Re: [Freesurfer] Beta values (resubmitting)

[Douglas N. Greve]

oh, yes, that is correct for DOSS

On 4/26/2022 3:38 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Ok.
In this case I used the DOSS model (I tested the interaction before 
and it was not significant). So wouldn't the two groups have the same 
slope?

But the beta values extraction file has only 3 lines (image below).


To extract the beta values I used this command:
mri_segstats --seg 
lh.CU_CI_CSF_doss.glmdir/cortisol.diff/perm.th20.neg.sig.ocn.mgh --i 
lh.CU_CI_CSF_doss.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.CU_CI_CSF.cortisol.beta.clusters.dat


Thank you so much,
Laura.


*De:* Douglas N. Greve 
*Enviado:* terça-feira, 26 de abril de 2022 15:01
*Para:* Laura Willers de Souza 
*Cc:* freesurfer@nmr.mgh.harvard.edu 
*Assunto:* Re: [Freesurfer] Beta values (resubmitting)
3rd line for the slope of CU, 4th line for the slope of CI

On 4/25/2022 4:03 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Thanks so much!

I would also like to confirm that I am interpreting the beta values 
correctly for a second model.


Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate 
effect.


The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)


The file with the beta values contains 3 lines (image below).

  * The first line would be the beta value for the intercept of the
1st group; the second line for the intercept of the 2nd group;
and the third line for the slope of the covariate?
  o Thus the glm equation for the 1st cluster would be:
  o 1st group  cortical thickness = 2.64 - 0.12X + n
  o 2nd group --- cortical thickness = 2.54 – 0.12X + n

Am I interpreting correctly?

Thank you very much for all the help!
*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil




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Re: [Freesurfer] Beta values (resubmitting)

[Laura Willers de Souza]

External Email - Use Caution

Ok.
In this case I used the DOSS model (I tested the interaction before and it was 
not significant). So wouldn't the two groups have the same slope?
But the beta values extraction file has only 3 lines (image below).
[cid:67fd98ba-4655-445d-bdc7-fd5bbb6e6bb2]

To extract the beta values I used this command:
mri_segstats --seg 
lh.CU_CI_CSF_doss.glmdir/cortisol.diff/perm.th20.neg.sig.ocn.mgh --i 
lh.CU_CI_CSF_doss.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.CU_CI_CSF.cortisol.beta.clusters.dat

Thank you so much,
Laura.


De: Douglas N. Greve 
Enviado: terça-feira, 26 de abril de 2022 15:01
Para: Laura Willers de Souza 
Cc: freesurfer@nmr.mgh.harvard.edu 
Assunto: Re: [Freesurfer] Beta values (resubmitting)

3rd line for the slope of CU, 4th line for the slope of CI

On 4/25/2022 4:03 PM, Laura Willers de Souza wrote:

External Email - Use Caution

Thanks so much!



I would also like to confirm that I am interpreting the beta values correctly 
for a second model.



Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate effect.




The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)


The file with the beta values contains 3 lines (image below).

[cid:part1.KvgY07aY.UPvnt0iC@mgh.harvard.edu]

  *   The first line would be the beta value for the intercept of the 1st 
group; the second line for the intercept of the 2nd group; and the third line 
for the slope of the covariate?
 *   Thus the glm equation for the 1st cluster would be:
 *   1st group  cortical thickness = 2.64 - 0.12X + n
 *   2nd group --- cortical thickness = 2.54 – 0.12X + n



Am I interpreting correctly?



Thank you very much for all the help!




Laura Willers de Souza


Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil





The information in this e-mail is intended only for the person to whom it is 
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Re: [Freesurfer] Beta values (resubmitting)

[Douglas N. Greve]

3rd line for the slope of CU, 4th line for the slope of CI

On 4/25/2022 4:03 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Thanks so much!

I would also like to confirm that I am interpreting the beta values 
correctly for a second model.


Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate 
effect.


The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)


The file with the beta values contains 3 lines (image below).

  * The first line would be the beta value for the intercept of the
1st group; the second line for the intercept of the 2nd group; and
the third line for the slope of the covariate?
  o Thus the glm equation for the 1st cluster would be:
  o 1st group  cortical thickness = 2.64 - 0.12X + n
  o 2nd group --- cortical thickness = 2.54 – 0.12X + n

Am I interpreting correctly?

Thank you very much for all the help!
*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


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 .
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Re: [Freesurfer] Beta values (resubmitting)

[Laura Willers de Souza]

External Email - Use Caution

Thanks so much!

I would also like to confirm that I am interpreting the beta values correctly 
for a second model.

Model 2: Two Groups, One Covariate

Contrasts (DOSS): difference between the group intercepts; covariate effect.


The fsgd file looks like this:

GroupDescriptorFile 1

Title CU_CI_CSF
MeasurementName thickness
Class CU
Class CI
Variables cortisolCSF
Input 011_S_0003_S9128 CI 2.397895273
Input 022_S_0004_S9233 CI 2.772588722
Input 011_S_0005_S9137 CU 3.044522438
Input 011_S_0008_S9196 CU 2.397895273
Input 011_S_0010_S8800 CI 2.151762203

... (n=300)

The file with the beta values contains 3 lines (image below).
[cid:image003.png@01D858C5.3392CD10]

  *   The first line would be the beta value for the intercept of the 1st 
group; the second line for the intercept of the 2nd group; and the third line 
for the slope of the covariate?
 *   Thus the glm equation for the 1st cluster would be:
 *   1st group  cortical thickness = 2.64 - 0.12X + n
 *   2nd group --- cortical thickness = 2.54 – 0.12X + n


Am I interpreting correctly?


Thank you very much for all the help!


Laura Willers de Souza

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


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Re: [Freesurfer] Beta values (resubmitting)

[Douglas N. Greve]

Yes, first line intercept, 2nd line slope

On 4/12/2022 3:44 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Hey! I'm resending this email because I think it got lost on the list.

Hello FreeSurfer Developers,

I'm extracting beta values​​from some analyzes and I would like toknow 
if I'm extracting and interpreting these values​​correctly.


To extract the beta values ​​I used this command:

mri_segstats 
--seglh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh--i 
lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 
--avgwflh.cortisol_CSF.beta.clusters.dat


The model consists of 1 group and 1 covariate.
I used the contrasts for intercept and slope.
The fsgd file looks like this:
GroupDescriptorFile 1
Title cortisol_CSF
Class Main
Variablescortisol_CSF
Input011_S_0003_S9128Main2.397895273
Input022_S_0004_S9233Main2.772588722
Input011_S_0005_S9137Main3.044522438
Input011_S_0008_S9196Main2.397895273
Input011_S_0010_S8800Main2.151762203
... (n=300)
The beta values ​​extraction file contains 2 lines (image below).

  *  Would the first line be the beta value for the intercept and the
second line for the slope?
  * Thus the glm equation for the 1st cluster would be: cortical
thickness = 2.57 - 0.12X + n
Is this correct?
Thank you very much in advance.
*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil



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[Freesurfer] Beta values (resubmitting)

[Laura Willers de Souza]

External Email - Use Caution

Hey! I'm resending this email because I think it got lost on the list.


Hello FreeSurfer Developers,



I'm extracting beta values ​​from some analyzes and I would like to know if I'm 
extracting and interpreting these values ​​correctly.



To extract the beta values ​​I used this command:

mri_segstats --seg 
lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i 
lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.cortisol_CSF.beta.clusters.dat



The model consists of 1 group and 1 covariate.

I used the contrasts for intercept and slope.

The fsgd file looks like this:



GroupDescriptorFile 1

Title cortisol_CSF

Class Main

Variables  cortisol_CSF

Input   011_S_0003_S9128   Main2.397895273

Input   022_S_0004_S9233   Main2.772588722

Input   011_S_0005_S9137   Main3.044522438

Input   011_S_0008_S9196   Main2.397895273

Input   011_S_0010_S8800   Main2.151762203

... (n=300)


The beta values ​​extraction file contains 2 lines (image below).

[cid:69d5a8c2-68b8-43ac-85f3-0448f1e3a0b5]

  *Would the first line be the beta value for the intercept and the second 
line for the slope?
  *   Thus the glm equation for the 1st cluster would be:cortical thickness 
= 2.57 - 0.12X + n

Is this correct?


Thank you very much in advance.


Laura Willers de Souza

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil

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Re: [Freesurfer] Beta values

[Laura Willers de Souza]

External Email - Use Caution

Sure! The fsgd file looks like this:



GroupDescriptorFile 1

Title cortisol_CSF

Class Main

Variables  cortisol_CSF

Input   011_S_0003_S9128   Main2.397895273

Input   022_S_0004_S9233   Main2.772588722

Input   011_S_0005_S9137   Main3.044522438

Input   011_S_0008_S9196   Main2.397895273

Input   011_S_0010_S8800   Main2.151762203

... (n=300)



Best,

Laura.





-



On 4/3/2022, Douglas N. Greve wrote:



Can you send the fsgd file?





On 4/1/2022, Laura Willers de Souza wrote:



Hello FreeSurfer Developers,


I'm extracting beta values ​​from some analyzes and I would like to know if I'm 
extracting and interpreting these values ​​correctly.



To extract the beta values ​​I used this command:
mri_segstats --seg 
lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i 
lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.cortisol_CSF.beta.clusters.dat



The model consists of 1 group and 1 covariate.

I used the contrasts for intercept and slope.

The beta values ​​extraction file contains 2 lines (image below).

[cid:228fe1e8-abaa-4279-83ec-5c81c3fb6a37]

  * Would the first line be the beta value for the intercept and the

second line for the slope?

  * Thus the glm equation for the 1st cluster would be:   cortical

thickness = 2.57 - 0.12X + n





Is this correct?

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Re: [Freesurfer] Beta values

[Douglas N. Greve]

Can you send the fsgd file?

On 4/1/2022 3:28 PM, Laura Willers de Souza wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm extracting beta values ​​from some analyzes and I would like to 
know if I'm extracting and interpreting these values ​​correctly.


To extract the beta values ​​I used this command:
mri_segstats --seg 
lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh 
--i lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.cortisol_CSF.beta.clusters.dat


The model consists of 1 group and 1 covariate.
I used the contrasts for intercept and slope.
The beta values ​​extraction file contains 2 lines (image below).

  * Would the first line be the beta value for the intercept and the
second line for the slope?
  * Thus the glm equation for the 1st cluster would be:   cortical
thickness = 2.57 - 0.12X + n


Is this correct?

Thanks in advance!

*Laura Willers de Souza *

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil


___
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The information in this e-mail is intended only for the person to whom it is 
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Beta values

[Laura Willers de Souza]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm extracting beta values ​​from some analyzes and I would like to know if I'm 
extracting and interpreting these values ​​correctly.

