Re: [Freesurfer] Using pre-segmented results

[Jordi Huguet]

External Email - Use Caution

Great, just what I was looking for!

Thanks Douglas,
Jordi

On Wed, Nov 27, 2019, 19:47 Greve, Douglas N.,Ph.D. 
wrote:

> It might work if you
> mkdir -p FOO/mri
> cp yourwm.mgz FOO/mri/wm.mgz
> cp inputdata.mgz FOO/mri/orig/001.mgz
> then run recon-all -s FOO -all
>
>
> On 11/27/2019 12:39 PM, Jordi Huguet wrote:
>
> External Email - Use Caution
> Hi Bruce,
>
> Many thanks for your reply.
>
> I understand from your answer that it could be done as follows (I am not
> an expert in FreeSurfer directives):
>
> a) run full FreeSurfer pipeline
> recon-all -s FOO
> b) insert pre-existing WM segmentation as wm.mgz (modifying the intensity
> values)
> c) re-run stages 15-23 and 24-31 (recon-all shall use my external
> segmentation as WM "edits")
> recon-all -s FOO -autorecon2-wm -autorecon3
>
> Is it possible however to just include the WM segmentation without
> executing a full early run of recon-all?
>
> Thanks,
> Jordi
>
>
> On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl 
> wrote:
>
>> Hi Jordi
>>
>> yes, this should be possible. You might need to run recon-all in stages
>> though. Although if you set the wm.mgz values from SPM to 255 and 1 (not
>> 0)
>> recon-all should detect them as "edits" and retain them
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 26 Nov 2019, Jordi Huguet wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Hi there,
>> > I wonder if its somehow possible to feed FreeSurfer's recon-all with
>> pre-existing segmented maps
>> > (based on prior segmentation procedure e.g. SPM or ANTs) to
>> "improve" FreeSurfer results.
>> >
>> > For some images I am working with the FreeSurfer's WM segmentation
>> output is not optimal so I am
>> > looking for alternatives to improve the final results on such specific
>> cases without requiring any
>> > manual intervention.
>> >
>> > Any comments, examples or shared reflections on this regard are kindly
>> welcome.
>> >
>> > Thanks in advance,
>> > Jordi Huguet
>> >
>> >___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
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[Freesurfer] 回复： Converting labels drew by freeview to volume Error: coordinate mismatch

[zorothus...@163.com]

External Email - Use CautionSorry i didn't make it clear. I mean the volume( nii file) converted by label does not match T1.___
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Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

[Bronwyn Overs]

External Email - Use Caution

Hi Kersten, 

No problem at al and thank you for your reply. 
While running my correction for multiple comparisons I store the df associated 
with each contrast vector using the following: 

[~,~,dflh] = find(F_lhstats.df(2,:)); 
[~,~,dfrh] = find(F_rhstats.df(2,:)); 
dfmodelh = {floor(mode(dflh))}; 
dfmoderh = {floor(mode(dfrh))}; 

So far the dfmodelh and dfmoderh have been identical. I then calculate the 
effect size for each cluster using the following steps: 
1. Derive the p-value from the Max threshold ('Max'), where p = 10 to the power 
of -abs(Max) 
2. Calculate the t-value associated with this p-value, using the relevant df 
for this contrast 
3. Calculate cohen's d using 't' and 'df', where d = (t*2)/(sqrt(df)) 

When the Max threshold is listed as -inf I cannot complete these calculations. 
Can you suggest an alternate method for generating effect sizes for these 
clusters? 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



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From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Thursday, November 28, 2019 12:29:18 AM 
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary 
file 



External Email - Use Caution 


Hi Bronwyn, Doug, 

sorry - I missed the other mail from two weeks ago (and have been absent for a 
few days), but I'm able to take a look now. 

You mention that your goal is to calculate effect sizes. Could you briefly let 
us know how you are planning to do it - this would help me to better understand 
the issue. 

