[Freesurfer] Qdec questions

[sabin khadka]

Hi all - When you get a significant cluster after doing monte-carlo simulation, 
we get peak vertex/Talairach coordinates and also saved in *summary files. Is 
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the 
significant clusters?

Thanks
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Re: [Freesurfer] Qdec Questions

[Douglas N Greve]

In your case you have HC listed first, so red/yellow means HC>SAD, blue 
means SAD>HC
doug





On 10/29/2013 11:03 PM, Ashley Shurick wrote:
> Hi Doug,
>
> Apologies, but I have a rather easy follow-up question that I can't 
> figure out:
>
> How do you interpret the effect in each significant region? A previous 
> post suggests using ctrl + left mouse click on a blob and examining 
> the plot of the data. However, for the model I am looking at ("Does 
> the thickness-ERQ correlation differ between HC and SAD?") I still 
> can't determine if cortical thinning represents HC attaching a representative plot here.
>
> Thank you,
>
> Ashley
>
>
> On Tue, Oct 29, 2013 at 10:25 AM, Ashley Shurick 
> mailto:ashley.shur...@gmail.com>> wrote:
>
> Thank you!
>
>
> On Tue, Oct 29, 2013 at 10:19 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> On 10/29/2013 01:10 PM, Ashley Shurick wrote:
> > Hi all,
> >
> > I'm running analyses in Qdec and want to verify a few things:
> >
> > 1. When comparing two groups (HC vs patients) I am including
> mean
> > cortical thickness as a covariate, using the following equation:
> >
> >
> > bh.thickness = (lh.thickness*lh.surfarea +
> rh.thickness*rh.surfarea) /
> > (lh.surfarea + rh.surfarea)
> >
> >
> > Is this the best way to calculate global mean thickness?
> Yes
> >
> >
> > 2. I want to regress out any effects of age, therefore I need to
> > demean the ages for my groups as a whole, and not perform this
> > calculation on each group separately, correct?
> Yes, in which case the test of the difference between groups
> will be
> done at an age equal to the mean of the ages.
> >
> > 3. I'm including questionnaires as a covariate of interest -
> do I need
> > to demean these values as well?
> When you do a test on a continuous covariate, that test will be
> unaffected by demeaning of the covariate. Demeaning will
> affect the
> difference between groups if you use a separate covariate for each
> group. If you have a single covariate across groups, demeaning
> will have
> no effect.
>
> doug
> >
> >
> > Thank you in advance for your help!
> >
> >
> > Ashley
> >
> >
> > --
> > Ashley A. Shurick
> > Ph.D. Candidate
> > Department of Psychology
> > Stanford University
> >
> >
> > ___
> > 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.
>
>
>

-- 
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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Re: [Freesurfer] Qdec Questions

[Douglas N Greve]

On 10/29/2013 01:10 PM, Ashley Shurick wrote:
> Hi all,
>
> I'm running analyses in Qdec and want to verify a few things:
>
> 1. When comparing two groups (HC vs patients) I am including mean 
> cortical thickness as a covariate, using the following equation:
>
>
> bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) / 
> (lh.surfarea + rh.surfarea)
>
>
> Is this the best way to calculate global mean thickness?
Yes
>
>
> 2. I want to regress out any effects of age, therefore I need to 
> demean the ages for my groups as a whole, and not perform this 
> calculation on each group separately, correct?
Yes, in which case the test of the difference between groups will be 
done at an age equal to the mean of the ages.
>
> 3. I'm including questionnaires as a covariate of interest - do I need 
> to demean these values as well?
When you do a test on a continuous covariate, that test will be 
unaffected by demeaning of the covariate. Demeaning will affect the 
difference between groups if you use a separate covariate for each 
group. If you have a single covariate across groups, demeaning will have 
no effect.

doug
>
>
> Thank you in advance for your help!
>
>
> Ashley
>
>
> -- 
> Ashley A. Shurick
> Ph.D. Candidate
> Department of Psychology
> Stanford University
>
>
> ___
> 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] Qdec Questions

[Ashley Shurick]

Hi all,

I'm running analyses in Qdec and want to verify a few things:

1. When comparing two groups (HC vs patients) I am including mean cortical
thickness as a covariate, using the following equation:


bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) /
(lh.surfarea + rh.surfarea)


Is this the best way to calculate global mean thickness?


2. I want to regress out any effects of age, therefore I need to demean the
ages for my groups as a whole, and not perform this calculation on each
group separately, correct?

3. I'm including questionnaires as a covariate of interest - do I need to
demean these values as well?


Thank you in advance for your help!


Ashley


-- 
Ashley A. Shurick
Ph.D. Candidate
Department of Psychology
Stanford University
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Re: [Freesurfer] QDEC questions

[Nick Schmansky]

Tudor,

To follow-up on the repeated analysis question: each 'Design' can be
named by changing the 'Design Name' text box on the 'Design' tab from
something other than 'Untitled', which has the effect of saving all
results to a directory of that name, so that you can revisit them later
(by loading results in freeview for instance).