To extract the beta values ​​I used this command:
mri_segstats --seg 
lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i 
lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.cortisol_CSF.beta.clusters.dat

The model consists of 1 group and 1 covariate.
I used the contrasts for intercept and slope.
The beta values ​​extraction file contains 2 lines (image below).
[cid:c5a3c332-10fc-4726-b15e-672b02ded1fa]

  *   Would the first line be the beta value for the intercept and the second 
line for the slope?
  *   Thus the glm equation for the 1st cluster would be:   cortical thickness 
= 2.57 - 0.12X + n

Is this correct?

Thanks in advance!

Laura Willers de Souza

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil
___
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
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Re: [Freesurfer] beta coefficients

[Douglas N. Greve]

I have not had time to do the math on this one. Rather than wait for me, 
you can just create your own design matrix with the regressors as 
reflected in your equation. Look at glmdir/Xg.dat for an example.


On 2/5/2021 3:14 AM, Marina Fernández wrote:


External Email - Use Caution

Dear experts,

In addition to t and p-value, I would like to report the beta 
coefficient of the fixed effects in the following regression equation 
for the vertex showing the max statistic within the cluster that 
survived multiple comparison correction:


y = β0 + β1*sex + β2*age + β3*(sex+age) + e

I know that beta.mgh contains the beta estimates corresponding to the 
intercepts of male and female and the slopes of age for each sex. 
However, what I need is the beta corresponding to the intercept (β0), 
and the beta for the slope of sex (β1), age (β2) and sex*age 
interaction (β3). I also


need the residual variance of the model (e), but rvar.mgh contains 4 
values, 2 for the intercepts and another two for the slopes. I would 
really appreciate if you could help me to obtain this information.


Thanks a lot in advance

Marina


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[Freesurfer] beta coefficients

[Marina Fernández]

External Email - Use Caution

Dear experts,



In addition to t and p-value, I would like to report the beta coefficient
of the fixed effects in the following regression equation for the vertex
showing the max statistic within the cluster that survived multiple
comparison correction:



y = β0 + β1*sex + β2*age + β3*(sex+age) + e



I know that beta.mgh contains the beta estimates corresponding to the
intercepts of male and female and the slopes of age for each sex. However,
what I need is the beta corresponding to the intercept (β0), and the beta
for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also

need the residual variance of the model (e), but rvar.mgh contains 4
values, 2 for the intercepts and another two for the slopes. I would really
appreciate if you could help me to obtain this information.



Thanks a lot in advance



Marina
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[Freesurfer] beta coefficient of the fixed effects

[Marina Fernández]

External Email - Use Caution

Dear Doug,



In addition to t and p-value, I would like to report the beta coefficient
of the fixed effects in the following regression equation for the vertex
showing the max statistic within the cluster that survived multiple
comparison correction:



y = β0 + β1*sex + β2*age + β3*(sex+age) + e



I know that beta.mgh contains the beta estimates corresponding to the
intercepts of male and female and the slopes of age for each sex. However,
what I need is the beta corresponding to the intercept (β0), and the beta
for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also
need the residual variance of the model (e), but rvar.mgh contains 4
values, 2 for the intercepts and another two for the slopes. I would really
appreciate if you could help me to obtain this information.



Thanks a lot in advance

Marina
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Re: [Freesurfer] beta testing FreeSurfer v7 beta: recon-all-status.log, samseg

[Douglas N. Greve]

Yes, if you want to run it now, use
samseg --i orig.mgz --i T2.mgz --o samsegdir
And don't use the T1.mgz
I have fixed this bug in the version that we will release. I mostly 
wanted to make sure that samseg itself would run.



On 2/25/2020 3:08 PM, Antonin Skoch wrote:


External Email - Use Caution

Dear experts,

I began to test beta v7 version of FreeSurfer.

I noticed that some entries in recon-all-status.log seem missing (i.e. 
white and pial surface placement - there is entry Cortical Parc while 
following entry is Refine Pial Surfs).


Running
samseg` --t1w $s/mri/T1.mgz --t2w $s/mri/T2.mgz --s $s --refmode t1w
exits with error in samseg2recon since command

set segvol = `find "$samsegdir" -iname "*crispSegmentation.nii" -print`

results with empty string set to segvol variable.

Antonin

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[Freesurfer] beta testing FreeSurfer v7 beta: recon-all-status.log, samseg

[Antonin Skoch]

External Email - Use Caution

Dear experts,


I began to test beta v7 version of FreeSurfer.


I noticed that some entries in recon-all-status.log seem missing (i.e. white 
and pial surface placement - there is entry Cortical Parc while following entry 
is Refine Pial Surfs).


Running 

samseg` --t1w $s/mri/T1.mgz --t2w $s/mri/T2.mgz --s $s --refmode t1w
exits with error in samseg2recon since command



set segvol = `find "$samsegdir" -iname "*crispSegmentation.nii" -print`


results with empty string set to segvol variable.


Antonin

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Re: [Freesurfer] Beta extraction

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

The betas are averages across subject, so you should not get one for 
each subject

On 2/27/19 4:34 PM, Jahan, Bushra wrote:
>
> When I ran the following command (with our data), I got the average 
> beta values for each segmentation i.e. only 5 beta values (as opposed 
> to 5 beta values for each subject).
>
>
> mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
> beta.clusters.dat
>
>
> That said, is it necessarily to run the previous command for each 
> subject  (in order to extract 5 beta values for each subject) or is 
> there way to extract betas for each subject from the group analysis?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Thursday, November 29, 2018 11:19:33 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Beta extraction
> Use something like
> mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
> beta.clusters.dat
>
> See mri_glmfit-sim --help for more info on the OCN file and mri_segstats
> --help for info on the avgwf file
>
>
> On 11/29/2018 04:40 PM, Jahan, Bushra wrote:
> > I am wondering how to extract beta values from the clusters of task
> > functional data, particularly output of the multiple comparisons
> > correction?
> >
> > Aava Jahan
> >
> >
> > ___
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[Freesurfer] Beta Extraction

[Jahan, Bushra]

When I ran the following command (with our data), I got the average beta values 
for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for 
each subject).


mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat


That said, is it necessarily to run the previous command for each subject  (in 
order to extract 5 beta values for each subject) or is there way to extract 
betas for each subject from the group analysis?

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Re: [Freesurfer] Beta extraction

[Jahan, Bushra]

When I ran the following command (with our data), I got the average beta values 
for each segmentation i.e. only 5 beta values (as opposed to 5 beta values for 
each subject).


mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat


That said, is it necessarily to run the previous command for each subject  (in 
order to extract 5 beta values for each subject) or is there way to extract 
betas for each subject from the group analysis?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Thursday, November 29, 2018 11:19:33 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Beta extraction

Use something like
mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
beta.clusters.dat

See mri_glmfit-sim --help for more info on the OCN file and mri_segstats
--help for info on the avgwf file


On 11/29/2018 04:40 PM, Jahan, Bushra wrote:
> I am wondering how to extract beta values from the clusters of task
> functional data, particularly output of the multiple comparisons
> correction?
>
> Aava Jahan
>
>
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[Freesurfer] Beta series method in FS?

[Hahn, Emily M.]

Hi, I am interested in using the beta series method 
(https://neuroscape.ucsf.edu/wp-content/uploads/publications/Rissman2004-Measuring-functional-connectivity-during-distinct-stages-of-a-cognitive-task.pdf)
 for intra-subject analysis. Is there a straightforward way to do this in 
FreeSurfer? 

I attempted and the following analysis (code starting @ foreach) and an error 
appeared at the selxavg3-sess step:
ERROR: condition ids are not contiguous

Should I include a positive contrast for each condition (i.e. instead of 
'-no-con-ok', use 'mkcontrast-sess -analysis $analysis -contrast $contrast -a 
$1_to_194') or is something else about the design erroneous? Thank you in 
advance for feedback.

Notes regarding the paradigm file:
(1) treats each condition type as a unique event (i.e. second column consists 
of numbers 1:194; $Nconditions = 194)
(2) stim weight == 1 (i.e. third column all ones) 

foreach cortices ( lh rh )

mkanalysis-sess \
-fsd $fsd \
-surface fsaverage $cortices \
-fwhm $FWHM \
-event-related \
-paradigm $paradigm \
-nconditions $Nconditions \
-spmhrf 0 \
-TR $TR \
-refeventdur $EVENT_DUR \
-nskip $Nskip \
-hpf $HPF \
-analysis bsm.analyses.$cortices \
-per-run \
-nuisreg $MC_nuis -1 \
-tpexclude $MCR_censor \
-force

end

foreach cortices ( lh rh )

selxavg3-sess \
-s $SUBJECT \
-analysis bsm.analyses.$cortices \
-no-con-ok

end

--
Emily M. Hahn | Clinical-Computational Research Coordinator
Division of Neurotherapeutics | A.A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital/Harvard Medical School
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Re: [Freesurfer] Beta extraction

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

Use something like
mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf 
beta.clusters.dat

See mri_glmfit-sim --help for more info on the OCN file and mri_segstats 
--help for info on the avgwf file


On 11/29/2018 04:40 PM, Jahan, Bushra wrote:
> I am wondering how to extract beta values from the clusters of task 
> functional data, particularly output of the multiple comparisons 
> correction?
>
> Aava Jahan
>
>
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[Freesurfer] Beta extraction

[Jahan, Bushra]

I am wondering how to extract beta values from the clusters of task functional 
data, particularly output of the multiple comparisons correction?

Aava Jahan
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Re: [Freesurfer] Beta-Zero Correction - No Phase File

[Afzal, Afsana]

Hi Doug, 

Thanks for getting back to me. I've tried mri_convert $Input_file --split 
$Output_file to split up the fieldmaps but I'm getting 6 to 12 different 
outputs (depending on the fieldmap) rather than just the mag and phase files 
which is what I was expecting. 

Have you encountered this before and is there another way to unpack the 
fieldmaps into just the mag and phase components? 

Thanks so much for you time, 

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2016 12:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Beta-Zero Correction - No Phase File

You can extract frames from a multi frame file with
mri_convert input.nii.gz --frame 0 output.frame0.nii.gz


On 07/12/2016 02:29 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm working with a dataset that outputs only one file (not two
> separate mag and phase files) for the fieldmap. The data was also
> collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx
> (not sure if this is the reason the fieldmaps are unpacking
> differently). I've attached the .dat file for one of the fieldmaps in
> this email.
>
> If there a way to separate out the mag and phase from the single
> fieldmap file so I can use epidewarp.fsl?
>
> Thanks,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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--
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] Beta-Zero Correction - No Phase File

[Douglas N Greve]

You can extract frames from a multi frame file with
mri_convert input.nii.gz --frame 0 output.frame0.nii.gz


On 07/12/2016 02:29 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm working with a dataset that outputs only one file (not two 
> separate mag and phase files) for the fieldmap. The data was also 
> collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx 
> (not sure if this is the reason the fieldmaps are unpacking 
> differently). I've attached the .dat file for one of the fieldmaps in 
> this email.
>
> If there a way to separate out the mag and phase from the single 
> fieldmap file so I can use epidewarp.fsl?
>
> Thanks,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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-- 
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] Beta-Zero Correction - No Phase File

[dgw]

If both phase and magnitude data are there, you could use fslroi to 
separate the images out into two separate files.

hth
d

On 7/14/16 9:52 AM, Afzal, Afsana wrote:
> Hi,
>
> Just wanted to follow up on the issue of just having one fieldmap file
> for beta-zero correction outlined below.
>
> Thanks for your help,
>
> Afsana
>
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
> [aaf...@mgh.harvard.edu]
> *Sent:* Tuesday, July 12, 2016 2:29 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Beta-Zero Correction - No Phase File
>
> Hi,
>
> I'm working with a dataset that outputs only one file (not two separate
> mag and phase files) for the fieldmap. The data was also collected on
> non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this
> is the reason the fieldmaps are unpacking differently). I've attached
> the .dat file for one of the fieldmaps in this email.
>
> If there a way to separate out the mag and phase from the single
> fieldmap file so I can use epidewarp.fsl?
>
> Thanks,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
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>
>
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> 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 
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] Beta-Zero Correction - No Phase File

[Afzal, Afsana]

Hi,

Just wanted to follow up on the issue of just having one fieldmap file for 
beta-zero correction outlined below.