Thanks, 

Kersten 

On Di, 2019-11-26 at 23:14 +, Greve, Douglas N.,Ph.D. wrote: 


can you send the cluster summary file? 

On 11/24/2019 7:09 PM, Bronwyn Overs wrote: 

BQ_BEGIN


External Email - Use Caution 
Hi Kersten, 

Following on from Douglas's reply, you may remember my analysis as I forwarded 
you some files in October (see [ 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html | 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html ] ). 
I followed your suggestions of removing the '--thmax 5' argument form 
'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap 
perfectly with the significance maps from the LME. However, now my largest 
clusters have a maximum threshold of '-inf' in my cluster summary files. Do you 
have any idea how to get around this problem so that I can use my max threshold 
values to calculate cluster-wise effect sizes? 




Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



[ https://twitter.com/neuraustralia | Twitter ] | [ 
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ 
http://www.neura.edu.au/help-research/subscribe | Subscribe ] 




From: "Greve, Douglas N.,Ph.D." [ mailto:dgr...@mgh.harvard.edu | 
 ] 
To: "Freesurfer support list" [ mailto:freesurfer@nmr.mgh.harvard.edu | 
 ] , "Kersten Diers, DZNE" [ 
mailto:kersten.di...@dzne.de | 
 ] 
Sent: Thursday, November 14, 2019 4:23:12 AM 
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary 
file 

I'll have to leave this one for Kersten as it appears that the LME stuff 
is generating and inf value 

On 11/12/19 7:05 PM, Bronwyn Overs wrote: 
> 
> External Email - Use Caution 
> 
> Hi Douglas, 
> 
> Yes I have looked at it in Freeview and I have attached a screenshot 
> for your reference. 
> 
> The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated 
> with a mass-univariate spatiotemporal model using 
> 'lme_mass_fit_EMinit' and then FDR correction was applied across both 
> hemispheres (lme_mass_FDR). I have provided analysis details and 
> syntax below. The B1B7 contrast represents the affect of years in cases. 
> 
> Sample: 
> Our sample includes 112 controls subjects, and 106 cases. All subjects 
> are aged between 12 and 30 years. 153 or these subjects have 2 
> time-points (77 control, 76 cases), while the remaining 65 individuals 
> have only 1 MRI time-point. We also have mixed ethnicites - 165 
> Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians). 
> 
> The QDEC file contains the following 6 variables: 
> 1. Y (years between scans) 
> 2. A (baseline age) 
> 3. G (group, 1=case, 0=control) 
> 4. S (sex, 1=female, 0=male) 
> 5. E1 (Ethnicity 1, 1=asian, 0=other) 
> 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other) 
> 
> Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)] 
> 

Re: [Freesurfer] Using pre-segmented results

[Greve, Douglas N.,Ph.D.]

It might work if you
mkdir -p FOO/mri
cp yourwm.mgz FOO/mri/wm.mgz
cp inputdata.mgz FOO/mri/orig/001.mgz
then run recon-all -s FOO -all


On 11/27/2019 12:39 PM, Jordi Huguet wrote:

External Email - Use Caution

Hi Bruce,

Many thanks for your reply.

I understand from your answer that it could be done as follows (I am not an 
expert in FreeSurfer directives):

a) run full FreeSurfer pipeline
recon-all -s FOO
b) insert pre-existing WM segmentation as wm.mgz (modifying the intensity 
values)
c) re-run stages 15-23 and 24-31 (recon-all shall use my external segmentation 
as WM "edits")
recon-all -s FOO -autorecon2-wm -autorecon3

Is it possible however to just include the WM segmentation without executing a 
full early run of recon-all?