Nick


On Thu, 2013-04-18 at 20:12 -0400, Douglas N Greve wrote:
> Here's part 1. I'll write until I have to catch my shuttle, answer the 
> rest tomorrow ...
> 
> On 04/18/2013 05:27 PM, Tudor Popescu wrote:
> > Apologies for my previous long email; if anyone gets a chance to look 
> > over the questions I'd be really grateful!
> > Many thanks indeed,
> > Tudor
> >
> > On 16 April 2013 19:40, Tudor Popescu  > > wrote:
> >
> > Thanks Nick, (and thanks Doug too for the answer to question 2.)
> >
> > It must indeed have been a disk-space issue, as running the
> > -qcache again, after clearing up some space, produced all the
> > expected .mgh files
> >
> > If I can follow up on two of my previous questions:
> >
> > 3) Not sure I understand your answer. So it seems discrete
> > variables, such as gender, cannot be taken as covariates or
> > nuisance variables, only as factors. But users might want to take
> > some discrete variables as covariates, rather than as factors, as
> > I might not be interested in their direct effect on the brain
> > measure but simply want to parcel out the variance that they
> > contribute. Are you suggesting that they should be taken as
> > factors even if they aren't of interest?
> >
> Yes. There is no real distinction between between something that is of 
> interest and something that is not. The way the software is set up, the 
> continuous factors can be listed as nuisance and get around the 
> limitation of only have two covariates.
> >
> >
> > 4) Does the ideal value of FWHM depend on the blob size in the
> > sense that if one expects small blobs in the results (how small?),
> > then one should use small FWHMs in QDEC, and large FWHMs if
> > expecting large blobs?
> >
> Yes.
> >
> >
> > I apologise for the amount of questions I keep asking, but I have
> > a few more:
> >
> > A) When trying repeated analyses (designs) in QDEC, do I need to
> > delete the output files of previous analyses, and/or restart QDEC
> > every time? Or are the results of each analysis displayed
> > correctly independently of previously-made analyses in the same
> > QDEC session? I'm asking because I see that, once the "Set using
> > FDR" button is pressed, the corrected t threshold remains in use
> > for subsequent analyses, but after restarting QDEC and redoing the
> > last analysis, the t threshold is no longer the same
> >
> Not sure, have to check. I think you can name the output folders 
> differently for each analysis. If you do not change the name, then the 
> output is totally deleted and recreated.
> >
> >
> > B) Must all QDEC analyses always be done for the two hemispheres
> > separately? Is there no analysis that can be done on the whole
> > brain, such that the t-value thresholds are FDR-corrected at the
> > whole-brain level?
> >
> There is none.
> >
> >
> > C) I would like to extract the cortical thickness of several
> > cortical ROIs including the IPS, IFG and SPL; I didn’t know
> > whether the Desikan-Killiany or the Destrieux atlas would be more
> > appropriate, but I tried the command given here
> > 
> > ,
> > hoping to obtain a table with the thickness of all ROIs from the
> > parcelation corresponding to the Destrieux atlas. However,
> > although the command results in the message "
> > lh.aparc.a2009.thickness.table", I found no such file anywhere in
> > my $SUBJECTS_DIR
> >
> Did it go into the directory that you ran the command from?
> >
> >
> > D) How should a regression-type analysis be made in QDEC, i.e. one
> > where I have a continuous predictor such as behavioural score,
> > whose correlation with the brain measure (cortical thickness) I
> > want to compare between my two groups? Because of QDEC's
> > preference for discrete variables as factors, it seems that only
> > ANOVA-type analyses can be done (i.e. effect of discrete factor(s)
> > on brain measure), rather than regression-type (i.e. correlation
> > between continuous factor and brain measure)
> >
> Enter it in as a covariate (continuous factor). QDEC will automatically 
> produce a contrast testing the difference in thickness/score slopes (ie, 
> an interaction between group factor and continuous factor).
> >
> >
> > E) The average brain with inflated cortex that results are
> > projected on – is this the same average that is 

Re: [Freesurfer] QDEC questions

[Douglas N Greve]

Here's part 1. I'll write until I have to catch my shuttle, answer the 
rest tomorrow ...