Thanks for your help,

Afsana


__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana 
[aaf...@mgh.harvard.edu]
Sent: Tuesday, July 12, 2016 2:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Beta-Zero Correction - No Phase File

Hi,

I'm working with a dataset that outputs only one file (not two separate mag and 
phase files) for the fieldmap. The data was also collected on non-Siemens 
scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the 
fieldmaps are unpacking differently). I've attached the .dat file for one of 
the fieldmaps in this email.

If there a way to separate out the mag and phase from the single fieldmap file 
so I can use epidewarp.fsl?

Thanks,

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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[Freesurfer] Beta-Zero Correction - No Phase File

[Afzal, Afsana]

Hi,

I'm working with a dataset that outputs only one file (not two separate mag and 
phase files) for the fieldmap. The data was also collected on non-Siemens 
scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the 
fieldmaps are unpacking differently). I've attached the .dat file for one of 
the fieldmaps in this email.

If there a way to separate out the mag and phase from the single fieldmap file 
so I can use epidewarp.fsl?

Thanks,

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


b0map-infodump.dat
Description: b0map-infodump.dat
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Re: [Freesurfer] beta value

[Xiaomin Yue]

Do you mean by contrasting a condition vs fixation?

Xiaomin




On Mon, May 18, 2015 at 7:07 AM -0700, Douglas Greve 
gr...@nmr.mgh.harvard.edu wrote:
Yes, but you have to set up the contrasts, it won't do it automatically

On 5/16/15 10:48 PM, Xiaomin Yue wrote:
 Hi,

 During the processing of functional data, can fsfast generate outputs
 of the significants for each beta values modeled in the design matrix?

 Thanks,
 XIaomin


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Re: [Freesurfer] beta value

[Douglas Greve]

yes

On 5/18/15 10:38 AM, Xiaomin Yue wrote:

Do you mean by contrasting a condition vs fixation?

Xiaomin




On Mon, May 18, 2015 at 7:07 AM -0700, Douglas Greve 
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


Yes, but you have to set up the contrasts, it won't do it automatically

On 5/16/15 10:48 PM, Xiaomin Yue wrote:

Hi,

During the processing of functional data, can fsfast generate outputs 
of the significants for each beta values modeled in the design matrix?


Thanks,
XIaomin


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Re: [Freesurfer] beta value

[Xiaomin Yue]

Thanks

Xiaomin




On Mon, May 18, 2015 at 9:15 AM -0700, Douglas Greve 
gr...@nmr.mgh.harvard.edu wrote:
yes

On 5/18/15 10:38 AM, Xiaomin Yue wrote:
 Do you mean by contrasting a condition vs fixation?

 Xiaomin




 On Mon, May 18, 2015 at 7:07 AM -0700, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Yes, but you have to set up the contrasts, it won't do it automatically

 On 5/16/15 10:48 PM, Xiaomin Yue wrote:
 Hi,

 During the processing of functional data, can fsfast generate outputs
 of the significants for each beta values modeled in the design matrix?

 Thanks,
 XIaomin


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[Freesurfer] beta value

[Xiaomin Yue]

Hi,
During the processing of functional data, can fsfast generate outputs of the 
significants for each beta values modeled in the design matrix?
Thanks,XIaomin___
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Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

I implemented the ROI percent signal change formula following the MarsBaR FAQ 
(http://marsbar.sourceforge.net/faq.html) but the values I'm getting seem too 
small (on the order of .0002%).  Basically the formula is the (beta * peak 
absolute value of the canonical HRF regressor * 100)/(run mean).  No 
derivatives in this case as it is a boxcar design.

I took the mean across all the runs since FSFAST uses the same regressor across 
the entire experiment (unlike SPM).
I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF as you 
suggested (where m equals the condition+1). 

Is it possible that I'm missing something in the scaling here?  Especially with 
a boxcar design, the signal change should be much larger than this for a 
significant cluster, I think.  For example, the peak HRF value for one of the 
conditions is 0.0092.  If the betas are already scaled according to the peak 
value, then it would come out as .02%, which is more reasonable, although still 
too small.

Thanks for your help with this!

Joe



On May 31, 2013, at 5:02 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 
 Oh, right, it is probably not there for subcortical. I don't know what I 
 would have to do to write it out. It won't be something that happens 
 before I get back from HBM. Can you remind me after HBM?
 doug
 
 On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values 
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the 
 surface-based lh and rh spaces.  For the subcortical volume-based 
 analysis I don't see the corresponding corrected voxel p-values being 
 available?
 
 On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com wrote:
 
 
 On May 31, 2013, at 12:11 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but
 I have a remaining question:
 
 I assume the contents of sig.nii.gz (which I assume are the vertex
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected
 vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is
 corrected on a voxelwise basis (the th13 is just part of the name 
 but it
 should be the same regardless of the threshold you choose)
 doug
 
 Excellent!  Thanks!  :)
 
 
 Thanks again for your patience!
 
 Joe
 
 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:
 
 Just to make sure I'm doing this right, I'm going to summarize what
 I've taken away from your answers and to ask some new questions. In
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
 from the group level analysis to generate a mask for each cluster of
 interest.
 Then I could extract the value of the voxels from each
 subject's cespct file for each contrast, average them across the
 cluster ROI, then average them across each subject, to generate the
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from
 the cache.th20.pos/neg.sig.cluster.summary files from the group level
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get
 this information?
 I can use these coordinates to get the peak voxel T by getting the
 value from the group level F.nii.gz file and taking its square root.
 How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel
 coordinates into the Atlas coordinates to look up the putative BA and
 landmarks (unless there is a better way with Freesurfer?  I'm seeing
 some references to some BA labels in the forum but it doesn't look
 like this is a complete set yet?).
 
 Sorry for all these questions!  I got some nice results from FSFAST
 and would like to get them written up.
 
 Cheers!
 
 Joe
 
 
 
 
 On May 29, 2013, at 10:53 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

then I get on the order of .02% difference between the contrasted conditions.
The run mean values are in my expected ballpark of about 100 or so.
The condition betas are just very very small.
Or perhaps this is typical of FSFAST analyses?

On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 
 The beta's have already been scaled. What do you get if you just 
 beta/runmean ?
 
 
 
 On 07/17/2013 01:45 PM, Joseph Dien wrote:
 I implemented the ROI percent signal change formula following the 
 MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values 
 I'm getting seem too small (on the order of .0002%).  Basically the 
 formula is the (beta * peak absolute value of the canonical HRF 
 regressor * 100)/(run mean).  No derivatives in this case as it is a 
 boxcar design.
 
 I took the mean across all the runs since FSFAST uses the same 
 regressor across the entire experiment (unlike SPM).
 I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF 
 as you suggested (where m equals the condition+1).
 
 Is it possible that I'm missing something in the scaling here? 
 Especially with a boxcar design, the signal change should be much 
 larger than this for a significant cluster, I think.  For example, the 
 peak HRF value for one of the conditions is 0.0092.  If the betas are 
 already scaled according to the peak value, then it would come out as 
 .02%, which is more reasonable, although still too small.
 
 Thanks for your help with this!
 
 Joe
 
 
 
 On May 31, 2013, at 5:02 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 Oh, right, it is probably not there for subcortical. I don't know what I
 would have to do to write it out. It won't be something that happens
 before I get back from HBM. Can you remind me after HBM?
 doug
 
 On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
 surface-based lh and rh spaces.  For the subcortical volume-based
 analysis I don't see the corresponding corrected voxel p-values being
 available?
 
 On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:
 
 
 On May 31, 2013, at 12:11 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but
 I have a remaining question:
 
 I assume the contents of sig.nii.gz (which I assume are the vertex
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected
 vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is
 corrected on a voxelwise basis (the th13 is just part of the name
 but it
 should be the same regardless of the threshold you choose)
 doug
 
 Excellent!  Thanks!  :)
 
 
 Thanks again for your patience!
 
 Joe
 
 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:
 
 Just to make sure I'm doing this right, I'm going to summarize what
 I've taken away from your answers and to ask some new questions. In
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
 from the group level analysis to generate a mask for each cluster of
 interest.
 Then I could extract the value of the voxels from each
 subject's cespct file for each contrast, average them across the
 cluster ROI, then average them across each subject, to generate the
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from
 the cache.th20.pos/neg.sig.cluster.summary files from the group 
 level
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can 
 I get
 this information?
 I can use these coordinates to get the peak voxel T by getting the
 value from the group level F.nii.gz file and taking its square root.
 How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel
 coordinates into the Atlas coordinates to look up the putative 
 BA and
 landmarks (unless there is a better way with 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

It's a boxcar design so 20.265.

  mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh 
-fwhm 5 -event-related  -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 
-refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 
-tpexclude tpexclude.dat

On Jul 17, 2013, at 3:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 when you ran mkanalysis-sess, what did you set --refeventdur to?
 On 07/17/2013 02:50 PM, Joseph Dien wrote:
 then I get on the order of .02% difference between the contrasted conditions.
 The run mean values are in my expected ballpark of about 100 or so.
 The condition betas are just very very small.
 Or perhaps this is typical of FSFAST analyses?
 
 On Jul 17, 2013, at 2:00 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 The beta's have already been scaled. What do you get if you just
 beta/runmean ?
 
 
 
 On 07/17/2013 01:45 PM, Joseph Dien wrote:
 I implemented the ROI percent signal change formula following the
 MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values
 I'm getting seem too small (on the order of .0002%).  Basically the
 formula is the (beta * peak absolute value of the canonical HRF
 regressor * 100)/(run mean).  No derivatives in this case as it is a
 boxcar design.
 
 I took the mean across all the runs since FSFAST uses the same
 regressor across the entire experiment (unlike SPM).
 I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF
 as you suggested (where m equals the condition+1).
 
