Re: [Freesurfer] mixed models and longitudinal streaming

[Angela Favaro]

thank you!


Martin Reuter  ha scritto:

> Hi Angela,
>
> to get the fs_write_Y to work, you would first need to set
> mri.volsz(4) = 1
> (to tell it to write only  a single frame).
>
> But for writing significance maps, you can use fs_write_fstats (as you did).
>
> Usually you don't describe the data, but simply capture the overlay of
> the p values on the surface and show the images. In the text you can of
> course reference the cortical ROI. You usually don't smooth significance
> maps, but instead you can use a different smoothing level for the inputs
> (Y, thickness), which is different.
>
> For correction you would compute the FDR and use the result as a cutoff
> (FDR thresholded , so only what survives at the specified level is shown).
> Here it makes sense to combine left and right hemisphere. Something like
> this:
>
> % FDR correct, then use - log10(pth) in tksurfer
> P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ];
> G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ];
> [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0);
> pcor = -log10(pth)
>
>
> The significance map does include a sign, so that you know in what
> direction the effect goes. Having opposite signs for linear and
> quadratic is possible (meaning that the quadratic term goes in the
> opposite direction as the linear term). For example there could be a
> linear effect with age (atrophy, linear term is negative= higher age
> with smaller thickness) that slows down at higher ages (quadratic term
> is positive, a floor effect).
>
> Best, Martin
>
> On 04/20/2016 04:50 PM, Angela Favaro wrote:
>> I was finally able to run linear mixed models with my data - thank you
>> very much Martin for your precious help!
>>
>> No I would need some help/advice for visualization and description of
>> my results
>>
>> The command fs_write_Y(sided_pval,mri,'spval.mgh') is not working on
>> my matlab. This is the message error:
>> Error using reshape
>> To RESHAPE the number of elements must not change.
>> Error in fs_write_Y (line 21)
>> save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
>>
>> so, I have used the command:
>> fs_write_fstats(F_rhstats_lin,mri,'sig.mgh','sig')
>> to export the findings, as described in the wiki. However, how can I
>> describe my data, in terms of measure of the clusters, MNI coordinates
>> and statistical values? and is it possible to smooth the image?
>>
>> In addition, this map is 'uncorrected' for multiple testing. How can I
>> perform this correction?
>>
>> I am testing null hypothesis of no group differences in the rate of
>> change over time between two groups and I found significant
>> differences both using quadratic effects (time per time per group) and
>> linear effects (time per group) in the same model (with one random
>> effect, that appeared to perform better than the model with 2 RF). The
>> map of the first analysis appeared in blue in Freeview, whereas the
>> map for linear effects appeared in red. Does sig.mgh include the sign
>> of the difference? and is it possible that the two analyses have
>> opposite sign? am I doing something wrong?
>>
>> Thank you!
>>
>> Angela
>>
>>
>>
>>
>>
>>
>> Martin Reuter  ha scritto:
>>
>>> Actually I am just adding a fix for this submitted by a user (thanks
>>> Knut) , so it should work with modern versions soon.
>>>
>>> Best, Martin
>>>
>>> On 04/06/2016 11:02 AM, Martin Reuter wrote:
 Hi Angela,

 newer versions of matlab don't support the old matlabpool comands any
 longer. You need to use an older matlab version (less than 8.2.0.29).

 Best, Martin

 On 04/05/2016 06:06 PM, Angela Favaro wrote:
> Hi Martin, thank you for your help.
> I still have problems in running mixed models analyses. Do I need some
> additional toolbox in matlab? (I did not find this information in the
> web)
> I tried to run the module in two versions of matlab, but the same
> problem occurr.
>
> I used these commands:
> [M,Y,ni] = sortData(M,1,Y,sID)
> X = [ones(length(M),1) M M(:,1).*M(:,2)]
>
> [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)
>
> this is the error message:
> Undefined function 'matlabpool' for input
> arguments of type 'char'.
>
> Error in lme_mass_fit_init (line 74)
> if (prs==1) || (matlabpool('size') ~= prs)
>
> Error in lme_mass_fit_EMinit (line 69)
> [Theta1,Re1] =
> lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
>
> What can it be the problem?
> the matrices seem to be OK (and M has the same number of rows as Y
> (and as the sID)).
>
> thank you for any help!
>
> Angela
>
>
>
>
> Martin Reuter  ha scritto:
>
>> Hi Angela,
>>
>> the smooth function seems to be part of the curve fitting toolbox
>> http://www.mathworks.com/help/curvefit/smooth.html
>> so 

Re: [Freesurfer] lme model for within-subjects repeated measures design

[Martin Reuter]

Thanks,

what I mean is in order to quantify a treatment effect for the subjects 
that received treatment at T0, you would need another scan before that 
(Tminus1). You would need three time points:


group1: baseline, placebo, treatment
group2: baseline, treatment, placebo

you could then test if treatment or placebo differs from baseline.

If you assume that the ordering is not important, you could use a binary 
variable (drug / placebo) instead of time in LME and control for the 
time delta as a co-variate. This may make sense, as you are not really 
interested in change / time unit.


Another model would be to use time as usual in LME and add drug as a 
time varying covariate. I am not a statistician, so I don't really know 
what would be best in your case.