On 04/18/2013 05:27 PM, Tudor Popescu wrote:
> Apologies for my previous long email; if anyone gets a chance to look 
> over the questions I'd be really grateful!
> Many thanks indeed,
> Tudor
>
> On 16 April 2013 19:40, Tudor Popescu  > wrote:
>
> Thanks Nick, (and thanks Doug too for the answer to question 2.)
>
> It must indeed have been a disk-space issue, as running the
> -qcache again, after clearing up some space, produced all the
> expected .mgh files
>
> If I can follow up on two of my previous questions:
>
> 3) Not sure I understand your answer. So it seems discrete
> variables, such as gender, cannot be taken as covariates or
> nuisance variables, only as factors. But users might want to take
> some discrete variables as covariates, rather than as factors, as
> I might not be interested in their direct effect on the brain
> measure but simply want to parcel out the variance that they
> contribute. Are you suggesting that they should be taken as
> factors even if they aren't of interest?
>
Yes. There is no real distinction between between something that is of 
interest and something that is not. The way the software is set up, the 
continuous factors can be listed as nuisance and get around the 
limitation of only have two covariates.
>
>
> 4) Does the ideal value of FWHM depend on the blob size in the
> sense that if one expects small blobs in the results (how small?),
> then one should use small FWHMs in QDEC, and large FWHMs if
> expecting large blobs?
>
Yes.
>
>
> I apologise for the amount of questions I keep asking, but I have
> a few more:
>
> A) When trying repeated analyses (designs) in QDEC, do I need to
> delete the output files of previous analyses, and/or restart QDEC
> every time? Or are the results of each analysis displayed
> correctly independently of previously-made analyses in the same
> QDEC session? I'm asking because I see that, once the "Set using
> FDR" button is pressed, the corrected t threshold remains in use
> for subsequent analyses, but after restarting QDEC and redoing the
> last analysis, the t threshold is no longer the same
>
Not sure, have to check. I think you can name the output folders 
differently for each analysis. If you do not change the name, then the 
output is totally deleted and recreated.
>
>
> B) Must all QDEC analyses always be done for the two hemispheres
> separately? Is there no analysis that can be done on the whole
> brain, such that the t-value thresholds are FDR-corrected at the
> whole-brain level?
>
There is none.
>
>
> C) I would like to extract the cortical thickness of several
> cortical ROIs including the IPS, IFG and SPL; I didn’t know
> whether the Desikan-Killiany or the Destrieux atlas would be more
> appropriate, but I tried the command given here
> 
> ,
> hoping to obtain a table with the thickness of all ROIs from the
> parcelation corresponding to the Destrieux atlas. However,
> although the command results in the message "
> lh.aparc.a2009.thickness.table", I found no such file anywhere in
> my $SUBJECTS_DIR
>
Did it go into the directory that you ran the command from?
>
>
> D) How should a regression-type analysis be made in QDEC, i.e. one
> where I have a continuous predictor such as behavioural score,
> whose correlation with the brain measure (cortical thickness) I
> want to compare between my two groups? Because of QDEC's
> preference for discrete variables as factors, it seems that only
> ANOVA-type analyses can be done (i.e. effect of discrete factor(s)
> on brain measure), rather than regression-type (i.e. correlation
> between continuous factor and brain measure)
>
Enter it in as a covariate (continuous factor). QDEC will automatically 
produce a contrast testing the difference in thickness/score slopes (ie, 
an interaction between group factor and continuous factor).
>
>
> E) The average brain with inflated cortex that results are
> projected on – is this the same average that is normally used in
> most papers, or does the inflating algorithm differ? And is the
> colour-coding the same (dark gray = sulci, light gray = gyri)?
>
It is mostly the same. Some papers may display on the pial or the white 
or do a custom inflation to keep some of the gyral shape instead of 
having it so smooth. The colors I assume are the same.

whew! made it through all of them before my shuttle.
doug

>
>
>
> On 15 April 2013 23:52, Nick Schmansky  > wrote:
>
> Tudor,
>
> In the recon-all.log, it has this line:
> ER

Re: [Freesurfer] QDEC questions

[Tudor Popescu]

Apologies for my previous long email; if anyone gets a chance to look over
the questions I'd be really grateful!
Many thanks indeed,
Tudor

On 16 April 2013 19:40, Tudor Popescu  wrote:

> Thanks Nick, (and thanks Doug too for the answer to question 2.)
>
> It must indeed have been a disk-space issue, as running the -qcache again,
> after clearing up some space, produced all the expected .mgh files
>
> If I can follow up on two of my previous questions:
>
> 3) Not sure I understand your answer. So it seems discrete variables, such
> as gender, cannot be taken as covariates or nuisance variables, only as
> factors. But users might want to take some discrete variables as
> covariates, rather than as factors, as I might not be interested in their
> direct effect on the brain measure but simply want to parcel out the
> variance that they contribute. Are you suggesting that they should be taken
> as factors even if they aren't of interest?
>
> 4) Does the ideal value of FWHM depend on the blob size in the sense that
> if one expects small blobs in the results (how small?), then one should use
> small FWHMs in QDEC, and large FWHMs if expecting large blobs?
>
> I apologise for the amount of questions I keep asking, but I have a few
> more:
>
> A) When trying repeated analyses (designs) in QDEC, do I need to delete
> the output files of previous analyses, and/or restart QDEC every time? Or
> are the results of each analysis displayed correctly independently of
> previously-made analyses in the same QDEC session? I'm asking because I see
> that, once the "Set using FDR" button is pressed, the corrected t threshold
> remains in use for subsequent analyses, but after restarting QDEC and
> redoing the last analysis, the t threshold is no longer the same
>
> B) Must all QDEC analyses always be done for the two hemispheres
> separately? Is there no analysis that can be done on the whole brain, such
> that the t-value thresholds are FDR-corrected at the whole-brain level?
>
> C) I would like to extract the cortical thickness of several cortical ROIs
> including the IPS, IFG and SPL; I didn’t know whether the Desikan-Killiany
> or the Destrieux atlas would be more appropriate, but I tried the command
> given 
> here,
> hoping to obtain a table with the thickness of all ROIs from the
> parcelation corresponding to the Destrieux atlas. However, although the
> command results in the message " lh.aparc.a2009.thickness.table", I found
> no such file anywhere in my $SUBJECTS_DIR
>
> D) How should a regression-type analysis be made in QDEC, i.e. one where I
> have a continuous predictor such as behavioural score, whose correlation
> with the brain measure (cortical thickness) I want to compare between my
> two groups? Because of QDEC's preference for discrete variables as factors,
> it seems that only ANOVA-type analyses can be done (i.e. effect of discrete
> factor(s) on brain measure), rather than regression-type (i.e. correlation
> between continuous factor and brain measure)
>
> E) The average brain with inflated cortex that results are projected on –
> is this the same average that is normally used in most papers, or does the
> inflating algorithm differ? And is the colour-coding the same (dark gray =
> sulci, light gray = gyri)?
>
>
>
> On 15 April 2013 23:52, Nick Schmansky  wrote:
>
>> Tudor,
>>
>> In the recon-all.log, it has this line:
>> ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
>>
>> but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
>> correctly, so this indicates to me that it might have run out of disk
>> space.  is that the case?
>>
>> to answer the others:
>> 2. not sure
>> 3. you can select discrete can a regular variate along with your main
>> variate.  'nuisance' variates are like any other.
>> 4. depends on the expected 'blob' size
>> 5. the selection of fwhm in qdec corresponds directly with the values
>> selected by qcache (they are one-to-one related, ie the 10mm fwhm values
>> created by qcache are used by the 10mm fwhm selection in qdec).
>>
>> Nick
>>
>>
>>
>> On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
>> > Dear experts,
>> >
>> > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
>> > misbehaving, and so after running a first whole-brain group cortical
>> > thickness analysis on my structural data, I have some questions:
>> >
>> > 1. After running recon-all with the –qcache flag (i.e. presmoothing),
>> > files of the type lh.thickness.*.mgh were created for all 38 subjects
>> > (19 in each group), however files of the type rh.thickness.*.mgh were
>> > not created for 5 out of the 19 subjects of the first group. Log files
>> > recon-all-status.log and recon-all.log (attached, for one of those 5
>> > subjects) both mention that the process ran on Mar22nd ended with
>> > errors, although I can't quite see what

Re: [Freesurfer] QDEC questions

[Tudor Popescu]

Thanks Nick, (and thanks Doug too for the answer to question 2.)

It must indeed have been a disk-space issue, as running the -qcache again,
after clearing up some space, produced all the expected .mgh files

If I can follow up on two of my previous questions:

3) Not sure I understand your answer. So it seems discrete variables, such
as gender, cannot be taken as covariates or nuisance variables, only as
factors. But users might want to take some discrete variables as
covariates, rather than as factors, as I might not be interested in their
direct effect on the brain measure but simply want to parcel out the
variance that they contribute. Are you suggesting that they should be taken
as factors even if they aren't of interest?

4) Does the ideal value of FWHM depend on the blob size in the sense that
if one expects small blobs in the results (how small?), then one should use
small FWHMs in QDEC, and large FWHMs if expecting large blobs?

I apologise for the amount of questions I keep asking, but I have a few
more:

A) When trying repeated analyses (designs) in QDEC, do I need to delete the
output files of previous analyses, and/or restart QDEC every time? Or are
the results of each analysis displayed correctly independently of
previously-made analyses in the same QDEC session? I'm asking because I see
that, once the "Set using FDR" button is pressed, the corrected t threshold
remains in use for subsequent analyses, but after restarting QDEC and
redoing the last analysis, the t threshold is no longer the same

B) Must all QDEC analyses always be done for the two hemispheres
separately? Is there no analysis that can be done on the whole brain, such
that the t-value thresholds are FDR-corrected at the whole-brain level?

C) I would like to extract the cortical thickness of several cortical ROIs
including the IPS, IFG and SPL; I didn’t know whether the Desikan-Killiany
or the Destrieux atlas would be more appropriate, but I tried the command
given 
here,
hoping to obtain a table with the thickness of all ROIs from the
parcelation corresponding to the Destrieux atlas. However, although the
command results in the message " lh.aparc.a2009.thickness.table", I found
no such file anywhere in my $SUBJECTS_DIR

D) How should a regression-type analysis be made in QDEC, i.e. one where I
have a continuous predictor such as behavioural score, whose correlation
with the brain measure (cortical thickness) I want to compare between my
two groups? Because of QDEC's preference for discrete variables as factors,
it seems that only ANOVA-type analyses can be done (i.e. effect of discrete
factor(s) on brain measure), rather than regression-type (i.e. correlation
between continuous factor and brain measure)

E) The average brain with inflated cortex that results are projected on –
is this the same average that is normally used in most papers, or does the
inflating algorithm differ? And is the colour-coding the same (dark gray =
sulci, light gray = gyri)?