 Is it possible that I'm missing something in the scaling here?
 Especially with a boxcar design, the signal change should be much
 larger than this for a significant cluster, I think.  For example, the
 peak HRF value for one of the conditions is 0.0092.  If the betas are
 already scaled according to the peak value, then it would come out as
 .02%, which is more reasonable, although still too small.
 
 Thanks for your help with this!
 
 Joe
 
 
 
 On May 31, 2013, at 5:02 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 Oh, right, it is probably not there for subcortical. I don't know what I
 would have to do to write it out. It won't be something that happens
 before I get back from HBM. Can you remind me after HBM?
 doug
 
 On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
 surface-based lh and rh spaces.  For the subcortical volume-based
 analysis I don't see the corresponding corrected voxel p-values being
 available?
 
 On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:
 
 
 On May 31, 2013, at 12:11 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but
 I have a remaining question:
 
 I assume the contents of sig.nii.gz (which I assume are the vertex
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected
 vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is
 corrected on a voxelwise basis (the th13 is just part of the name
 but it
 should be the same regardless of the threshold you choose)
 doug
 
 Excellent!  Thanks!  :)
 
 
 Thanks again for your patience!
 
 Joe
 
 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:
 
 Just to make sure I'm doing this right, I'm going to summarize what
 I've taken away from your answers and to ask some new questions. In
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
 from the group level analysis to generate a mask for each cluster of
 interest.
 Then I could extract the value of the voxels from each
 subject's cespct file for each contrast, average them across the
 cluster ROI, then average them across each subject, to generate the
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from
 the cache.th20.pos/neg.sig.cluster.summary files 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

It's a little complicated.  Basically there were eight runs, comprising four 
conditions (me, we, you1, you2) each with two adjoining runs.  For the 
analysis, I merged each of the pairs into a single run and added a nuisance 
regressor to account for the difference in run means.  There were a total of 
four different kinds of boxcars (AR, CS, EM, MP).  So 4x4=16 conditions.  There 
was also a covariate of non-interest to mark the switch point for each boxcar, 
one for each run, so 20 total.

The 7 nuisance regressors are six movement covariates plus one to account for 
merging eight runs into four (it consists of 1 for the first half and -1 for 
the second, so the difference in the run means).  I'm using the movement 
covariates from a prior SPM run since ARTdetect (for detecting bad volumes) 
isn't set up for AFNI style data.  From all published accounts the different 
movement detection routines yield similar enough results that it shouldn't be a 
problem (consistent with what I found when I compared them for this dataset).

You're thinking that collinearity could have reduced the effect sizes?  When I 
correlate the X.X regressor matrix, the 20 predictors don't correlate by more 
than about .2 at worst.  I do see greater correlations with some of the 
nuisance regressors (as high as the .4 range).  Are my betas unusually small 
for FSFAST analyses?  They did come up clusterwise significant at least. Or 
should I not worry?  I'm not sure what to expect from FSFAST analyses.

Thanks!

Joe


On Jul 17, 2013, at 3:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 why do you have 20 conditions? And what are the 7 nuisance regressors?
 
 On 07/17/2013 03:54 PM, Joseph Dien wrote:
 It's a boxcar design so 20.265.
 
 mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh 
 -fwhm 5 -event-related-paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 
 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 
 7 -tpexclude tpexclude.dat
 
 On Jul 17, 2013, at 3:50 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 when you ran mkanalysis-sess, what did you set --refeventdur to?
 On 07/17/2013 02:50 PM, Joseph Dien wrote:
 then I get on the order of .02% difference between the contrasted 
 conditions.
 The run mean values are in my expected ballpark of about 100 or so.
 The condition betas are just very very small.
 Or perhaps this is typical of FSFAST analyses?
 
 On Jul 17, 2013, at 2:00 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 The beta's have already been scaled. What do you get if you just
 beta/runmean ?
 
 
 
 On 07/17/2013 01:45 PM, Joseph Dien wrote:
 I implemented the ROI percent signal change formula following the
 MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values
 I'm getting seem too small (on the order of .0002%).  Basically the
 formula is the (beta * peak absolute value of the canonical HRF
 regressor * 100)/(run mean).  No derivatives in this case as it is a
 boxcar design.
 
 I took the mean across all the runs since FSFAST uses the same
 regressor across the entire experiment (unlike SPM).
 I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF
 as you suggested (where m equals the condition+1).
 
 Is it possible that I'm missing something in the scaling here?
 Especially with a boxcar design, the signal change should be much
 larger than this for a significant cluster, I think.  For example, the
 peak HRF value for one of the conditions is 0.0092.  If the betas are
 already scaled according to the peak value, then it would come out as
 .02%, which is more reasonable, although still too small.
 
 Thanks for your help with this!
 
 Joe
 
 
 
 On May 31, 2013, at 5:02 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 Oh, right, it is probably not there for subcortical. I don't know 
 what I
 would have to do to write it out. It won't be something that happens
 before I get back from HBM. Can you remind me after HBM?
 doug
 
 On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the
 surface-based lh and rh spaces.  For the subcortical volume-based
 analysis I don't see the corresponding corrected voxel p-values 
 being
 available?
 
 On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com mailto:jdie...@mac.com
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:
 
 
 On May 31, 2013, at 12:11 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

Oh, right, the nuisance regressors are given a separate regressor for 
each run. I had forgotten!

On 07/17/2013 04:55 PM, Joseph Dien wrote:

 On Jul 17, 2013, at 4:50 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 On 07/17/2013 04:48 PM, Joseph Dien wrote:
 The single nuisance regressor models the difference between the merged
 runs.  So if the first run had a mean of 90 and the second run had a
 mean of 110 then the merged run mean would be 100.  The nuisance
 regressor has 1s for the volumes of the first run and -1s for the
 volumes of the second run so it ends up with a beta value of 10, thus
 accounting for the difference between these two sets of volumes.  I
 think it does make sense.
 Do you do this in a single regressor? So you would have a +1 -1 pattern
 repeated 4 times? I think to make it work, you would need 4 regressors.
 In any event, FSFAST will do the right thing, so maybe it is not 
 important.


 Looking at the X.X file, it did create four nuisance regressors.  I'm 
 really impressed with how well FSFAST handles all this!  :)


 In any case, while it was necessary to do so for my original SPM
 analyses since it uses a separate covariates for each run, after
 working through the FSFAST procedures with your help I see that is not
 the case for FSFAST (a single regressor models a given condition in
 all the runs).  I'll try doing as you suggest to see what difference
 it makes.

 It is indeed cognitive areas and the manipulations are subtle social
 cognition manipulations so perhaps not surprising after all.

 I'll send you the paradigm file separately.

 Thanks for taking the time to look into this!

 Joe


 On Jul 17, 2013, at 4:38 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 It is not necessary or beneficial to combine the runs in this way.
 FSFAST will do all this for you and keep account of all the runs and
 transitions. FSFAST will put in regressors to fit each of the run 
 means.
 The single regressor you have is not the right way to hand this (at
 least I don't understand how it works). It could be that the low %
 signal change is related to the colinearity between the task waveform
 and the mean regressors. Can you set things up in the way that FSFAST
 expects them and don't use any nuisance regressors?

 Also, in what area are you looking at the percent change? .02% sounds
 very small, but may be if it is in some cognitive area, maybe it is ok.
 If it is in visual cortex, then it looks way too low.

 Also, can you send the paradigm file?

 doug




 On 07/17/2013 04:27 PM, Joseph Dien wrote:
 It's a little complicated.  Basically there were eight runs,
 comprising four conditions (me, we, you1, you2) each with two
 adjoining runs.  For the analysis, I merged each of the pairs into a
 single run and added a nuisance regressor to account for the
 difference in run means.  There were a total of four different kinds
 of boxcars (AR, CS, EM, MP).  So 4x4=16 conditions.  There was also a
 covariate of non-interest to mark the switch point for each boxcar,
 one for each run, so 20 total.

 The 7 nuisance regressors are six movement covariates plus one to
 account for merging eight runs into four (it consists of 1 for the
 first half and -1 for the second, so the difference in the run means).
 I'm using the movement covariates from a prior SPM run since
 ARTdetect (for detecting bad volumes) isn't set up for AFNI style
 data.  From all published accounts the different movement detection
 routines yield similar enough results that it shouldn't be a problem
 (consistent with what I found when I compared them for this dataset).

 You're thinking that collinearity could have reduced the effect sizes?
 When I correlate the X.X regressor matrix, the 20 predictors don't
 correlate by more than about .2 at worst.  I do see greater
 correlations with some of the nuisance regressors (as high as the .4
 range).  Are my betas unusually small for FSFAST analyses?  They did
 come up clusterwise significant at least. Or should I not worry?  I'm
 not sure what to expect from FSFAST analyses.

 Thanks!

 Joe


 On Jul 17, 2013, at 3:58 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 why do you have 20 conditions? And what are the 7 nuisance 
 regressors?

 On 07/17/2013 03:54 PM, Joseph Dien wrote:
 It's a boxcar design so 20.265.

 mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface 
 fsaverage lh
 -fwhm 5 -event-related-paradigm CPA1.par -nconditions 20 -spmhrf 
 0 -TR
 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg 
 nuisreg2.dat
 7 -tpexclude tpexclude.dat

 On Jul 17, 2013, at 3:50 PM, Douglas N Greve s.
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

On 05/30/2013 04:37 PM, Joseph Dien wrote:
 Just to make sure I'm doing this right, I'm going to summarize what 
 I've taken away from your answers and to ask some new questions. In 
 order to present the results, I need two things:

 1) A set of histograms (with error bars) for each cluster figure to 
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition 
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
 from the group level analysis to generate a mask for each cluster of 
 interest.
 Then I could extract the value of the voxels from each 
 subject's cespct file for each contrast, average them across the 
 cluster ROI, then average them across each subject, to generate the 
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
I don't understand. If you don't have a cluster for a contrast, how are 
you defining the cluster? From another contrast?


 2) A results table with the headings:

 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark

 I can get the first two from 
 the cache.th20.pos/neg.sig.cluster.summary files from the group level 
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group level sig.nii.gz 
 file.  Is this FWE corrected?  If not, how can I get this information?
What do you mean? The cluster p-value is corrected, why do you need the 
max p and why does it need to be corrected?
 I can use these coordinates to get the peak voxel T by getting the 
 value from the group level F.nii.gz file and taking its square root. 
  How can I get the sign of the T statistic?
Same as the sign of gamma.mgh
 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing 
 some references to some BA labels in the forum but it doesn't look 
 like this is a complete set yet?).
Some of the BA labels are in FS, but not nearly all of them
doug

 Sorry for all these questions!  I got some nice results from FSFAST 
 and would like to get them written up.

 Cheers!

 Joe




 On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 On 5/29/13 10:42 PM, Joseph Dien wrote:

 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Hi Joe,

 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.

 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an index
 somewhere as to which beta weight is which?  Or if not, how are they
 organized?
 For the first level analysis, the first N beta weights correspond 
 to the
 N conditions in the paradigm file. The rest are nuisance variables.