Cheers, Martin



On 04/21/2016 06:08 PM, Martina Papmeyer wrote:

Hi Martin

Thank you very much for your response!  To clarify the design: There 
are 44 subjects, all have been scanned twice and thus have repeated 
measures of cortical thickness. 22 subjects were first (T0) scanned 2 
hours after a placebo treatment. Some days later, the identical 
subjects were scanned again (T1) but this time 2 hours after a "real" 
treatment. The other 22 subjects were scanned first (T0) after "real" 
treatment and then some days later after placebo treatment. The 
interval between T0 and T1 varies between subjects which I would like 
to take into account into my analyses. The time between receiving 
placebo/real treatment and MRI acquisition is identical among all 
subjects (2hours) and thus not of concern.


Thank you very much for your help! Best, Martina

Sent from my iPad

On 21 Apr 2016, at 22:09, Martin Reuter > wrote:



Hi Martina,

so you don't have a baseline (no treatment) measurement? If you have 
a treatment at T0, you mean during an interval before T0, right? But 
since you did not scan before that treatment, you cannot quantify 
that change? The design is not clear to me.


About the random effect (with only two time points and two groups) I 
think having the intercept is enough.


Best, Martin


On 04/18/2016 11:51 AM, martina.papme...@puk.unibe.ch wrote:


Dear FreeSurfer experts

I have one question regarding my data analysis and would be 
extremely thankful for any advice!


My data-set is as follows: I have repeated measures (time point 0 
(T0), time point 1 (T1)) of several subjects. All individuals 
underwent an intervention at one of the time points and a placebo 
condition at the other time point in a fully randomized fashion. 
Thus, half of the subjects received treatment at T0 and half of them 
at T1. I am interested in the putative effect of the intervention on 
cortical thickness in a ROI. A major challenge is that the time 
between T0 and T1 varies between individuals and that I expect the 
time to impact on my dependent variable and to likely interact with 
the condition (treatment versus placebo).


I thought about conducting a simple repeated-measures ANOVA. 
However, as stated, I want to take the time between the two sessions 
into account. I also thought about an analysis of rates or percent 
changes. However, this approach does not model the correlation among 
the repeated measures and is thus associated with a reduction in power.


Accordingly, I am trying to use lme models to analyse my data. Since 
I have no between-group variable but a within-subjects design, I am 
concerned if my thoughts are correct and would be grateful for feedback.


I ran the longitudinal FS stream and followed the longitudinal lme 
model tutorial. I propose the following lme model with one random 
factor: thickness = intercept (random factor) + time since baseline 
+ ICV + condition (placebo or treatment) + timeXcondition + Age 
(does not change across time interval) + gender


The analysis finishes with 0% non-covergence. Can you tell me if my 
model is suitable given the fact that it is a within-subjects 
design? I also started wondering if it was possible to model time as 
a random factor but I think that I read that this is not suitable if 
you only have two groups (in my case: conditions).


Thank you very much for help and advice!

All best wishes, Martina

Universitäre Psychiatrische Dienste Bern (UPD)
*Universitätsklinik für Psychiatrie und Psychotherapie*
Systemische Neurowissenschaften der Psychopathologie
Zentrum für Translationale Forschung
Dr. phil. Martina Papmeyer, Wissenschaftliche Mitarbeiterin
Bolligenstrasse 111, CH-3000 Bern 60
Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961
Mail: martina.papme...@puk.unibe.ch
www.puk.unibe.ch



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


--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for 

Re: [Freesurfer] lme model for within-subjects repeated measures design

[Martina Papmeyer]

Hi Martin 

Thank you very much for your response!  To clarify the design: There are 44 
subjects, all have been scanned twice and thus have repeated measures of 
cortical thickness. 22 subjects were first (T0) scanned 2 hours after a placebo 
treatment. Some days later, the identical subjects were scanned again (T1) but 
this time 2 hours after a "real" treatment. The other 22 subjects were scanned 
first (T0) after "real" treatment and then some days later after placebo 
treatment. The interval between T0 and T1 varies between subjects which I would 
like to take into account into my analyses. The time between receiving 
placebo/real treatment and MRI acquisition is identical among all subjects 
(2hours) and thus not of concern. 