On 15 April 2013 23:52, Nick Schmansky  wrote:

> Tudor,
>
> In the recon-all.log, it has this line:
> ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
>
> but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
> correctly, so this indicates to me that it might have run out of disk
> space.  is that the case?
>
> to answer the others:
> 2. not sure
> 3. you can select discrete can a regular variate along with your main
> variate.  'nuisance' variates are like any other.
> 4. depends on the expected 'blob' size
> 5. the selection of fwhm in qdec corresponds directly with the values
> selected by qcache (they are one-to-one related, ie the 10mm fwhm values
> created by qcache are used by the 10mm fwhm selection in qdec).
>
> Nick
>
>
>
> On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
> > Dear experts,
> >
> > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
> > misbehaving, and so after running a first whole-brain group cortical
> > thickness analysis on my structural data, I have some questions:
> >
> > 1. After running recon-all with the –qcache flag (i.e. presmoothing),
> > files of the type lh.thickness.*.mgh were created for all 38 subjects
> > (19 in each group), however files of the type rh.thickness.*.mgh were
> > not created for 5 out of the 19 subjects of the first group. Log files
> > recon-all-status.log and recon-all.log (attached, for one of those 5
> > subjects) both mention that the process ran on Mar22nd ended with
> > errors, although I can't quite see what that was
> >
> >
> >
> > 2. When I take age as a continuous factor (covariate), the list of
> > clusters in my results look dramatically different from the clusters
> > that I get for the same contrast ran without the covariate. Why is
> > that, given that normally adding a covariate very rarely changes the
> > results by a great

Re: [Freesurfer] QDEC questions

[Douglas Greve]

For #2, it is hard to say without seeing the design. I would not say 
that covariates should not change the results (otherwise one would not 
add them), especially age. If you have a balanced design, then one would 
hope that adding age would reduce the residual noise and show more of an 
effect. But if you have a very narrow age range, then "age" can look 
like a constant which would be colinear with the actual group 
designations and so reduce activation.
doug



On 4/15/13 5:52 PM, Nick Schmansky wrote:
> Tudor,
>
> In the recon-all.log, it has this line:
> ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
>
> but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
> correctly, so this indicates to me that it might have run out of disk
> space.  is that the case?
>
> to answer the others:
> 2. not sure
> 3. you can select discrete can a regular variate along with your main
> variate.  'nuisance' variates are like any other.
> 4. depends on the expected 'blob' size
> 5. the selection of fwhm in qdec corresponds directly with the values
> selected by qcache (they are one-to-one related, ie the 10mm fwhm values
> created by qcache are used by the 10mm fwhm selection in qdec).
>
> Nick
>
>
>
> On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
>> Dear experts,
>>
>> Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
>> misbehaving, and so after running a first whole-brain group cortical
>> thickness analysis on my structural data, I have some questions:
>>
>> 1. After running recon-all with the –qcache flag (i.e. presmoothing),
>> files of the type lh.thickness.*.mgh were created for all 38 subjects
>> (19 in each group), however files of the type rh.thickness.*.mgh were
>> not created for 5 out of the 19 subjects of the first group. Log files
>> recon-all-status.log and recon-all.log (attached, for one of those 5
>> subjects) both mention that the process ran on Mar22nd ended with
>> errors, although I can't quite see what that was
>>
>>
>>
>> 2. When I take age as a continuous factor (covariate), the list of
>> clusters in my results look dramatically different from the clusters
>> that I get for the same contrast ran without the covariate. Why is
>> that, given that normally adding a covariate very rarely changes the
>> results by a great deal? Also in my case, I had quite a narrow (and
>> well-balanced between the groups) age range!
>>
>>   
>>
>> 3. I know that discrete factors cannot be taken as nuisance factors,
>> but it seems they also can't be taken as covariates. How does one,
>> then, control for the effects of e.g. gender in a group comparison?
>>
>>
>> 4. When should values other than 10 be used for the FWHM parameter of
>> the smoothing?
>>
>>
>> 5. How come QDEC allows you to set the FWHM parameter, when in fact it
>> is also set in the qcache stage of recon-all, which precedes QDEC?
>>
>>
>> Many thanks in advance!!
>>
>> Tudor
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
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>
>

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Re: [Freesurfer] QDEC questions

[Nick Schmansky]

Tudor,

In the recon-all.log, it has this line:
ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh

but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
correctly, so this indicates to me that it might have run out of disk
space.  is that the case?

to answer the others:
2. not sure
3. you can select discrete can a regular variate along with your main
variate.  'nuisance' variates are like any other.
4. depends on the expected 'blob' size
5. the selection of fwhm in qdec corresponds directly with the values
selected by qcache (they are one-to-one related, ie the 10mm fwhm values
created by qcache are used by the 10mm fwhm selection in qdec).