 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is 
 computed as the simple contrast (ces) and as a percent of the 
 baseline at the voxel (cespct, cesvarpct).

 2) In order to extract the cluster, it looks like I would
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
 volume where the voxels are tagged with the number of the
 corresponding cluster.
 Is that  from a group analysis?


 Yes, that's right.

 I could then use that to generate masks to extract the information I
 need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file
 there (something.y.ocn.dat) that has a value for each subject in the
 rows and a value for each cluster in the columns.


 I see it.  Are these values already scaled as percent signal change? 
  If so, that would be wonderful!  :)
 Only if you specified it when you ran isxconcat-sess. Note that the 
 non-scaled values are actually scaled to percent of grand mean 
 intensity.

 Is that correct?

 3) The final information that I would need is the canonical hrf shape
 generated by FSFAST for a single event.  I guess I could generate 
 that
 by setting up a dummy analysis run with a single event of the desired
 duration and then look in the X variable in the resulting X.mat file?
 try this
 plot(X.runflac(1).flac.ev(2).tirf, 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but 
 I have a remaining question:

 I assume the contents of sig.nii.gz (which I assume are the vertex 
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected 
 vertex p-values?  Or are only clusterwise corrections available?
There should be something like cache.th13.abs.sig.voxel.mgh which is 
corrected on a voxelwise basis (the th13 is just part of the name but it 
should be the same regardless of the threshold you choose)
doug

 Thanks again for your patience!

 Joe

 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com wrote:

 Just to make sure I'm doing this right, I'm going to summarize what 
 I've taken away from your answers and to ask some new questions. In 
 order to present the results, I need two things:

 1) A set of histograms (with error bars) for each cluster figure to 
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition 
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
 from the group level analysis to generate a mask for each cluster of 
 interest.
 Then I could extract the value of the voxels from each 
 subject's cespct file for each contrast, average them across the 
 cluster ROI, then average them across each subject, to generate the 
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.

 2) A results table with the headings:

 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark

 I can get the first two from 
 the cache.th20.pos/neg.sig.cluster.summary files from the group level 
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group 
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get 
 this information?
 I can use these coordinates to get the peak voxel T by getting the 
 value from the group level F.nii.gz file and taking its square root. 
  How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing 
 some references to some BA labels in the forum but it doesn't look 
 like this is a complete set yet?).

 Sorry for all these questions!  I got some nice results from FSFAST 
 and would like to get them written up.

 Cheers!

 Joe




 On May 29, 2013, at 10:53 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 On 5/29/13 10:42 PM, Joseph Dien wrote:

 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:

 Hi Joe,

 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.

 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an index
 somewhere as to which beta weight is which?  Or if not, how are they
 organized?
 For the first level analysis, the first N beta weights correspond 
 to the
 N conditions in the paradigm file. The rest are nuisance variables.


 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is 
 computed as the simple contrast (ces) and as a percent of the 
 baseline at the voxel (cespct, cesvarpct).

 2) In order to extract the cluster, it looks like I would
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
 volume where the voxels are tagged with the number of the
 corresponding cluster.
 Is that  from a group analysis?


 Yes, that's right.

 I could then use that to generate masks to extract the information I
 need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file
 there (something.y.ocn.dat) that has a value for each subject in the
 rows and a value for each cluster in the columns.


 I see it.  Are these values already scaled as percent signal 
 change?  If so, that would be wonderful!  :)
 Only if you specified it when you ran isxconcat-sess. Note that the 
 non-scaled values are actually scaled to percent of grand mean 
 intensity.

 Is that correct?

 3) The final 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

On May 31, 2013, at 12:09 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 
 On 05/30/2013 04:37 PM, Joseph Dien wrote:
 Just to make sure I'm doing this right, I'm going to summarize what 
 I've taken away from your answers and to ask some new questions. In 
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to 
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition 
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
 from the group level analysis to generate a mask for each cluster of 
 interest.
 Then I could extract the value of the voxels from each 
 subject's cespct file for each contrast, average them across the 
 cluster ROI, then average them across each subject, to generate the 
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 I don't understand. If you don't have a cluster for a contrast, how are 
 you defining the cluster? From another contrast?
 

Well, what the reviewer told me to do is if I present a figure with a 
significant cluster for one condition, I should use that as an ROI to calculate 
the %age signal change for all four conditions and present it as a bar chart as 
part of the figure.  I think she wanted to be able to get a more qualitative 
sense of the data patterns.

 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from 
 the cache.th20.pos/neg.sig.cluster.summary files from the group level 
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group level sig.nii.gz 
 file.  Is this FWE corrected?  If not, how can I get this information?
 What do you mean? The cluster p-value is corrected, why do you need the 
 max p and why does it need to be corrected?

Well, as I understand it, the drawback of clusterwise statistics is that while 
it assures you that the cluster passes muster as not being due to random chance 
(at 95% confidence), it doesn't provide any assurances at the voxel level (or 
in this case the vertex level) as it is likely that a cluster is composed of 
both signal and noise and you don't know which part is which.  So if a cluster 
covers both BA44 and BA45 (for example), you can't be sure whether the 
activation involves BA44, BA45, or both.  A voxelwise correction is more 
conservative but if it provides significance, it does allow for this kind of 
interpretation.

 I can use these coordinates to get the peak voxel T by getting the 
 value from the group level F.nii.gz file and taking its square root. 
 How can I get the sign of the T statistic?
 Same as the sign of gamma.mgh

Ah, great!

 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing 
 some references to some BA labels in the forum but it doesn't look 
 like this is a complete set yet?).
 Some of the BA labels are in FS, but not nearly all of them
 doug

No problem!  I worked out that I can use the talairach.nii file made available 
by the Talairach Daemon folks.


 
 Sorry for all these questions!  I got some nice results from FSFAST 
 and would like to get them written up.
 
 Cheers!
 
 Joe
 
 
 
 
 On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Hi Joe,
 
 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an index
 somewhere as to which beta weight is which?  Or if not, how are they
 organized?
 For the first level analysis, the first N beta weights correspond 
 to the
 N conditions in the paradigm file. The rest are nuisance variables.
 
 
 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is 
 computed as the simple contrast (ces) and as a percent of the 
 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but 
 I have a remaining question:
 
 I assume the contents of sig.nii.gz (which I assume are the vertex 
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected 
 vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is 
 corrected on a voxelwise basis (the th13 is just part of the name but it 
 should be the same regardless of the threshold you choose)
 doug

Excellent!  Thanks!  :)

 
 Thanks again for your patience!
 
 Joe
 
 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com wrote:
 
 Just to make sure I'm doing this right, I'm going to summarize what 
 I've taken away from your answers and to ask some new questions. In 
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to 
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition 
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
 from the group level analysis to generate a mask for each cluster of 
 interest.
 Then I could extract the value of the voxels from each 
 subject's cespct file for each contrast, average them across the 
 cluster ROI, then average them across each subject, to generate the 
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from 
 the cache.th20.pos/neg.sig.cluster.summary files from the group level 
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group 
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get 
 this information?
 I can use these coordinates to get the peak voxel T by getting the 
 value from the group level F.nii.gz file and taking its square root. 
 How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing 
 some references to some BA labels in the forum but it doesn't look 
 like this is a complete set yet?).
 
 Sorry for all these questions!  I got some nice results from FSFAST 
 and would like to get them written up.
 
 Cheers!
 
 Joe
 
 
 
 
 On May 29, 2013, at 10:53 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Hi Joe,
 
 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an index
 somewhere as to which beta weight is which?  Or if not, how are they
 organized?
 For the first level analysis, the first N beta weights correspond 
 to the
 N conditions in the paradigm file. The rest are nuisance variables.
 
 
 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is 
 computed as the simple contrast (ces) and as a percent of the 
 baseline at the voxel (cespct, cesvarpct).
 
 2) In order to extract the cluster, it looks like I would
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
 volume where the voxels are tagged with the number of the
 corresponding cluster.
 Is that  from a group analysis?
 
 
 Yes, that's right.
 
 I could then use that to generate masks to extract the information I
 need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file
 there (something.y.ocn.dat) that has a value for each subject in the
 rows and a value for each cluster in the columns.
 
 
 I see it.  Are these values already scaled as percent signal 
 change?  If so, that would be wonderful!  :)
 Only if you specified it when you ran 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

It looks like the corrected vertex p-values (ex: 
cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh 
and rh spaces.  For the subcortical volume-based analysis I don't see the 
corresponding corrected voxel p-values being available?

On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com wrote:

 
 On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 wrote:
 
 
 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but 
 I have a remaining question:
 
 I assume the contents of sig.nii.gz (which I assume are the vertex 
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected 
 vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is 
 corrected on a voxelwise basis (the th13 is just part of the name but it 
 should be the same regardless of the threshold you choose)
 doug
 
 Excellent!  Thanks!  :)
 
 
 Thanks again for your patience!
 
 Joe
 
 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com wrote:
 
 Just to make sure I'm doing this right, I'm going to summarize what 
 I've taken away from your answers and to ask some new questions. In 
 order to present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to 
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition 
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot 
 from the group level analysis to generate a mask for each cluster of 
 interest.
 Then I could extract the value of the voxels from each 
 subject's cespct file for each contrast, average them across the 
 cluster ROI, then average them across each subject, to generate the 
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings:
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from 
 the cache.th20.pos/neg.sig.cluster.summary files from the group level 
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group 
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get 
 this information?
 I can use these coordinates to get the peak voxel T by getting the 
 value from the group level F.nii.gz file and taking its square root. 
 How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing 
 some references to some BA labels in the forum but it doesn't look 
 like this is a complete set yet?).
 
 Sorry for all these questions!  I got some nice results from FSFAST 
 and would like to get them written up.
 
 Cheers!
 
 Joe
 
 
 
 
 On May 29, 2013, at 10:53 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 Hi Joe,
 
 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an index
 somewhere as to which beta weight is which?  Or if not, how are they
 organized?
 For the first level analysis, the first N beta weights correspond 
 to the
 N conditions in the paradigm file. The rest are nuisance variables.
 
 
 Ah, very good!  In order to compute the percent signal change 
 statistic (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  
 I'm also going to need the beta weights for the session mean 
 regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is 
 computed as the simple contrast (ces) and as a percent of the 
 baseline at the voxel (cespct, cesvarpct).
 
 2) In order to extract the cluster, it looks like I would
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a
 volume where the voxels are tagged with the number of the
 corresponding cluster.
 Is that  from a group analysis?
 
 
 Yes, that's right.
 
 I could then use that to generate masks to extract the information I
 need for each cluster from beta.nii.gz.
 If this is 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

Oh, right, it is probably not there for subcortical. I don't know what I 
would have to do to write it out. It won't be something that happens 
before I get back from HBM. Can you remind me after HBM?
doug

On 05/31/2013 04:44 PM, Joseph Dien wrote:
 It looks like the corrected vertex p-values 
 (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the 
 surface-based lh and rh spaces.  For the subcortical volume-based 
 analysis I don't see the corresponding corrected voxel p-values being 
 available?