Thank you very much for your help! Best, Martina 

Sent from my iPad

> On 21 Apr 2016, at 22:09, Martin Reuter  wrote:
> 
> Hi Martina,
> 
> so you don't have a baseline (no treatment) measurement? If you have a 
> treatment at T0, you mean during an interval before T0, right? But since you 
> did not scan before that treatment, you cannot quantify that change? The 
> design is not clear to me.
> 
> About the random effect (with only two time points and two groups) I think 
> having the intercept is enough.
> 
> Best, Martin
> 
> 
>> On 04/18/2016 11:51 AM, martina.papme...@puk.unibe.ch wrote:
>> Dear FreeSurfer experts
>>  
>> I have one question regarding my data analysis and would be extremely 
>> thankful for any advice!
>>  
>> My data-set is as follows: I have repeated measures (time point 0 (T0), time 
>> point 1 (T1)) of several subjects. All individuals underwent an intervention 
>> at one of the time points and a placebo condition at the other time point in 
>> a fully randomized fashion. Thus, half of the subjects received treatment at 
>> T0 and half of them at T1. I am interested in the putative effect of the 
>> intervention on cortical thickness in a ROI. A major challenge is that the 
>> time between T0 and T1 varies between individuals and that I expect the time 
>> to impact on my dependent variable and to likely interact with the condition 
>> (treatment versus placebo).
>>  
>> I thought about conducting a simple repeated-measures ANOVA. However, as 
>> stated, I want to take the time between the two sessions into account. I 
>> also thought about an analysis of rates or percent changes. However, this 
>> approach does not model the correlation among the repeated measures and is 
>> thus associated with a reduction in power.
>>  
>> Accordingly, I am trying to use lme models to analyse my data. Since I have 
>> no between-group variable but a within-subjects design, I am concerned if my 
>> thoughts are correct and would be grateful for feedback.
>>  
>> I ran the longitudinal FS stream and followed the longitudinal lme model 
>> tutorial. I propose the following lme model with one random factor: 
>> thickness = intercept (random factor) + time since baseline + ICV + 
>> condition (placebo or treatment) + timeXcondition + Age (does not change 
>> across time interval) + gender
>>  
>> The analysis finishes with 0% non-covergence. Can you tell me if my model is 
>> suitable given the fact that it is a within-subjects design? I also started 
>> wondering if it was possible to model time as a random factor but I think 
>> that I read that this is not suitable if you only have two groups (in my 
>> case: conditions).
>>  
>> Thank you very much for help and advice!
>>  
>> All best wishes, Martina
>>  
>>  
>>  
>>  
>> Universitäre Psychiatrische Dienste Bern (UPD)
>> Universitätsklinik für Psychiatrie und Psychotherapie
>> Systemische Neurowissenschaften der Psychopathologie
>> Zentrum für Translationale Forschung
>> Dr. phil. Martina Papmeyer, Wissenschaftliche Mitarbeiterin
>> Bolligenstrasse 111, CH-3000 Bern 60
>> Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961
>> Mail: martina.papme...@puk.unibe.ch 
>> www.puk.unibe.ch
>>  
>>  
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Martin Reuter, PhD
> Assistant Professor of Radiology, Harvard Medical School
> Assistant Professor of Neurology, Harvard Medical School
> A.A.Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Research Affiliate, CSAIL, MIT
> Phone: +1-617-724-5652
> Web  : http://reuter.mit.edu 
> ___
> 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
> 

Re: [Freesurfer] white matter edits not incorporated

[Bruce Fischl]

yes, I think that's what V6 does I think
On Thu, 21 Apr 2016, dgw wrote:


Hi,

I solved it (with help from a colleague) by just calling the
individual mri_make_surfaces command separately (adjusting the
nowhite), and
the subsequent ones through the flair pial command. I am now running
-make all, to finish the rest (note it did miss one step in the
re-start: it didn't re-run mris_calc, for bug hunting purposes), I
will re-run after it finishes.

Thanks everyone!
d

On Thu, Apr 21, 2016 at 4:55 PM, Bruce Fischl
 wrote:

Hi Mike

yes, I think it is fixed. Daniel: can you try out dev and see if it fixes
this for you?
Bruce




On Thu, 21 Apr 2016, Harms, Michael wrote:



That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).

I think some of the subsequent back-and-forth with Bruce and Nick was off
the list, so I’ve included the key email (where Bruce diagnosed the
problem) below.

Has this been fixed in the forthcoming FS 6.0?

thanks,
-MH

 snip 

ok, I see what's going on. Here is the sequence of calls:

1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh

Makes the white surface *without* using the aparc. Because there are a
string of "hypointensity" labels in the aseg, the white surface is frozen
in these locations.

2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh

internally recreates the white surface but doesn't save it. The frozen
vertices are allowed to move since the aparc *is* used in this call, and
the vertices are deemed to be in real cortical regions.

The pial surface then starts from the (inwards deformed but not written to
disk) white surface, and then settles inside the white surface that is on
disk.

I'm not sure how we settled on this logic. Why recreate the white surface?
Why not run with -nowhite -orig_pial white? That way the algorithm uses
the
white surface that the user can see and things should be consistent

Bruce

 end-snip 



--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/21/16, 9:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgw"  wrote:

Hi,

I followed the advice, and the White Matter surface looks much better;
however, now the pial surface is crossing the white matter surface.

I ran the following:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8

for those at Martinos the new subjid should indicate the new path.

I've attached a screenshot. Thank you in advance for any advice you can
give.

Thank You,
Dan

On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:


Hi Bruce,

Thanks! I'll give it a whirl.

d

On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
 wrote:


Hi Daniel

the problems isn't that it it's ignoring the wm edits, it is that it
starts
the orig surface out there, but then retracts to the (same) visible
gray/white boundary that it found in the first place. For this type of
lesion I think what you should do is also edit those voxels in the
aseg.mgz
and change them to right-lesion. This should freeze the white surface
there
I think. If it doesn't, let me know and I'll fix it.

cheers
Bruce


On Tue, 19 Apr 2016, dgw wrote:


Here is the log for the most recent -autorecon2-wm call:

Thanks!
d

On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
 wrote:


can you send us the recon-all.log? I don't see an obvious reason why
it
wouldn't have worked
On Tue, 19 Apr 2016, dgw wrote:


Just to follow up, I have tried several different options with
recon-all to get the white matter edits to stick on this participant,
and it doesn't seem to be working:

re-editing wm.mgz and running recon-all -autorecon2-wm
re-editing wm.mgz and running recon-all -make all

I can't seem to get any appreciable change in the white matter
surface. I have attached a screenshot, for an example.

hth
d


On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:


Hi,

I recently edited a brain with a gyral cyst, carefully filling the
cyst with white matter in the wm.mgz. Unfortunately after running:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8

none of the edits were incorporated.