Nick



On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
> Dear experts,
> 
> Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
> misbehaving, and so after running a first whole-brain group cortical
> thickness analysis on my structural data, I have some questions:
> 
> 1. After running recon-all with the –qcache flag (i.e. presmoothing),
> files of the type lh.thickness.*.mgh were created for all 38 subjects
> (19 in each group), however files of the type rh.thickness.*.mgh were
> not created for 5 out of the 19 subjects of the first group. Log files
> recon-all-status.log and recon-all.log (attached, for one of those 5
> subjects) both mention that the process ran on Mar22nd ended with
> errors, although I can't quite see what that was
> 
> 
> 
> 2. When I take age as a continuous factor (covariate), the list of
> clusters in my results look dramatically different from the clusters
> that I get for the same contrast ran without the covariate. Why is
> that, given that normally adding a covariate very rarely changes the
> results by a great deal? Also in my case, I had quite a narrow (and
> well-balanced between the groups) age range!
> 
>  
> 
> 3. I know that discrete factors cannot be taken as nuisance factors,
> but it seems they also can't be taken as covariates. How does one,
> then, control for the effects of e.g. gender in a group comparison?
> 
> 
> 4. When should values other than 10 be used for the FWHM parameter of
> the smoothing? 
> 
> 
> 5. How come QDEC allows you to set the FWHM parameter, when in fact it
> is also set in the qcache stage of recon-all, which precedes QDEC?
> 
> 
> Many thanks in advance!!
> 
> Tudor
> ___
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[Freesurfer] Qdec Questions

[mdkrue...@uwalumni.com]

Freesurfers-

When running analysis in qdec is it possible to use each individual
subjects brain volume (white matter + gray matter) as a covariate? If so,
what would be the easiest way to go about getting this information.

Best-
Michael

-- 
Michael D. Kruepke
PhD - University of Illinois at Urbana-Champaign
BA - Psych - University of Wisconsin-Madison
mdkrue...@gmail.com
(262)-483-7449
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Re: [Freesurfer] QDec questions

[Douglas N Greve]

Yes, see the answer to your first question below.
doug

krista kelly wrote:
> Am I able to do vertex-by-vertex analyses using freesurfer if I have 
> more than 2 discrete variables? If so, how?
>
> Is it also ok to use the unsmoothed data when doing surface area label 
> analyses?
>
> Thanks!
>
> On Tue, Oct 18, 2011 at 3:14 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Sorry, I meant to say that you cannot use QDEC with more than 2
> discrete variables (you have 3). You do not need to extract data
> from the smoothed thickness files, but the results you get from
> your ROI analysis may then differ a bit from that you get from the
> QDEC analysis.
> doug
>
> krista kelly wrote:
>
> Thanks Doug! Just a few more things:
>
> I only have two groups, so my contrast was wrong. Should it
> only be 1 -1, even if I have other variables I want to control
> for? Or should I have a contrast file for each discrete variable?
>
> How would I extract the smoothed data using mri_anatomical_stats?
>
> I realize the importance of smoothing data while doing a
> vertex-by-vertex analysis in QDec, but if I'm doing an ROI
> analysis by extracting the average thickness in a certain
> label (i.e. v1), is it necessary to do the stats on the
> smoothed data from each participant?
>
> Thanks!
>
>
> On Tue, Oct 18, 2011 at 2:23 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
>
>krista kelly wrote:
>
>Hi, just wondering if anyone has any advice on the
> following
>questions:
>
>I'm using QDEC to analyze cortical thickness differences
>between groups and I have a few questions:
>
>1) There are a few variables that I need to control
> for. First
>variable is scanner - I used two different scanners of
>different field strengths (1.5T GE and 3T Siemens) so I
> wanted
>to control for scanner. I also wanted to control for
> age and
>gender. Here's my ideal design setup:
>
>discrete variables - groups, scanner, gender
>nuisance variable - age
>
>contrast would be 1 -1 0 0 0 0
>I realize that scanner, gender, and group are all discrete
>variables, and that age would be a continuous one.
> However, in
>the design tab, I am not able to select all 3 discrete
>variables (groups, scanner, and gender). Should I designate
>scanner or gender as a nuisance variable instead? Would it
>matter which one I use as the nuisance variable?
> Possible setup:
>
>discrete vars - groups, scanner
>nuisance vars - age, gender
>
>contrast - 1 -1 0 0 (Correct?)
>
>Unfortunately, you cannot use QDEC if you have three groups.
>You'll have to create an FSGD file and contrasts by hand,
> then run
>mri_glmfit. Do a search for FSGD on our wiki and go to the
>examples page. I think there is an example there for what
> you want
>to do.
>
>
>2) If I use DODS, should I demean the ages if age is a
>nuisance variable?
>
>You should actually test whether there is an interaction
> between
>age and your group contrast of interest (using the DODS
> model). If
>there is not interaction, then switch to a DOSS where demeaning
>does not matter.
>
>
>3) If I use a smoothing kernel during the analysis, then
>create an ROI and map that ROI to each individual subject,
>will the resulting .stats file in each subjects stats
> folder
>reflect the smoothed data or does mapping onto each ROI
> just
>extract the raw unsmoothed data from each vertex?
>
>It depends on how you do the extraction. If you are using
>mris_anatomical_stats on each individual's unsmoothed data,
> then
>it will reflect the unsmoothed.
>
>doug
>
>
>Thanks!
>Krista
>  
>  
> 
>
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> 
> >
>
>  
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Re: [Freesurfer] QDec questions

[Douglas N Greve]