 On May 31, 2013, at 2:46 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com wrote:


 On May 31, 2013, at 12:11 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 On 05/31/2013 01:49 AM, Joseph Dien wrote:
 I was able to make more progress so I'm mostly good at this point but
 I have a remaining question:

 I assume the contents of sig.nii.gz (which I assume are the vertex
 p-values) are not FWE corrected.  Is it possible to get FWE-corrected
 vertex p-values?  Or are only clusterwise corrections available?
 There should be something like cache.th13.abs.sig.voxel.mgh which is
 corrected on a voxelwise basis (the th13 is just part of the name 
 but it
 should be the same regardless of the threshold you choose)
 doug

 Excellent!  Thanks!  :)


 Thanks again for your patience!

 Joe

 On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com 
 mailto:jdie...@mac.com
 mailto:jdie...@mac.com wrote:

 Just to make sure I'm doing this right, I'm going to summarize what
 I've taken away from your answers and to ask some new questions. In
 order to present the results, I need two things:

 1) A set of histograms (with error bars) for each cluster figure to
 show the % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition
 where the cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
 from the group level analysis to generate a mask for each cluster of
 interest.
 Then I could extract the value of the voxels from each
 subject's cespct file for each contrast, average them across the
 cluster ROI, then average them across each subject, to generate the
 histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.

 2) A results table with the headings:

 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark

 I can get the first two from
 the cache.th20.pos/neg.sig.cluster.summary files from the group level
 analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group
 level sig.nii.gz file.  Is this FWE corrected?  If not, how can I get
 this information?
 I can use these coordinates to get the peak voxel T by getting the
 value from the group level F.nii.gz file and taking its square root.
 How can I get the sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel
 coordinates into the Atlas coordinates to look up the putative BA and
 landmarks (unless there is a better way with Freesurfer?  I'm seeing
 some references to some BA labels in the forum but it doesn't look
 like this is a complete set yet?).

 Sorry for all these questions!  I got some nice results from FSFAST
 and would like to get them written up.

 Cheers!

 Joe




 On May 29, 2013, at 10:53 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:


 On 5/29/13 10:42 PM, Joseph Dien wrote:

 On May 29, 2013, at 11:40 AM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 Hi Joe,

 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with
 FS-Fast in order to compute percentage signal change.

 1) I see a file called beta.nii.gz that appears to have the beta
 weight information.  It has a four dimensional structure and the
 fourth dimension appears to be the beta weights.  Is there an 
 index
 somewhere as to which beta weight is which?  Or if not, how 
 are they
 organized?
 For the first level analysis, the first N beta weights correspond
 to the
 N conditions in the paradigm file. The rest are nuisance variables.


 Ah, very good!  In order to compute the percent signal change
 statistic (I'm following the MarsBaR approach:
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  

 I'm also going to need the beta weights for the session mean
 regressors.  How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is
 computed as the simple contrast (ces) and as a percent of the
 baseline at the voxel (cespct, cesvarpct).

 2) In order to extract the cluster, it 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

Just to make sure I'm doing this right, I'm going to summarize what I've taken 
away from your answers and to ask some new questions. In order to present the 
results, I need two things:

1) A set of histograms (with error bars) for each cluster figure to show the % 
signal change for each of the four contrasts of interest.
The cache.th20.pos.y.ocn.dat file only gives it for the condition where the 
cluster was significant so I can't use that.
So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the 
group level analysis to generate a mask for each cluster of interest.
Then I could extract the value of the voxels from each subject's cespct file 
for each contrast, average them across the cluster ROI, then average them 
across each subject, to generate the histogram?
This would suffice to give me the %age signal change?
I would be doing these computations in Matlab using MRIread.

2) A results table with the headings: 

Cluster p (FWE corrected)
Cluster size
Peak Voxel p (FWE corrected)
Peak Voxel T
Peak Voxel Coords
BA
Anatomical Landmark

I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files 
from the group level analysis.
I can get the peak voxel coordinates from the summary files as well.
I can use this to get the peak voxel p from the group level sig.nii.gz file.  
Is this FWE corrected?  If not, how can I get this information?
I can use these coordinates to get the peak voxel T by getting the value from 
the group level F.nii.gz file and taking its square root.  How can I get the 
sign of the T statistic?
I can use the Lancaster transform to convert the MNI305 peak voxel coordinates 
into the Atlas coordinates to look up the putative BA and landmarks (unless 
there is a better way with Freesurfer?  I'm seeing some references to some BA 
labels in the forum but it doesn't look like this is a complete set yet?).

Sorry for all these questions!  I got some nice results from FSFAST and would 
like to get them written up.

Cheers!

Joe




On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:

 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 wrote:
 
 Hi Joe,
 
 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with 
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta 
 weight information.  It has a four dimensional structure and the 
 fourth dimension appears to be the beta weights.  Is there an index 
 somewhere as to which beta weight is which?  Or if not, how are they 
 organized?
 For the first level analysis, the first N beta weights correspond to the 
 N conditions in the paradigm file. The rest are nuisance variables.
 
 
 Ah, very good!  In order to compute the percent signal change statistic (I'm 
 following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  I'm also going to need the beta weights for the session mean regressors.  
 How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is computed as the 
 simple contrast (ces) and as a percent of the baseline at the voxel (cespct, 
 cesvarpct).
 
 2) In order to extract the cluster, it looks like I would 
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a 
 volume where the voxels are tagged with the number of the 
 corresponding cluster.
 Is that  from a group analysis?
 
 
 Yes, that's right.
 
 I could then use that to generate masks to extract the information I 
 need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file 
 there (something.y.ocn.dat) that has a value for each subject in the 
 rows and a value for each cluster in the columns.
 
 
 I see it.  Are these values already scaled as percent signal change?  If so, 
 that would be wonderful!  :)
 Only if you specified it when you ran isxconcat-sess. Note that the 
 non-scaled values are actually scaled to percent of grand mean intensity.
 
 Is that correct?
 
 3) The final information that I would need is the canonical hrf shape 
 generated by FSFAST for a single event.  I guess I could generate that 
 by setting up a dummy analysis run with a single event of the desired 
 duration and then look in the X variable in the resulting X.mat file?
 try this
 plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)
 
 
 Perfect!  :)
 
 Sorry for all the questions!
 
 Joe
 
 
 
 
 
 
 Joseph Dien,
 Senior Research Scientist
 University of Maryland
 
 E-mail: jdie...@mac.com mailto:jdie...@mac.com
 Phone: 301-226-8848
 Fax: 301-226-8811
 http://joedien.com//
 
 
 
 
 
 
 
 
 
 
 
 
 
 ___
 Freesurfer mailing list
 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

I was able to make more progress so I'm mostly good at this point but I have a 
remaining question:

I assume the contents of sig.nii.gz (which I assume are the vertex p-values) 
are not FWE corrected.  Is it possible to get FWE-corrected vertex p-values?  
Or are only clusterwise corrections available?

Thanks again for your patience!

Joe

On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com wrote:

 Just to make sure I'm doing this right, I'm going to summarize what I've 
 taken away from your answers and to ask some new questions. In order to 
 present the results, I need two things:
 
 1) A set of histograms (with error bars) for each cluster figure to show the 
 % signal change for each of the four contrasts of interest.
 The cache.th20.pos.y.ocn.dat file only gives it for the condition where the 
 cluster was significant so I can't use that.
 So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the 
 group level analysis to generate a mask for each cluster of interest.
 Then I could extract the value of the voxels from each subject's cespct file 
 for each contrast, average them across the cluster ROI, then average them 
 across each subject, to generate the histogram?
 This would suffice to give me the %age signal change?
 I would be doing these computations in Matlab using MRIread.
 
 2) A results table with the headings: 
 
 Cluster p (FWE corrected)
 Cluster size
 Peak Voxel p (FWE corrected)
 Peak Voxel T
 Peak Voxel Coords
 BA
 Anatomical Landmark
 
 I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files 
 from the group level analysis.
 I can get the peak voxel coordinates from the summary files as well.
 I can use this to get the peak voxel p from the group level sig.nii.gz file.  
 Is this FWE corrected?  If not, how can I get this information?
 I can use these coordinates to get the peak voxel T by getting the value from 
 the group level F.nii.gz file and taking its square root.  How can I get the 
 sign of the T statistic?
 I can use the Lancaster transform to convert the MNI305 peak voxel 
 coordinates into the Atlas coordinates to look up the putative BA and 
 landmarks (unless there is a better way with Freesurfer?  I'm seeing some 
 references to some BA labels in the forum but it doesn't look like this is a 
 complete set yet?).
 
 Sorry for all these questions!  I got some nice results from FSFAST and would 
 like to get them written up.
 
 Cheers!
 
 Joe
 
 
 
 
 On May 29, 2013, at 10:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
 
 
 On 5/29/13 10:42 PM, Joseph Dien wrote:
 
 On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu 
 wrote:
 
 Hi Joe,
 
 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with 
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta 
 weight information.  It has a four dimensional structure and the 
 fourth dimension appears to be the beta weights.  Is there an index 
 somewhere as to which beta weight is which?  Or if not, how are they 
 organized?
 For the first level analysis, the first N beta weights correspond to the 
 N conditions in the paradigm file. The rest are nuisance variables.
 
 
 Ah, very good!  In order to compute the percent signal change statistic 
 (I'm following the MarsBaR approach: 
 http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
  I'm also going to need the beta weights for the session mean regressors.  
 How are the nuisance regressors organized?
 You can just use the meanfunc.nii.gz. Also, each contrasts is computed as 
 the simple contrast (ces) and as a percent of the baseline at the voxel 
 (cespct, cesvarpct).
 
 2) In order to extract the cluster, it looks like I would 
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a 
 volume where the voxels are tagged with the number of the 
 corresponding cluster.
 Is that  from a group analysis?
 
 
 Yes, that's right.
 
 I could then use that to generate masks to extract the information I 
 need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file 
 there (something.y.ocn.dat) that has a value for each subject in the 
 rows and a value for each cluster in the columns.
 
 
 I see it.  Are these values already scaled as percent signal change?  If 
 so, that would be wonderful!  :)
 Only if you specified it when you ran isxconcat-sess. Note that the 
 non-scaled values are actually scaled to percent of grand mean intensity.
 
 Is that correct?
 
 3) The final information that I would need is the canonical hrf shape 
 generated by FSFAST for a single event.  I guess I could generate that 
 by setting up a dummy analysis run with a single event of the desired 
 duration and then look in the X variable in the resulting X.mat file?
 try this
 plot(X.runflac(1).flac.ev(2).tirf, 

Re: [Freesurfer] beta weights from FS-Fast analysis

[Douglas N Greve]

Hi Joe,

On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with 
 FS-Fast in order to compute percentage signal change.