Is the FLAIRpial flag incompatible with autorecon2-wm?

Is there some other misake?

I followed this guide


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
_freeview

Thanks,
Dan




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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] white matter edits not incorporated

[dgw]

Hi,

I solved it (with help from a colleague) by just calling the
individual mri_make_surfaces command separately (adjusting the
nowhite), and
the subsequent ones through the flair pial command. I am now running
-make all, to finish the rest (note it did miss one step in the
re-start: it didn't re-run mris_calc, for bug hunting purposes), I
will re-run after it finishes.

Thanks everyone!
d

On Thu, Apr 21, 2016 at 4:55 PM, Bruce Fischl
 wrote:
> Hi Mike
>
> yes, I think it is fixed. Daniel: can you try out dev and see if it fixes
> this for you?
> Bruce
>
>
>
>
> On Thu, 21 Apr 2016, Harms, Michael wrote:
>
>>
>> That looks very similar in principle to something I posted back in Oct.
>> 2014 (“pial surface crossing white”).
>>
>> I think some of the subsequent back-and-forth with Bruce and Nick was off
>> the list, so I’ve included the key email (where Bruce diagnosed the
>> problem) below.
>>
>> Has this been fixed in the forthcoming FS 6.0?
>>
>> thanks,
>> -MH
>>
>>  snip 
>>
>> ok, I see what's going on. Here is the sequence of calls:
>>
>> 1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
>> L408_base lh
>>
>> Makes the white surface *without* using the aparc. Because there are a
>> string of "hypointensity" labels in the aseg, the white surface is frozen
>> in these locations.
>>
>> 2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
>> lh
>>
>> internally recreates the white surface but doesn't save it. The frozen
>> vertices are allowed to move since the aparc *is* used in this call, and
>> the vertices are deemed to be in real cortical regions.
>>
>> The pial surface then starts from the (inwards deformed but not written to
>> disk) white surface, and then settles inside the white surface that is on
>> disk.
>>
>> I'm not sure how we settled on this logic. Why recreate the white surface?
>> Why not run with -nowhite -orig_pial white? That way the algorithm uses
>> the
>> white surface that the user can see and things should be consistent
>>
>> Bruce
>>
>>  end-snip 
>>
>>
>>
>> --
>> Michael Harms, Ph.D.
>>
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 4/21/16, 9:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>> dgw" > dgwake...@gmail.com> wrote:
>>
>> Hi,
>>
>> I followed the advice, and the White Matter surface looks much better;
>> however, now the pial surface is crossing the white matter surface.
>>
>> I ran the following:
>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>> -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
>>
>> for those at Martinos the new subjid should indicate the new path.
>>
>> I've attached a screenshot. Thank you in advance for any advice you can
>> give.
>>
>> Thank You,
>> Dan
>>
>> On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
>>>
>>> Hi Bruce,
>>>
>>> Thanks! I'll give it a whirl.
>>>
>>> d
>>>
>>> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>>>  wrote:

 Hi Daniel

 the problems isn't that it it's ignoring the wm edits, it is that it
 starts
 the orig surface out there, but then retracts to the (same) visible
 gray/white boundary that it found in the first place. For this type of
 lesion I think what you should do is also edit those voxels in the
 aseg.mgz
 and change them to right-lesion. This should freeze the white surface
 there
 I think. If it doesn't, let me know and I'll fix it.

 cheers
 Bruce


 On Tue, 19 Apr 2016, dgw wrote:

> Here is the log for the most recent -autorecon2-wm call:
>
> Thanks!
> d
>
> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>  wrote:
>>
>> can you send us the recon-all.log? I don't see an obvious reason why
>> it
>> wouldn't have worked
>> On Tue, 19 Apr 2016, dgw wrote:
>>
>>> Just to follow up, I have tried several different options with
>>> recon-all to get the white matter edits to stick on this participant,
>>> and it doesn't seem to be working:
>>>
>>> re-editing wm.mgz and running recon-all -autorecon2-wm
>>> re-editing wm.mgz and running recon-all -make all
>>>
>>> I can't seem to get any appreciable change in the white matter
>>> surface. I have attached a screenshot, for an example.
>>>
>>> hth
>>> d
>>>
>>>
>>> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:

 Hi,

 I recently edited a brain with a gyral cyst, carefully filling the
 cyst with white matter in the wm.mgz. Unfortunately 

Re: [Freesurfer] white matter edits not incorporated

[Bruce Fischl]

Hi Mike

yes, I think it is fixed. Daniel: can you try out dev and see if it fixes 
this for you?

Bruce



On Thu, 21 Apr 2016, Harms, Michael wrote:



That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).