Sorry, I meant to say that you cannot use QDEC with more than 2 discrete 
variables (you have 3). You do not need to extract data from the 
smoothed thickness files, but the results you get from your ROI analysis 
may then differ a bit from that you get from the QDEC analysis.
doug

krista kelly wrote:
> Thanks Doug! Just a few more things:
>
> I only have two groups, so my contrast was wrong. Should it only be 1 
> -1, even if I have other variables I want to control for? Or should I 
> have a contrast file for each discrete variable?
>
> How would I extract the smoothed data using mri_anatomical_stats?
>
> I realize the importance of smoothing data while doing a 
> vertex-by-vertex analysis in QDec, but if I'm doing an ROI analysis by 
> extracting the average thickness in a certain label (i.e. v1), is it 
> necessary to do the stats on the smoothed data from each participant?
>
> Thanks!
>
>
> On Tue, Oct 18, 2011 at 2:23 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
> krista kelly wrote:
>
> Hi, just wondering if anyone has any advice on the following
> questions:
>
> I'm using QDEC to analyze cortical thickness differences
> between groups and I have a few questions:
>
> 1) There are a few variables that I need to control for. First
> variable is scanner - I used two different scanners of
> different field strengths (1.5T GE and 3T Siemens) so I wanted
> to control for scanner. I also wanted to control for age and
> gender. Here's my ideal design setup:
>
> discrete variables - groups, scanner, gender
> nuisance variable - age
>
> contrast would be 1 -1 0 0 0 0
> I realize that scanner, gender, and group are all discrete
> variables, and that age would be a continuous one. However, in
> the design tab, I am not able to select all 3 discrete
> variables (groups, scanner, and gender). Should I designate
> scanner or gender as a nuisance variable instead? Would it
> matter which one I use as the nuisance variable? Possible setup:
>
> discrete vars - groups, scanner
> nuisance vars - age, gender
>
> contrast - 1 -1 0 0 (Correct?)
>
> Unfortunately, you cannot use QDEC if you have three groups.
> You'll have to create an FSGD file and contrasts by hand, then run
> mri_glmfit. Do a search for FSGD on our wiki and go to the
> examples page. I think there is an example there for what you want
> to do.
>
>
> 2) If I use DODS, should I demean the ages if age is a
> nuisance variable?
>
> You should actually test whether there is an interaction between
> age and your group contrast of interest (using the DODS model). If
> there is not interaction, then switch to a DOSS where demeaning
> does not matter.
>
>
> 3) If I use a smoothing kernel during the analysis, then
> create an ROI and map that ROI to each individual subject,
> will the resulting .stats file in each subjects stats folder
> reflect the smoothed data or does mapping onto each ROI just
> extract the raw unsmoothed data from each vertex?
>
> It depends on how you do the extraction. If you are using
> mris_anatomical_stats on each individual's unsmoothed data, then
> it will reflect the unsmoothed.
>
> doug
>
>
> Thanks!
> Krista
> 
> 
>
> ___
> 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
> 
>
>
>
> 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.
>
>

-- 
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

_

Re: [Freesurfer] QDec questions

[Douglas N Greve]

krista kelly wrote:
> Hi, just wondering if anyone has any advice on the following questions:
>
> I'm using QDEC to analyze cortical thickness differences between 
> groups and I have a few questions:
>
> 1) There are a few variables that I need to control for. First 
> variable is scanner - I used two different scanners of different field 
> strengths (1.5T GE and 3T Siemens) so I wanted to control for scanner. 
> I also wanted to control for age and gender. Here's my ideal design 
> setup:
>
> discrete variables - groups, scanner, gender
> nuisance variable - age
>
> contrast would be 1 -1 0 0 0 0 
>
> I realize that scanner, gender, and group are all discrete variables, 
> and that age would be a continuous one. However, in the design tab, I 
> am not able to select all 3 discrete variables (groups, scanner, and 
> gender). Should I designate scanner or gender as a nuisance variable 
> instead? Would it matter which one I use as the nuisance variable? 
> Possible setup:
>
> discrete vars - groups, scanner
> nuisance vars - age, gender
>
> contrast - 1 -1 0 0 (Correct?)
Unfortunately, you cannot use QDEC if you have three groups. You'll have 
to create an FSGD file and contrasts by hand, then run mri_glmfit. Do a 
search for FSGD on our wiki and go to the examples page. I think there 
is an example there for what you want to do.
>
> 2) If I use DODS, should I demean the ages if age is a nuisance variable?
You should actually test whether there is an interaction between age and 
your group contrast of interest (using the DODS model). If there is not 
interaction, then switch to a DOSS where demeaning does not matter.
>
> 3) If I use a smoothing kernel during the analysis, then create an ROI 
> and map that ROI to each individual subject, will the resulting .stats 
> file in each subjects stats folder reflect the smoothed data or does 
> mapping onto each ROI just extract the raw unsmoothed data from each 
> vertex?
It depends on how you do the extraction. If you are using 
mris_anatomical_stats on each individual's unsmoothed data, then it will 
reflect the unsmoothed.

doug
>
> Thanks!
> Krista
> 
>
> ___
> 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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[Freesurfer] QDec questions

[krista kelly]

Hi, just wondering if anyone has any advice on the following questions:

I'm using QDEC to analyze cortical thickness differences between groups and
I have a few questions:

1) There are a few variables that I need to control for. First variable is
scanner - I used two different scanners of different field strengths (1.5T
GE and 3T Siemens) so I wanted to control for scanner. I also wanted to
control for age and gender. Here's my ideal design setup:

discrete variables - groups, scanner, gender
nuisance variable - age

contrast would be 1 -1 0 0 0 0

I realize that scanner, gender, and group are all discrete variables, and
that age would be a continuous one. However, in the design tab, I am not
able to select all 3 discrete variables (groups, scanner, and gender).
Should I designate scanner or gender as a nuisance variable instead? Would
it matter which one I use as the nuisance variable? Possible setup:

discrete vars - groups, scanner
nuisance vars - age, gender

contrast - 1 -1 0 0 (Correct?)