 1) I see a file called beta.nii.gz that appears to have the beta 
 weight information.  It has a four dimensional structure and the 
 fourth dimension appears to be the beta weights.  Is there an index 
 somewhere as to which beta weight is which?  Or if not, how are they 
 organized?
For the first level analysis, the first N beta weights correspond to the 
N conditions in the paradigm file. The rest are nuisance variables.

 2) In order to extract the cluster, it looks like I would 
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a 
 volume where the voxels are tagged with the number of the 
 corresponding cluster.
Is that  from a group analysis?

 I could then use that to generate masks to extract the information I 
 need for each cluster from beta.nii.gz.
If this is from a group analysis, then there should already be a file 
there (something.y.ocn.dat) that has a value for each subject in the 
rows and a value for each cluster in the columns.

 Is that correct?

 3) The final information that I would need is the canonical hrf shape 
 generated by FSFAST for a single event.  I guess I could generate that 
 by setting up a dummy analysis run with a single event of the desired 
 duration and then look in the X variable in the resulting X.mat file?
try this
plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)

 Sorry for all the questions!

 Joe




 

 Joseph Dien,
 Senior Research Scientist
 University of Maryland

 E-mail: jdie...@mac.com mailto:jdie...@mac.com
 Phone: 301-226-8848
 Fax: 301-226-8811
 http://joedien.com//













 ___
 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.

Re: [Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:

 Hi Joe,
 
 On 05/29/2013 01:00 AM, Joseph Dien wrote:
 I need to extract the beta weights from a cluster identified with 
 FS-Fast in order to compute percentage signal change.
 
 1) I see a file called beta.nii.gz that appears to have the beta 
 weight information.  It has a four dimensional structure and the 
 fourth dimension appears to be the beta weights.  Is there an index 
 somewhere as to which beta weight is which?  Or if not, how are they 
 organized?
 For the first level analysis, the first N beta weights correspond to the 
 N conditions in the paradigm file. The rest are nuisance variables.
 

Ah, very good!  In order to compute the percent signal change statistic (I'm 
following the MarsBaR approach: 
http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated)
 I'm also going to need the beta weights for the session mean regressors.  How 
are the nuisance regressors organized?

 2) In order to extract the cluster, it looks like I would 
 use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a 
 volume where the voxels are tagged with the number of the 
 corresponding cluster.
 Is that  from a group analysis?
 

Yes, that's right.

 I could then use that to generate masks to extract the information I 
 need for each cluster from beta.nii.gz.
 If this is from a group analysis, then there should already be a file 
 there (something.y.ocn.dat) that has a value for each subject in the 
 rows and a value for each cluster in the columns.
 

I see it.  Are these values already scaled as percent signal change?  If so, 
that would be wonderful!  :)

 Is that correct?
 
 3) The final information that I would need is the canonical hrf shape 
 generated by FSFAST for a single event.  I guess I could generate that 
 by setting up a dummy analysis run with a single event of the desired 
 duration and then look in the X variable in the resulting X.mat file?
 try this
 plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf)
 

Perfect!  :)

 Sorry for all the questions!
 
 Joe
 
 
 
 
 
 
 Joseph Dien,
 Senior Research Scientist
 University of Maryland
 
 E-mail: jdie...@mac.com mailto:jdie...@mac.com
 Phone: 301-226-8848
 Fax: 301-226-8811
 http://joedien.com//
 
 
 
 
 
 
 
 
 
 
 
 
 
 ___
 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.
 




Joseph Dien,
Senior Research Scientist
University of Maryland 

E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//











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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] beta weights from FS-Fast analysis

[Joseph Dien]

I need to extract the beta weights from a cluster identified with FS-Fast in 
order to compute percentage signal change.  

1) I see a file called beta.nii.gz that appears to have the beta weight 
information.  It has a four dimensional structure and the fourth dimension 
appears to be the beta weights.  Is there an index somewhere as to which beta 
weight is which?  Or if not, how are they organized?

2) In order to extract the cluster, it looks like I would use mri_label2vol to 
convert cache.th20.neg.sig.ocn.annot into a volume where the voxels are tagged 
with the number of the corresponding cluster.

I could then use that to generate masks to extract the information I need for 
each cluster from beta.nii.gz.

Is that correct?

3) The final information that I would need is the canonical hrf shape generated 
by FSFAST for a single event.  I guess I could generate that by setting up a 
dummy analysis run with a single event of the desired duration and then look in 
the X variable in the resulting X.mat file?

Sorry for all the questions!

Joe






Joseph Dien,
Senior Research Scientist
University of Maryland 

E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//











___
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.

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Joerg Pfannmoeller]

Found a fix for that problem:

http://www.mathworks.com/matlabcentral/newsreader/view_thread/284776



On Tue, 14 May 2013 14:14:31 -0400
Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:

 Joerg,
 
 I'm guessing you have some matlab setup script that has run prior to the
 freesurfer setup.  I see this output:
 /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6
 
 which is not something freesurfer would link against or require.
 normally it should use /usr/lib64/libstdc++.so.6.
 
 try running this prior to sourcing the freesurfer setup:
 
 setenv LD_LIBRARY_PATH 
 
 Glad to see 5.3 works otherwise.  Thanks for testing it.
 
 Nick
 
 
 
 On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote:
  Unfortunately encountered a problem in fs-fast stream during execution of 
  selxavg3-sess. Added a relevant part of the log file below:
  
  
 
  sxa3pwd =
  
  /home/...removed...
  
   
  sxa3cmd =
  
  /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis 
  harm.sm0.mni305
  
   /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
   
  
  #@# session02 ###
  /home/...removed.../freesurfer_fMRT/session02
  -
  $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
  /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
  /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
  /usr/local/freesurfer/matlab/MRIread.m
  -
  outtop = /home/...removed.../freesurfer_fMRT
  Extension format = nii.gz
   1 stim-v-base.mat
  nruns = 1
  autostimdur = 
  
  
  outanadir = 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305
  Found 45239/537168 ( 8.4) voxels in mask
  Creating Design Matrix
   ... creation time =  0.009 sec
  DoMCFit = 1
  ntptot = 100, nX = 8, DOF = 92
  Saving X matrix to 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat
  XCond = 444.207 (normalized)
  Computing compensation for resdual AR1 bias
   1  -0.5  -0.493933(t=0.004964)
   2  -0.25  -0.269463(t=0.00648)
   3  0  -0.0514275(t=0.00734)
   4  0.25  0.155364(t=0.008221)
   5  0.5  0.337574(t=0.009058)
  AR1 Correction M: 0.0769642 1.19552
  Computing contrast matrices
  OLS Beta Pass 
run 1t= 0.0
  Global Mean   725.29
  Global In-Mask Mean = 725.295 (694.97)
  Rescale Target = 100
  RescaleFactor = 0.137875
  OLS Residual Pass 
run 1t= 0.0
  Saving rho1
  Smoothing ACF
  /usr/local/freesurfer/bin/mri_fwhm --mask 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz
   --i 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
   --o 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
   --fwhm 20.00 --smooth-only
  /usr/local/freesurfer/bin/mri_fwhm: 
  /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version 
  `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm)
  /usr/local/freesurfer/bin/mri_fwhm: 
  /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version 
  `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm)
  
  ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz
   --i 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
   --o 
  /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
   --fwhm 20.00 --smooth-only
   --
  ERROR: fast_selxavg3() failed\n
  
  
  
  Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04.
  
  
  
  
  
  
  On Tue, 14 May 2013 08:28:05 +0200
  Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:
  
   Tested recon-all tonight on lubuntu 13.04. I did not encounter any 
   problems. Also freeview runs without an error for the subject bert.
   
   
   
   On Mon, 13 May 2013 14:40:10 +0200
   Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote:
   
Just for completeness, I refer to my first contribution:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html

















On Mon, 13 May 2013 13:58:30 +0200
Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:

 Hello Nick,
 
 just installed and tested the BETA version. Up to now no problem 
 encountered. Recon-all is just running as a test (using -use-gpu). OS 
 is Lubuntu 13.04. I report on the segmentation as soon as it is 
 finished.
 
 So long Joerg
 
 On Sun, 12 May 2013 22:41:25 -0400 (EDT)
 Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
 
  Fedora 18, Ubuntu 13 and Gentoo 64 users,
  
  another beta of the upcoming v5.3 is available here:
  
  

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Joerg Pfannmoeller]

Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. 
Also freeview runs without an error for the subject bert.



On Mon, 13 May 2013 14:40:10 +0200
Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote:

 Just for completeness, I refer to my first contribution:
 
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 On Mon, 13 May 2013 13:58:30 +0200
 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:
 
  Hello Nick,
  
  just installed and tested the BETA version. Up to now no problem 
  encountered. Recon-all is just running as a test (using -use-gpu). OS is 
  Lubuntu 13.04. I report on the segmentation as soon as it is finished.
  
  So long Joerg
  
  On Sun, 12 May 2013 22:41:25 -0400 (EDT)
  Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
  
   Fedora 18, Ubuntu 13 and Gentoo 64 users,
   
   another beta of the upcoming v5.3 is available here:
   
   ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
   
   this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
   who wished to test that the segfault problem in v5.2 and the prior beta
   v5.3 is fixed.  Your help in testing this release is appreciated.
   
   Thanks,
   
   Nick
   
   
   
   
   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.
   
  
  
  -- 
  Joerg Pfannmoeller pfannmo...@uni-greifswald.de
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 -- 
 pfannmo...@uni-greifswald.de
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Joerg Pfannmoeller]

Unfortunately encountered a problem in fs-fast stream during execution of 
selxavg3-sess. Added a relevant part of the log file below:


   
sxa3pwd =

/home/...removed...

 
sxa3cmd =

/usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis 
harm.sm0.mni305

 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
 

#@# session02 ###
/home/...removed.../freesurfer_fMRT/session02
-
$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/usr/local/freesurfer/matlab/MRIread.m
-
outtop = /home/...removed.../freesurfer_fMRT
Extension format = nii.gz
 1 stim-v-base.mat
nruns = 1
autostimdur = 


outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305
Found 45239/537168 ( 8.4) voxels in mask
Creating Design Matrix
 ... creation time =  0.009 sec
DoMCFit = 1
ntptot = 100, nX = 8, DOF = 92
Saving X matrix to 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat
XCond = 444.207 (normalized)
Computing compensation for resdual AR1 bias
 1  -0.5  -0.493933(t=0.004964)
 2  -0.25  -0.269463(t=0.00648)
 3  0  -0.0514275(t=0.00734)
 4  0.25  0.155364(t=0.008221)
 5  0.5  0.337574(t=0.009058)
AR1 Correction M: 0.0769642 1.19552
Computing contrast matrices
OLS Beta Pass 
  run 1t= 0.0
Global Mean   725.29
Global In-Mask Mean = 725.295 (694.97)
Rescale Target = 100
RescaleFactor = 0.137875
OLS Residual Pass 
  run 1t= 0.0
Saving rho1
Smoothing ACF
/usr/local/freesurfer/bin/mri_fwhm --mask 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz 
--i 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
 --o 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
 --fwhm 20.00 --smooth-only
/usr/local/freesurfer/bin/mri_fwhm: 
/usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version 
`GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm)
/usr/local/freesurfer/bin/mri_fwhm: 
/usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.9' 
not found (required by /usr/local/freesurfer/bin/mri_fwhm)

ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz 
--i 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
 --o 
/home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
 --fwhm 20.00 --smooth-only
 --
ERROR: fast_selxavg3() failed\n



Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04.






