PM, Adam Martersteck wrote:
>> > > Hi Freesurer experts,
>> > >
>> > > I’m looking to censor (drop volumes) from my resting state fMRI
>> time
>> > > series that violate a predetermined motion and signal threshold
>> (FD
>> > > and DVARS). I've already determined which volumes violate X and Y
>> > > criteria.
>> > >
>> > > Is there a way to to tell FS to "ignore" these time points in the
>> > > analysis such as in preproc-sess or mkanalysis-sess?
>> > >
>> > > If there is not and if I were to drop the volumes directly from
>> > the 4D
>> > > file before starting any pre-processing and analysis  – would
>> > that be
>> > > a problem for finding and regressing the auto-correlation in the
>> > time
>> > > series?
>> > >
>> > > Thanks!
>> > > Adam
>> > >
>> > >
>> > > ___
>> > > 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: 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 > vard.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
>> > 

Re: [Freesurfer] resting state motion censoring

[Adam Martersteck]

Hi Freesurfer team & Doug,

Just thought I'd check back in as you had asked! Any thoughts on censoring
resting state volumes for fcseedcorr?

Thanks,
Adam

On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve  wrote:

> Currently there is no way to do this. But it might not be hard to add.
> If I don't get back in a couple of weeks, send me a reminder.
>
>
> On 02/14/2018 12:13 PM, Adam Martersteck wrote:
> > Just a quick follow-up question,
> > For FD/DVARS or other "censoring" criteria -- using -tpexclusion
> > worked great for surface based analysis with mkanalsysis and selxavg3.
> > Is there a way to do this for seed-to-seed analysis (fcseedcor)?
> >
> > Thanks!
> >
> > On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve
> > > wrote:
> >
> > Yes,you need a time point exclusion file (-tpexclude filename
> > option to
> > mkanalysis-sess). Run mkanalysis with -help to get more info on how
> to
> > create it.
> >
> > On 01/25/2018 04:43 PM, Adam Martersteck wrote:
> > > Hi Freesurer experts,
> > >
> > > I’m looking to censor (drop volumes) from my resting state fMRI
> time
> > > series that violate a predetermined motion and signal threshold (FD
> > > and DVARS). I've already determined which volumes violate X and Y
> > > criteria.
> > >
> > > Is there a way to to tell FS to "ignore" these time points in the
> > > analysis such as in preproc-sess or mkanalysis-sess?
> > >
> > > If there is not and if I were to drop the volumes directly from
> > the 4D
> > > file before starting any pre-processing and analysis  – would
> > that be
> > > a problem for finding and regressing the auto-correlation in the
> > time
> > > series?
> > >
> > > Thanks!
> > > Adam
> > >
> > >
> > > ___
> > > 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: 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  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: 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
>
___
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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

Re: [Freesurfer] resting state motion censoring

[Douglas N Greve]

Currently there is no way to do this. But it might not be hard to add. 
If I don't get back in a couple of weeks, send me a reminder.


On 02/14/2018 12:13 PM, Adam Martersteck wrote:
> Just a quick follow-up question,
> For FD/DVARS or other "censoring" criteria -- using -tpexclusion 
> worked great for surface based analysis with mkanalsysis and selxavg3. 
> Is there a way to do this for seed-to-seed analysis (fcseedcor)?
>
> Thanks!
>
> On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve 
> > wrote:
>
> Yes,you need a time point exclusion file (-tpexclude filename
> option to
> mkanalysis-sess). Run mkanalysis with -help to get more info on how to
> create it.
>
> On 01/25/2018 04:43 PM, Adam Martersteck wrote:
> > Hi Freesurer experts,
> >
> > I’m looking to censor (drop volumes) from my resting state fMRI time
> > series that violate a predetermined motion and signal threshold (FD
> > and DVARS). I've already determined which volumes violate X and Y
> > criteria.
> >
> > Is there a way to to tell FS to "ignore" these time points in the
> > analysis such as in preproc-sess or mkanalysis-sess?
> >
> > If there is not and if I were to drop the volumes directly from
> the 4D
> > file before starting any pre-processing and analysis  – would
> that be
> > a problem for finding and regressing the auto-correlation in the
> time
> > series?
> >
> > Thanks!
> > Adam
> >
> >
> > ___
> > 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: 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.
>
>
>
>
> ___
> 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: 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/

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

Re: [Freesurfer] resting state motion censoring

[Adam Martersteck]

Just a quick follow-up question,
For FD/DVARS or other "censoring" criteria -- using -tpexclusion worked
great for surface based analysis with mkanalsysis and selxavg3. Is there a
way to do this for seed-to-seed analysis (fcseedcor)?

Thanks!

On Thu, Jan 25, 2018 at 4:00 PM, Douglas N Greve 
wrote:

> Yes,you need a time point exclusion file (-tpexclude filename option to
> mkanalysis-sess). Run mkanalysis with -help to get more info on how to
> create it.
>
> On 01/25/2018 04:43 PM, Adam Martersteck wrote:
> > Hi Freesurer experts,
> >
> > I’m looking to censor (drop volumes) from my resting state fMRI time
> > series that violate a predetermined motion and signal threshold (FD
> > and DVARS). I've already determined which volumes violate X and Y
> > criteria.
> >
> > Is there a way to to tell FS to "ignore" these time points in the
> > analysis such as in preproc-sess or mkanalysis-sess?
> >
> > If there is not and if I were to drop the volumes directly from the 4D
> > file before starting any pre-processing and analysis  – would that be
> > a problem for finding and regressing the auto-correlation in the time
> > series?
> >
> > Thanks!
> > Adam
> >
> >
> > ___
> > 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: 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.
>
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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.

Re: [Freesurfer] resting state motion censoring

[Douglas N Greve]

Yes,you need a time point exclusion file (-tpexclude filename option to 
mkanalysis-sess). Run mkanalysis with -help to get more info on how to 
create it.

On 01/25/2018 04:43 PM, Adam Martersteck wrote:
> Hi Freesurer experts,
>
> I’m looking to censor (drop volumes) from my resting state fMRI time 
> series that violate a predetermined motion and signal threshold (FD 
> and DVARS). I've already determined which volumes violate X and Y 
> criteria.
>
> Is there a way to to tell FS to "ignore" these time points in the 
> analysis such as in preproc-sess or mkanalysis-sess?
>
> If there is not and if I were to drop the volumes directly from the 4D 
> file before starting any pre-processing and analysis  – would that be 
> a problem for finding and regressing the auto-correlation in the time 
> series?
>
> Thanks!
> Adam
>
>
> ___
> 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: 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/

___
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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.