2) If I use DODS, should I demean the ages if age is a nuisance variable?

3) If I use a smoothing kernel during the analysis, then create an ROI and
map that ROI to each individual subject, will the resulting .stats file in
each subjects stats folder reflect the smoothed data or does mapping onto
each ROI just extract the raw unsmoothed data from each vertex?

Thanks!
Krista
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Re: [Freesurfer] Qdec questions

[Martin Kavec]

Thanks for the replay, Nick!

On Monday 27 October 2008 16:48:26 Nick Schmansky wrote:
> Martin,
>
> To answer question 1, the fsaverage surface is used as a target surface
> to which the data (ie thickness) of each subject in the group is sampled
> and then smoothed, so the accuracy of the recon of the fsaverage subject
> itself is not relevant to accuracy of the group analysis.

Thanks, it's clear now.

>
> For 2., unfortunately, the only way to get qdec to recognize ?h.pial_lgi
> is via the 'hack' that you mention: renaming the files as 'thickness'.
> A feature to be added to qdec is the reading of a text configuration
> file to allow selection of arbitrary surface data files into the qdec
> menu.  Actually, I think I might implement that feature this week, as I
> hate that hack

Sorry, I could not come up with something more pleasant.
:D

> , and can post this version of qdec for you if you want. 

That would be great, though I do not want to press you!

> For 3., I think you are in new territory here, the first to do this, so
> you will have to experiment.  Although 0mm smoothing, as you suggest,
> seems reasonable.

OK. I'll give it a try!

Thanks,

Martin
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Re: [Freesurfer] Qdec questions

[Nick Schmansky]

Martin,

To answer question 1, the fsaverage surface is used as a target surface
to which the data (ie thickness) of each subject in the group is sampled
and then smoothed, so the accuracy of the recon of the fsaverage subject
itself is not relevant to accuracy of the group analysis.

For 2., unfortunately, the only way to get qdec to recognize ?h.pial_lgi
is via the 'hack' that you mention: renaming the files as 'thickness'.
A feature to be added to qdec is the reading of a text configuration
file to allow selection of arbitrary surface data files into the qdec
menu.  Actually, I think I might implement that feature this week, as I
hate that hack, and can post this version of qdec for you if you want.

To create the smoothed ?h.pial_lgi files, you would do this:

recon-all -s subjid -qcache -measure pial_lgi

and it will create the fsaverage sampled and smoothed data for each
subject.

For 3., I think you are in new territory here, the first to do this, so
you will have to experiment.  Although 0mm smoothing, as you suggest,
seems reasonable.

Nick


On Sun, 2008-10-26 at 21:41 +0100, Martin Kavec wrote:
> Hello all,
> 
> I have started with a group analysis using qdec and have some questions:
> 
> 1. loading fsaverage into tkmedit along with rh.white and lh.white surprised 
> me that the pial surfaces do not run under the skull, as I see it on a single 
> subject but copy the white matter. It is also correct, but it looks a bit 
> odd. I suppose that this is a result of averaged out WM, but my concern is 
> whether it can anyhow affect the analysis
> 
> 2. I am interested in group analysis of LGI. I do not see however ?h.pial_lgi 
> in fsaverage. Also when I run qdec, lgi is not among the parameters available 
> for testing. I could backup say the thickness files and than rename my lgi 
> results as thickness, but if there is a more straightforward solution I would 
> like to avoid this trouble
> 
>  3. Since lgi is for each vertex calculated over a certain diameter, thus has 
> inherent smoothing. Therefore I would tend to use 0 smoothing in GLM. What do 
> you think about this idea?
> 
> Thanks,
> 
> Martin
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> 

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[Freesurfer] Qdec questions

[Martin Kavec]

Hello all,

I have started with a group analysis using qdec and have some questions:

1. loading fsaverage into tkmedit along with rh.white and lh.white surprised 
me that the pial surfaces do not run under the skull, as I see it on a single 
subject but copy the white matter. It is also correct, but it looks a bit 
odd. I suppose that this is a result of averaged out WM, but my concern is 
whether it can anyhow affect the analysis

2. I am interested in group analysis of LGI. I do not see however ?h.pial_lgi 
in fsaverage. Also when I run qdec, lgi is not among the parameters available 
for testing. I could backup say the thickness files and than rename my lgi 
results as thickness, but if there is a more straightforward solution I would 
like to avoid this trouble

 3. Since lgi is for each vertex calculated over a certain diameter, thus has 
inherent smoothing. Therefore I would tend to use 0 smoothing in GLM. What do 
you think about this idea?

Thanks,

Martin
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