Thanks,
Jordi


On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Jordi

yes, this should be possible. You might need to run recon-all in stages
though. Although if you set the wm.mgz values from SPM to 255 and 1 (not 0)
recon-all should detect them as "edits" and retain them

cheers
Bruce


On Tue, 26 Nov 2019, Jordi Huguet wrote:

>
> External Email - Use Caution
>
> Hi there,
> I wonder if its somehow possible to feed FreeSurfer's recon-all with 
> pre-existing segmented maps
> (based on prior segmentation procedure e.g. SPM or ANTs) to "improve" 
> FreeSurfer results.
>
> For some images I am working with the FreeSurfer's WM segmentation output is 
> not optimal so I am
> looking for alternatives to improve the final results on such specific cases 
> without requiring any
> manual intervention.
>
> Any comments, examples or shared reflections on this regard are kindly 
> welcome.
>
> Thanks in advance,
> Jordi Huguet
>
>___
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Re: [Freesurfer] Using pre-segmented results

[Jordi Huguet]

External Email - Use Caution

Hi Bruce,

Many thanks for your reply.

I understand from your answer that it could be done as follows (I am not an
expert in FreeSurfer directives):

a) run full FreeSurfer pipeline
recon-all -s FOO
b) insert pre-existing WM segmentation as wm.mgz (modifying the intensity
values)
c) re-run stages 15-23 and 24-31 (recon-all shall use my external
segmentation as WM "edits")
recon-all -s FOO -autorecon2-wm -autorecon3

Is it possible however to just include the WM segmentation without
executing a full early run of recon-all?

Thanks,
Jordi


On Tue, Nov 26, 2019 at 3:08 PM Bruce Fischl 
wrote:

> Hi Jordi
>
> yes, this should be possible. You might need to run recon-all in stages
> though. Although if you set the wm.mgz values from SPM to 255 and 1 (not
> 0)
> recon-all should detect them as "edits" and retain them
>
> cheers
> Bruce
>
>
> On Tue, 26 Nov 2019, Jordi Huguet wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi there,
> > I wonder if its somehow possible to feed FreeSurfer's recon-all with
> pre-existing segmented maps
> > (based on prior segmentation procedure e.g. SPM or ANTs) to
> "improve" FreeSurfer results.
> >
> > For some images I am working with the FreeSurfer's WM segmentation
> output is not optimal so I am
> > looking for alternatives to improve the final results on such specific
> cases without requiring any
> > manual intervention.
> >
> > Any comments, examples or shared reflections on this regard are kindly
> welcome.
> >
> > Thanks in advance,
> > Jordi Huguet
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Applying -qcache following manual edits

[Greve, Douglas N.,Ph.D.]

yes, in fact, what you have done is the preferred method. Just run recon-all 
with -qcache instead of -all (or any other directive). Also note that qdec is 
not very flexible, so you may want to use the command line stream.

On 11/27/2019 10:21 AM, Marisa Cathryn Ross wrote:

External Email - Use Caution
Hello,

We have a large set of images that have been processed in FS 6.0 (on linux) 
with manual edits for all stages of recon-all. We would like to utilize the 
QDEC package to do group analyses, but did not have the -qcache flag in our 
pipeline when we ran recon-all.

Is it possible to create the necessary fsaverage files without losing the 
manual edits? We have never generated these files, as -qcache has not been 
designated previously in our pipeline. If this is possible, how should we go 
about re-running recon-all with -qcache so as to not lose the manual edits?

Thank you,
Marisa Ross

--
Marisa C. Ross, MPA
PhD Candidate
Neuroscience and Public Policy Program
University of Wisconsin-Madison
mro...@wisc.edu




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Re: [Freesurfer] Converting labels drew by freeview to volume Error: coordinate mismatch

[Greve, Douglas N.,Ph.D.]

I'm not sure what the problem is. You say that they match when you load the T1 
and the sc. If so, what is the problem?

On 11/27/2019 7:57 AM, zorothustra wrote:

External Email - Use Caution

Hello Freesurfer Developers,

I'm trying to get superior colliculus' ROI mannually by freeview. I load 
"orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw 
the ROI and save it as a label file. After that I use "mri_label2vol --label 
sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial 
structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii 
--s SUB --regheader --noedit --reg register.dat", and it worked, but the 
coordinate mismatch, much different from the SC's position in the T1 space( 
Load T1.nii as volume and SC.label as ROI in freeview, and they are matched).
Can anyone help me? Thank you!