I think some of the subsequent back-and-forth with Bruce and Nick was off
the list, so I’ve included the key email (where Bruce diagnosed the
problem) below.

Has this been fixed in the forthcoming FS 6.0?

thanks,
-MH

 snip 

ok, I see what's going on. Here is the sequence of calls:

1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh

Makes the white surface *without* using the aparc. Because there are a
string of "hypointensity" labels in the aseg, the white surface is frozen
in these locations.

2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh

internally recreates the white surface but doesn't save it. The frozen
vertices are allowed to move since the aparc *is* used in this call, and
the vertices are deemed to be in real cortical regions.

The pial surface then starts from the (inwards deformed but not written to
disk) white surface, and then settles inside the white surface that is on
disk.

I'm not sure how we settled on this logic. Why recreate the white surface?
Why not run with -nowhite -orig_pial white? That way the algorithm uses
the
white surface that the user can see and things should be consistent

Bruce

 end-snip 



--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/21/16, 9:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgw"  wrote:

Hi,

I followed the advice, and the White Matter surface looks much better;
however, now the pial surface is crossing the white matter surface.

I ran the following:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8

for those at Martinos the new subjid should indicate the new path.

I've attached a screenshot. Thank you in advance for any advice you can
give.

Thank You,
Dan

On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:

Hi Bruce,

Thanks! I'll give it a whirl.

d

On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
 wrote:

Hi Daniel

the problems isn't that it it's ignoring the wm edits, it is that it
starts
the orig surface out there, but then retracts to the (same) visible
gray/white boundary that it found in the first place. For this type of
lesion I think what you should do is also edit those voxels in the
aseg.mgz
and change them to right-lesion. This should freeze the white surface
there
I think. If it doesn't, let me know and I'll fix it.

cheers
Bruce


On Tue, 19 Apr 2016, dgw wrote:


Here is the log for the most recent -autorecon2-wm call:

Thanks!
d

On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
 wrote:

can you send us the recon-all.log? I don't see an obvious reason why
it
wouldn't have worked
On Tue, 19 Apr 2016, dgw wrote:


Just to follow up, I have tried several different options with
recon-all to get the white matter edits to stick on this participant,
and it doesn't seem to be working:

re-editing wm.mgz and running recon-all -autorecon2-wm
re-editing wm.mgz and running recon-all -make all

I can't seem to get any appreciable change in the white matter
surface. I have attached a screenshot, for an example.

hth
d


On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:

Hi,

I recently edited a brain with a gyral cyst, carefully filling the
cyst with white matter in the wm.mgz. Unfortunately after running:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8

none of the edits were incorporated.

Is the FLAIRpial flag incompatible with autorecon2-wm?

Is there some other misake?

I followed this guide

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
_freeview

Thanks,
Dan



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Re: [Freesurfer] mixed models and longitudinal streaming

[Martin Reuter]

Hi Angela,

to get the fs_write_Y to work, you would first need to set
mri.volsz(4) = 1
(to tell it to write only  a single frame).

But for writing significance maps, you can use fs_write_fstats (as you did).

Usually you don't describe the data, but simply capture the overlay of 
the p values on the surface and show the images. In the text you can of 
course reference the cortical ROI. You usually don't smooth significance 
maps, but instead you can use a different smoothing level for the inputs 
(Y, thickness), which is different.

For correction you would compute the FDR and use the result as a cutoff 
(FDR thresholded , so only what survives at the specified level is shown).
Here it makes sense to combine left and right hemisphere. Something like 
this:

% FDR correct, then use - log10(pth) in tksurfer
P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ];
G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ];
[detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0);
pcor = -log10(pth)


The significance map does include a sign, so that you know in what 
direction the effect goes. Having opposite signs for linear and 
quadratic is possible (meaning that the quadratic term goes in the 
opposite direction as the linear term). For example there could be a 
linear effect with age (atrophy, linear term is negative= higher age 
with smaller thickness) that slows down at higher ages (quadratic term 
is positive, a floor effect).

Best, Martin

On 04/20/2016 04:50 PM, Angela Favaro wrote:
> I was finally able to run linear mixed models with my data - thank you
> very much Martin for your precious help!
>
> No I would need some help/advice for visualization and description of
> my results
>
> The command fs_write_Y(sided_pval,mri,'spval.mgh') is not working on
> my matlab. This is the message error:
> Error using reshape
> To RESHAPE the number of elements must not change.
> Error in fs_write_Y (line 21)
> save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
>
> so, I have used the command:
> fs_write_fstats(F_rhstats_lin,mri,'sig.mgh','sig')
> to export the findings, as described in the wiki. However, how can I
> describe my data, in terms of measure of the clusters, MNI coordinates
> and statistical values? and is it possible to smooth the image?
>
> In addition, this map is 'uncorrected' for multiple testing. How can I
> perform this correction?
>
> I am testing null hypothesis of no group differences in the rate of
> change over time between two groups and I found significant
> differences both using quadratic effects (time per time per group) and
> linear effects (time per group) in the same model (with one random
> effect, that appeared to perform better than the model with 2 RF). The
> map of the first analysis appeared in blue in Freeview, whereas the
> map for linear effects appeared in red. Does sig.mgh include the sign
> of the difference? and is it possible that the two analyses have
> opposite sign? am I doing something wrong?
>
> Thank you!
>
> Angela
>
>
>
>
>
>
> Martin Reuter  ha scritto:
>
>> Actually I am just adding a fix for this submitted by a user (thanks
>> Knut) , so it should work with modern versions soon.
>>
>> Best, Martin
>>
>> On 04/06/2016 11:02 AM, Martin Reuter wrote:
>>> Hi Angela,
>>>
>>> newer versions of matlab don't support the old matlabpool comands any
>>> longer. You need to use an older matlab version (less than 8.2.0.29).
>>>
>>> Best, Martin
>>>
>>> On 04/05/2016 06:06 PM, Angela Favaro wrote:
 Hi Martin, thank you for your help.
 I still have problems in running mixed models analyses. Do I need some
 additional toolbox in matlab? (I did not find this information in the
 web)
 I tried to run the module in two versions of matlab, but the same
 problem occurr.