1)FreeSurfer version: freesurfer-local-build-dev-20191104
2)platform: Ubuntu 18.04







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[Freesurfer] Using individual atlas in PETSurfer

[Boris Rauchmann]

External Email - Use Caution

Dear all,

I have a LUT, a gca file for subcortical segmentation and two gcs files for
parcellation available. How can I get SUVRs for both the cortical and
subcortical structures?

I  tried using xcerebralseg to create a individual segmentation to replace
the apas+head.mgz but when I'm using gtmseg I only managed it to get
results for the cortical parcellation using a annot created from the two
gcs files (--ctx-annot atlas --ctab LUT). Can someone help me with this?

Best,
Boris
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[Freesurfer] Applying -qcache following manual edits

[Marisa Cathryn Ross]

External Email - Use Caution

Hello,

We have a large set of images that have been processed in FS 6.0 (on linux) 
with manual edits for all stages of recon-all. We would like to utilize the 
QDEC package to do group analyses, but did not have the -qcache flag in our 
pipeline when we ran recon-all.

Is it possible to create the necessary fsaverage files without losing the 
manual edits? We have never generated these files, as -qcache has not been 
designated previously in our pipeline. If this is possible, how should we go 
about re-running recon-all with -qcache so as to not lose the manual edits?

Thank you,
Marisa Ross

--
Marisa C. Ross, MPA
PhD Candidate
Neuroscience and Public Policy Program
University of Wisconsin-Madison
mro...@wisc.edu

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Re: [Freesurfer] freeview parallelized binary

[Hoopes, Andrew]

Hi Dustin,

The freeview binaries that we ship are the same binaries installed on the 
cluster. You should try specifying the number of threads available to openmp by 
setting the OMP_NUM_THREADS env variable to something like 4 or 8 on your local 
machine to see if this makes a difference.

Best,
Andrew


From:  on behalf of "Clark, Dustin 
Christopher" 
Reply-To: FS Help 
Date: Tuesday, November 26, 2019 at 9:43 AM
To: FS Help 
Subject: [Freesurfer] freeview parallelized binary


External Email - Use Caution
Hello,

We recently noticed freeview on the MGH cluster was using multiple cores when 
loading niftis, however, our local installation only uses one core when loading 
the same nifiti. Is it possible to get access to this freeview binary or the 
source code to build it for parallelization on our system? Thank you,

Dustin Clark
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Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

[Diers, Kersten /DZNE]

External Email - Use Caution

Hi Bronwyn, Doug,

sorry - I missed the other mail from two weeks ago (and have been absent for  a 
few days), but I'm able to take a look now.

You mention that your goal is to calculate effect sizes. Could you briefly let 
us know how you are planning to do it - this would help me to better understand 
the issue.

Thanks,

Kersten

On Di, 2019-11-26 at 23:14 +, Greve, Douglas N.,Ph.D. wrote:
can you send the cluster summary file?

On 11/24/2019 7:09 PM, Bronwyn Overs wrote:

External Email - Use Caution

Hi Kersten,

Following on from Douglas's reply, you may remember my analysis as I forwarded 
you some files in October (see 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html). I 
followed your suggestions of removing the '--thmax 5' argument form 
'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap 
perfectly with the significance maps from the LME. However, now my largest 
clusters have a maximum threshold of '-inf' in my cluster summary files. Do you 
have any idea how to get around this problem so that I can use my max threshold 
values to calculate cluster-wise effect sizes?



Kind regards,


Bronwyn Overs

Research Assistant

[cid:1574861358.21520.14.camel@dzne.de]


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725


neura.edu.au 


Twitter | 
Facebook | 
Subscribe




From: "Greve, Douglas N.,Ph.D." 