 I used these commands:
 [M,Y,ni] = sortData(M,1,Y,sID)
 X = [ones(length(M),1) M M(:,1).*M(:,2)]

 [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3)

 this is the error message:
 Undefined function 'matlabpool' for input
 arguments of type 'char'.

 Error in lme_mass_fit_init (line 74)
 if (prs==1) || (matlabpool('size') ~= prs)

 Error in lme_mass_fit_EMinit (line 69)
 [Theta1,Re1] =
 lme_mass_fit_init(X,Zcols,Y,ni,[],prs);

 What can it be the problem?
 the matrices seem to be OK (and M has the same number of rows as Y
 (and as the sID)).

 thank you for any help!

 Angela




 Martin Reuter  ha scritto:

> Hi Angela,
>
> the smooth function seems to be part of the curve fitting toolbox
> http://www.mathworks.com/help/curvefit/smooth.html
> so either that is missing, or your version is too old.
> You can skip the lowess Plot (it is just for initially checking the data).
>
>
> Make sure your M has the same number of rows as your Y (and as the sID).

Re: [Freesurfer] lme model for within-subjects repeated measures design

[Martin Reuter]

Hi Martina,

so you don't have a baseline (no treatment) measurement? If you have a 
treatment at T0, you mean during an interval before T0, right? But since 
you did not scan before that treatment, you cannot quantify that change? 
The design is not clear to me.


About the random effect (with only two time points and two groups) I 
think having the intercept is enough.


Best, Martin


On 04/18/2016 11:51 AM, martina.papme...@puk.unibe.ch wrote:


Dear FreeSurfer experts

I have one question regarding my data analysis and would be extremely 
thankful for any advice!


My data-set is as follows: I have repeated measures (time point 0 
(T0), time point 1 (T1)) of several subjects. All individuals 
underwent an intervention at one of the time points and a placebo 
condition at the other time point in a fully randomized fashion. Thus, 
half of the subjects received treatment at T0 and half of them at T1. 
I am interested in the putative effect of the intervention on cortical 
thickness in a ROI. A major challenge is that the time between T0 and 
T1 varies between individuals and that I expect the time to impact on 
my dependent variable and to likely interact with the condition 
(treatment versus placebo).


I thought about conducting a simple repeated-measures ANOVA. However, 
as stated, I want to take the time between the two sessions into 
account. I also thought about an analysis of rates or percent changes. 
However, this approach does not model the correlation among the 
repeated measures and is thus associated with a reduction in power.


Accordingly, I am trying to use lme models to analyse my data. Since I 
have no between-group variable but a within-subjects design, I am 
concerned if my thoughts are correct and would be grateful for feedback.


I ran the longitudinal FS stream and followed the longitudinal lme 
model tutorial. I propose the following lme model with one random 
factor: thickness = intercept (random factor) + time since baseline + 
ICV + condition (placebo or treatment) + timeXcondition + Age (does 
not change across time interval) + gender


The analysis finishes with 0% non-covergence. Can you tell me if my 
model is suitable given the fact that it is a within-subjects design? 
I also started wondering if it was possible to model time as a random 
factor but I think that I read that this is not suitable if you only 
have two groups (in my case: conditions).


Thank you very much for help and advice!

All best wishes, Martina

Universitäre Psychiatrische Dienste Bern (UPD)
*Universitätsklinik für Psychiatrie und Psychotherapie*
Systemische Neurowissenschaften der Psychopathologie
Zentrum für Translationale Forschung
Dr. phil. Martina Papmeyer, Wissenschaftliche Mitarbeiterin
Bolligenstrasse 111, CH-3000 Bern 60
Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961
Mail: martina.papme...@puk.unibe.ch
www.puk.unibe.ch



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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] Qdec interface issue

[Sahil Bajaj]

Hello,

I am working on measuring cortical thickness of a patient group. I am using
Ubuntu 14.04

Somehow, if I use command line to perform the analysis, Freesurfer/qdec is
working fine but if I use Qdec interface, it works fine initially but when
I switch to display window, it doesn't allow me to change/edit FDR
p-values, threshold min and max, although I can click on all the options on
display window e.g. inflated, pial, white, etc.

Also, when I tried to do the same on other computer (Mac), it works fine
for me.

I was wondering if this is because of video card problem or something. The
thing is it was working before for some time, then after a computer crash,
it no longer works. We replaced the video card but are still experiencing
the same problem.

At this point I would welcome any suggestions.

Thanks,
Sahil

-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] white matter edits not incorporated

[Bruce Fischl]

Hi Daniel

I'm out if town , can you remind me next week? This is fixed in v6 I think if 
you want to just run the pial stuff in it
Bruce 

> On Apr 21, 2016, at 10:41 AM, dgw  wrote:
> 
> Hi,
> 
> I followed the advice, and the White Matter surface looks much better;
> however, now the pial surface is crossing the white matter surface.
> 
> I ran the following:
> /usr/local/freesurfer/stable5_3_0/bin/recon-all
> -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
> 
> for those at Martinos the new subjid should indicate the new path.
> 
> I've attached a screenshot. Thank you in advance for any advice you can give.
> 
> Thank You,
> Dan
> 
>> On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
>> Hi Bruce,
>> 
>> Thanks! I'll give it a whirl.
>> 
>> d
>> 
>> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>>  wrote:
>>> Hi Daniel
>>> 
>>> the problems isn't that it it's ignoring the wm edits, it is that it starts
>>> the orig surface out there, but then retracts to the (same) visible
>>> gray/white boundary that it found in the first place. For this type of
>>> lesion I think what you should do is also edit those voxels in the aseg.mgz
>>> and change them to right-lesion. This should freeze the white surface there
>>> I think. If it doesn't, let me know and I'll fix it.
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
 On Tue, 19 Apr 2016, dgw wrote:
 
 Here is the log for the most recent -autorecon2-wm call:
 
 Thanks!
 d
 
 On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
  wrote:
> can you send us the recon-all.log? I don't see an obvious reason why it
> wouldn't have worked
>> On Tue, 19 Apr 2016, dgw wrote:
>> 
>> Just to follow up, I have tried several different options with
>> recon-all to get the white matter edits to stick on this participant,
>> and it doesn't seem to be working:
>> 
>> re-editing wm.mgz and running recon-all -autorecon2-wm
>> re-editing wm.mgz and running recon-all -make all
>> 
>> I can't seem to get any appreciable change in the white matter
>> surface. I have attached a screenshot, for an example.
>> 
>> hth
>> d
>> 
>> 
>>> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>>> Hi,
>>> 
>>> I recently edited a brain with a gyral cyst, carefully filling the
>>> cyst with white matter in the wm.mgz. Unfortunately after running:
>>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>> 
>>> none of the edits were incorporated.
>>> 
>>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>> 
>>> Is there some other misake?
>>> 
>>> I followed this guide
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>>> 
>>> Thanks,
>>> Dan
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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 
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> contains patient information, please contact the Partners Compliance 
> HelpLine at
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> properly
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Re: [Freesurfer] Hippocampal subfields, stuck?

[Eugenio Iglesias]

Dear Maximilià,
first of all, sorry for the late response.
We assume throughout the code that mv a.ext b.ext  will overwrite b.ext if it 
exists. If this is not the case in your system, maybe you could create an alias 
from 'mv' -> 'mv -f' before calling recon-all?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "BAUTISTA-PERPINYA Maximilià" 
To: "Freesurfer support list" 
Sent: Monday, April 18, 2016 9:35:05 AM
Subject: [Freesurfer] Hippocampal subfields, stuck?

Dear all experts,

I am running FS 6dev version. This is my recon-all comand: "recon-all 
-nuintensitycor-3T -i [directory] -s [subjectname] -all 
-hippocampal-subfields-T1".

Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. 
At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter 
whether I say y or n; it seems it gets stuck and doesn't progress at all. There 
is no cpu usage. Any recommendations? I have attached the hippocampal subfields 
log.

More info:
-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202

RedHat release: CentOS release 6.7 (Final)

Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64

-


--
Maximilià Bautista-Perpinyà, BSc
Master student at Joint Master in Neuroscience (JMN)
Université de Strasbourg (in partnership with Universität Freiburg and 
Universität Basel)
&
Master Intern at Biological and Personality Psychology Laboratory
Department of Psychology, Universität Freiburg

(+49) 015759302368
maximila.bautista-perpi...@etu.unistra.fr
maxbau...@gmail.com

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Re: [Freesurfer] white matter edits not incorporated

[Harms, Michael]

That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).

I think some of the subsequent back-and-forth with Bruce and Nick was off
the list, so I’ve included the key email (where Bruce diagnosed the
problem) below.

Has this been fixed in the forthcoming FS 6.0?

thanks,
-MH

 snip 

ok, I see what's going on. Here is the sequence of calls:

1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
L408_base lh

Makes the white surface *without* using the aparc. Because there are a
string of "hypointensity" labels in the aseg, the white surface is frozen
in these locations.

2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
lh

internally recreates the white surface but doesn't save it. The frozen
vertices are allowed to move since the aparc *is* used in this call, and
the vertices are deemed to be in real cortical regions.

The pial surface then starts from the (inwards deformed but not written to
disk) white surface, and then settles inside the white surface that is on
disk.

I'm not sure how we settled on this logic. Why recreate the white surface?
Why not run with -nowhite -orig_pial white? That way the algorithm uses
the
white surface that the user can see and things should be consistent

Bruce

 end-snip 



--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 4/21/16, 9:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgw"  wrote:

Hi,

I followed the advice, and the White Matter surface looks much better;
however, now the pial surface is crossing the white matter surface.