To: "Freesurfer support list" 
, 
"Kersten Diers, DZNE" 
Sent: Thursday, November 14, 2019 4:23:12 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

I'll have to leave this one for Kersten as it appears that the LME stuff
is generating and inf value

On 11/12/19 7:05 PM, Bronwyn Overs wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Yes I have looked at it in Freeview and I have attached a screenshot
> for your reference.
>
> The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated
> with a mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit' and then FDR correction was applied across both
> hemispheres (lme_mass_FDR). I have provided analysis details and
> syntax below. The B1B7 contrast represents the affect of years in cases.
>
> Sample:
> Our sample includes 112 controls subjects, and 106 cases. All subjects
> are aged between 12 and 30 years. 153 or these subjects have 2
> time-points (77 control, 76 cases), while the remaining 65 individuals
> have only 1 MRI time-point. We also have mixed ethnicites - 165
> Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
>
> The QDEC file contains the following 6 variables:
> 1. Y (years between scans)
> 2. A (baseline age)
> 3. G (group, 1=case, 0=control)
> 4. S (sex, 1=female, 0=male)
> 5. E1 (Ethnicity 1, 1=asian, 0=other)
> 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other)
>
> Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)]
>i.e. main effects for each of the qdec variables + an
> interaction term for years X group
>
> DVs: Cortical thickness, area and volume
>
> Model: Mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit'
> CODE:
>   % Read in surface files
>   [Y,mri] = fs_read_Y(mgh);
>   % Read in qdec file
>   Qdec = fReadQdec(qdec);
>   % Remove fsid from qdec
>   Qdec = rmQdecCol(Qdec,1);
>   % Store col 1 (fsid-base) in sID variable
>   sID = Qdec(2:end,1);
>   % Remove col 1 (fsid-base) from Qdec array
>   Qdec = rmQdecCol(Qdec,1);
>   % Convert Qdec to numeric matrix M
>   M = Qdec2num(Qdec);
>   % Sort data and evaluate design matrix
>   [M,Y,ni] = sortData(M,1,Y,sID);
>   X = eval([ones(length(M),1) M M(:,1).*M(:,3)])
>   % Compute vertex-wise temporal covariance estimates.
>   [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3);
>   %Segmentation and model fitting.
>   [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y,
> ni);
>   %Check surfaces.
>   surfcomp(Th0, RgMeans, sphere, fig1, fig2)
>
> Correction for multiple comparisons: FDR across both hemispheres
> CODE:
>   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);
>   altfdr(r,2) = num2cell(abs(log10(lme_mass_FDR(P,0.05;
>   pcor = -log10(pth);
>   [~,~,dflh] = find(F_lhstats.df(2,:));
>   [~,~,dfrh] = find(F_rhstats.df(2,:));
>   dfmodelh(r,2) = {floor(mode(dflh))};
>   dfmoderh(r,2) = {floor(mode(dfrh))};
>   thrlh(r,2) = {pcor};
>   thrrh(r,2) = {pcor};
>   [~,dc] = size(detvtx);
>   dvtx(r,2) = {dc};
>
> Kind regards,
>
>
> 

[Freesurfer] Converting labels drew by freeview to volume Error: coordinate mismatch

[zorothustra]

External Email - Use Caution

Hello Freesurfer Developers,


I'm trying to get superior colliculus' ROI mannually by freeview. I load 
"orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw 
the ROI and save it as a label file. After that I use "mri_label2vol --label 
sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial 
structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii 
--s SUB --regheader --noedit --reg register.dat", and it worked, but the 
coordinate mismatch, much different from the SC's position in the T1 space( 
Load T1.nii as volume and SC.label as ROI in freeview, and they are matched).
Can anyone help me? Thank you!


1)FreeSurfer version: freesurfer-local-build-dev-20191104
2)platform: Ubuntu 18.04___
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