I ran the following:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8

for those at Martinos the new subjid should indicate the new path.

I've attached a screenshot. Thank you in advance for any advice you can
give.

Thank You,
Dan

On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
> Hi Bruce,
>
> Thanks! I'll give it a whirl.
>
> d
>
> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>  wrote:
>> Hi Daniel
>>
>> the problems isn't that it it's ignoring the wm edits, it is that it
>>starts
>> the orig surface out there, but then retracts to the (same) visible
>> gray/white boundary that it found in the first place. For this type of
>> lesion I think what you should do is also edit those voxels in the
>>aseg.mgz
>> and change them to right-lesion. This should freeze the white surface
>>there
>> I think. If it doesn't, let me know and I'll fix it.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 19 Apr 2016, dgw wrote:
>>
>>> Here is the log for the most recent -autorecon2-wm call:
>>>
>>> Thanks!
>>> d
>>>
>>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>>  wrote:
 can you send us the recon-all.log? I don't see an obvious reason why
it
 wouldn't have worked
 On Tue, 19 Apr 2016, dgw wrote:

> Just to follow up, I have tried several different options with
> recon-all to get the white matter edits to stick on this participant,
> and it doesn't seem to be working:
>
> re-editing wm.mgz and running recon-all -autorecon2-wm
> re-editing wm.mgz and running recon-all -make all
>
> I can't seem to get any appreciable change in the white matter
> surface. I have attached a screenshot, for an example.
>
> hth
> d
>
>
> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>> Hi,
>>
>> I recently edited a brain with a gyral cyst, carefully filling the
>> cyst with white matter in the wm.mgz. Unfortunately after running:
>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>
>> none of the edits were incorporated.
>>
>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>
>> Is there some other misake?
>>
>> I followed this guide
>>
>>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
>>_freeview
>>
>> Thanks,
>> Dan
>
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 addressed. If you believe this e-mail was sent to you in error and
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 contains patient information, please contact the Partners Compliance
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 http://www.partners.org/complianceline . If the e-mail was 

Re: [Freesurfer] white matter edits not incorporated

[dgw]

Hi,

I followed the advice, and the White Matter surface looks much better;
however, now the pial surface is crossing the white matter surface.

I ran the following:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8

for those at Martinos the new subjid should indicate the new path.

I've attached a screenshot. Thank you in advance for any advice you can give.

Thank You,
Dan

On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
> Hi Bruce,
>
> Thanks! I'll give it a whirl.
>
> d
>
> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>  wrote:
>> Hi Daniel
>>
>> the problems isn't that it it's ignoring the wm edits, it is that it starts
>> the orig surface out there, but then retracts to the (same) visible
>> gray/white boundary that it found in the first place. For this type of
>> lesion I think what you should do is also edit those voxels in the aseg.mgz
>> and change them to right-lesion. This should freeze the white surface there
>> I think. If it doesn't, let me know and I'll fix it.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 19 Apr 2016, dgw wrote:
>>
>>> Here is the log for the most recent -autorecon2-wm call:
>>>
>>> Thanks!
>>> d
>>>
>>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>>  wrote:
 can you send us the recon-all.log? I don't see an obvious reason why it
 wouldn't have worked
 On Tue, 19 Apr 2016, dgw wrote:

> Just to follow up, I have tried several different options with
> recon-all to get the white matter edits to stick on this participant,
> and it doesn't seem to be working:
>
> re-editing wm.mgz and running recon-all -autorecon2-wm
> re-editing wm.mgz and running recon-all -make all
>
> I can't seem to get any appreciable change in the white matter
> surface. I have attached a screenshot, for an example.
>
> hth
> d
>
>
> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>> Hi,
>>
>> I recently edited a brain with a gyral cyst, carefully filling the
>> cyst with white matter in the wm.mgz. Unfortunately after running:
>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>
>> none of the edits were incorporated.
>>
>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>
>> Is there some other misake?
>>
>> I followed this guide
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>>
>> Thanks,
>> Dan
>
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[Freesurfer] Comparison of the slope of the pvr analysis between groups

[Sophie Maingault]

Dear FS experts,
There is  already a post about that but the concerned person never answered so 
there is no solution. 
I’m currently running per-vertex analyses with the --pvr flag of mri_glmfit 
command. I did correlations between 2 vertex-wise variables correcting for age. 
I also would like to compare the slope of the pvr between 2 groups: in my fsgd 
file I have the subject ID and the group.
I run the following command: mri_glmfit --y lh.1.448tvs.mgh --fsgd 
448_cate30.fsgd --C contrast1.mtx --surf fsaverage lh --cortex --glmdir 
glm.lh.12_448tvs --pvr lh.2.448tvs.mgh with contrast1.mtx = 0 0 -1 1. 
I get the following error: ERROR: dimension mismatch between X and contrast 
contrast1.mtx   X has 3 cols, C has 4 cols

Do you know where is my mistake and if it possible to do comparison of the 
slope of a pvr analysis between groups with mir_glmfit ?

Thank you for your help,
Best regards,
Sophie
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