On Tue, 14 May 2013 08:28:05 +0200
Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:

 Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems. 
 Also freeview runs without an error for the subject bert.
 
 
 
 On Mon, 13 May 2013 14:40:10 +0200
 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote:
 
  Just for completeness, I refer to my first contribution:
  
  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  On Mon, 13 May 2013 13:58:30 +0200
  Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:
  
   Hello Nick,
   
   just installed and tested the BETA version. Up to now no problem 
   encountered. Recon-all is just running as a test (using -use-gpu). OS is 
   Lubuntu 13.04. I report on the segmentation as soon as it is finished.
   
   So long Joerg
   
   On Sun, 12 May 2013 22:41:25 -0400 (EDT)
   Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
   
Fedora 18, Ubuntu 13 and Gentoo 64 users,

another beta of the upcoming v5.3 is available here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz

this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
who wished to test that the segfault problem in v5.2 and the prior beta
v5.3 is fixed.  Your help in testing this release is appreciated.

Thanks,

Nick




The information in this e-mail is intended only for the person to whom 
it is
addressed. If you believe this e-mail was sent to you in error and the 
e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you 
in error
but does not contain patient information, please contact the sender and 
properly
dispose of the e-mail.

   
   
   -- 
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   ___
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Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Nick Schmansky]

Joerg,

I'm guessing you have some matlab setup script that has run prior to the
freesurfer setup.  I see this output:
/usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6

which is not something freesurfer would link against or require.
normally it should use /usr/lib64/libstdc++.so.6.

try running this prior to sourcing the freesurfer setup:

setenv LD_LIBRARY_PATH 

Glad to see 5.3 works otherwise.  Thanks for testing it.

Nick



On Tue, 2013-05-14 at 15:17 +0200, Joerg Pfannmoeller wrote:
 Unfortunately encountered a problem in fs-fast stream during execution of 
 selxavg3-sess. Added a relevant part of the log file below:
 
 

 sxa3pwd =
 
 /home/...removed...
 
  
 sxa3cmd =
 
 /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./session02 -analysis 
 harm.sm0.mni305
 
  /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
  
 
 #@# session02 ###
 /home/...removed.../freesurfer_fMRT/session02
 -
 $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
 /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
 /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
 /usr/local/freesurfer/matlab/MRIread.m
 -
 outtop = /home/...removed.../freesurfer_fMRT
 Extension format = nii.gz
  1 stim-v-base.mat
 nruns = 1
 autostimdur = 
 
 
 outanadir = /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305
 Found 45239/537168 ( 8.4) voxels in mask
 Creating Design Matrix
  ... creation time =  0.009 sec
 DoMCFit = 1
 ntptot = 100, nX = 8, DOF = 92
 Saving X matrix to 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/Xtmp.mat
 XCond = 444.207 (normalized)
 Computing compensation for resdual AR1 bias
  1  -0.5  -0.493933(t=0.004964)
  2  -0.25  -0.269463(t=0.00648)
  3  0  -0.0514275(t=0.00734)
  4  0.25  0.155364(t=0.008221)
  5  0.5  0.337574(t=0.009058)
 AR1 Correction M: 0.0769642 1.19552
 Computing contrast matrices
 OLS Beta Pass 
   run 1t= 0.0
 Global Mean   725.29
 Global In-Mask Mean = 725.295 (694.97)
 Rescale Target = 100
 RescaleFactor = 0.137875
 OLS Residual Pass 
   run 1t= 0.0
 Saving rho1
 Smoothing ACF
 /usr/local/freesurfer/bin/mri_fwhm --mask 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz
  --i 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
  --o 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
  --fwhm 20.00 --smooth-only
 /usr/local/freesurfer/bin/mri_fwhm: 
 /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version 
 `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer/bin/mri_fwhm)
 /usr/local/freesurfer/bin/mri_fwhm: 
 /usr/local/matlab/R2008a/sys/os/glnxa64/libstdc++.so.6: version 
 `GLIBCXX_3.4.9' not found (required by /usr/local/freesurfer/bin/mri_fwhm)
 
 ERROR: /usr/local/freesurfer/bin/mri_fwhm --mask 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/mask.nii.gz
  --i 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.nii.gz
  --o 
 /home/...removed.../freesurfer_fMRT/session02/bold/harm.sm0.mni305/rho1mn.sm.nii.gz
  --fwhm 20.00 --smooth-only
  --
 ERROR: fast_selxavg3() failed\n
 
 
 
 Seemingly a problem with GLIBCXX_3.4.11. My OS is Lubuntu 13.04.
 
 
 
 
 
 
 On Tue, 14 May 2013 08:28:05 +0200
 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:
 
  Tested recon-all tonight on lubuntu 13.04. I did not encounter any 
  problems. Also freeview runs without an error for the subject bert.
  
  
  
  On Mon, 13 May 2013 14:40:10 +0200
  Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote:
  
   Just for completeness, I refer to my first contribution:
   
   http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   
   On Mon, 13 May 2013 13:58:30 +0200
   Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:
   
Hello Nick,

just installed and tested the BETA version. Up to now no problem 
encountered. Recon-all is just running as a test (using -use-gpu). OS 
is Lubuntu 13.04. I report on the segmentation as soon as it is 
finished.

So long Joerg

On Sun, 12 May 2013 22:41:25 -0400 (EDT)
Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:

 Fedora 18, Ubuntu 13 and Gentoo 64 users,
 
 another beta of the upcoming v5.3 is available here:
 
 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
 
 this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 
 users
 who wished to test that the segfault problem in v5.2 and the prior 
 beta
 v5.3 is fixed.  Your help in testing this release is appreciated.
 
 Thanks,
 
 Nick
 
 
 
 

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Marcos Martins da Silva]

Hi, all
I have just finnished my FS 5.3-Beta recon-all test in Fedora 18 and
compared to FS 5.2 in CentOS6. Both OS are installed in the same machine
but different HDs.
I used recon-all -all -hippo-subfield in the same subject for both runs
and it worked great. The time in both versions were  similar:



Fedora 18 (FS 5.3 Beta)
CentOS6 (FS 5.2 release)
Start
Tue May 14 02:09:57 2013
   Sun April 14 23:45:26
2013
End
Tue May 14 14:23:31 2013
   Mon April 15 12:50:12
2013
Processing time
12:13:34
13:04:46







As I said in previous post. tksurfer and tkmedit are all Ok. Freeview
runs but volumes and surfaces are misaligned.
Comparing the results  from recon-all, some like volume of the
hippocampi subfields and eTIV are identical but other numbers like Brain
Segmentation Volume are quite different. I am attaching aseg.stats from
both runs.

Em Dom, 2013-05-12 às 22:41 -0400, Nick Schmansky escreveu:

 Fedora 18, Ubuntu 13 and Gentoo 64 users,
 
 another beta of the upcoming v5.3 is available here:
 
 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
 
 this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
 who wished to test that the segfault problem in v5.2 and the prior beta
 v5.3 is fixed.  Your help in testing this release is appreciated.
 
 Thanks,
 
 Nick
 
 
 
 
 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.
 


# Title Segmentation Statistics 
# 
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/home/marcos/freesurfer/ASegStatsLUT.txt --subject gus 
# sysname  Linux
# hostname freesurfer
# machine  x86_64
# user marcos
# anatomy_type volume
# 
# SUBJECTS_DIR /home/marcos/freesurfer/subjects
# subjectname gus
# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1139453.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
Without Ventricles, 1122310.00, mm^3
# Measure BrainSegNotVentSurf, BrainSegVolNotVentSurf, Brain Segmentation 
Volume Without Ventricles from Surf, 1123071.316664, mm^3
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 
262768.814347, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 
266640.410169, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 529409.224516, 
mm^3
# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left hemisphere 
cortical white matter volume, 211530.623754, mm^3
# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right hemisphere 
cortical white matter volume, 214452.468393, mm^3
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical white 
matter volume, 425983.092148, mm^3
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume, 
63239.00, mm^3
# Measure TotalGray, TotalGrayVol, Total gray matter volume, 669867.224516, mm^3
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume, 
1033963.316664, mm^3
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial 
volume, 1020057.316664, mm^3
# Measure SupraTentorialNotVentVox, SupraTentorialVolNotVentVox, Supratentorial 
volume voxel count, 1017844.00, mm^3
# Measure Mask, MaskVol, Mask Volume, 1501537.00, mm^3
# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to 
eTIV, 0.757655, unitless
# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV, 0.998415, 
unitless
# Measure lhSurfaceHoles, lhSurfaceHoles, Number of defect holes in lh surfaces 
prior to fixing, 17, unitless
# Measure rhSurfaceHoles, rhSurfaceHoles, Number of defect holes in rh surfaces 
prior to fixing, 17, unitless
# Measure SurfaceHoles, SurfaceHoles, Total number of defect holes in surfaces 
prior to fixing, 34, unitless
# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial 
Volume, 1503920.190724, mm^3
# SegVolFile mri/aseg.mgz 
# SegVolFileTimeStamp  2013/04/15 05:59:23 
# ColorTable /home/marcos/freesurfer/ASegStatsLUT.txt 
# ColorTableTimeStamp 2013/02/26 03:23:16 
# InVolFile  mri/norm.mgz 
# InVolFileTimeStamp  2013/04/15 00:44:47 
# InVolFrame 

Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Joerg Pfannmoeller]

Hello Nick,

just installed and tested the BETA version. Up to now no problem encountered. 
Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I 
report on the segmentation as soon as it is finished.

So long Joerg

On Sun, 12 May 2013 22:41:25 -0400 (EDT)
Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:

 Fedora 18, Ubuntu 13 and Gentoo 64 users,
 
 another beta of the upcoming v5.3 is available here:
 
 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
 
 this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
 who wished to test that the segfault problem in v5.2 and the prior beta
 v5.3 is fixed.  Your help in testing this release is appreciated.
 
 Thanks,
 
 Nick
 
 
 
 
 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.
 


-- 
Joerg Pfannmoeller pfannmo...@uni-greifswald.de
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Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Jörg Pfannmöller]

Just for completeness, I refer to my first contribution:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html

















On Mon, 13 May 2013 13:58:30 +0200
Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote:

 Hello Nick,
 
 just installed and tested the BETA version. Up to now no problem encountered. 
 Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I 
 report on the segmentation as soon as it is finished.
 
 So long Joerg
 
 On Sun, 12 May 2013 22:41:25 -0400 (EDT)
 Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
 
  Fedora 18, Ubuntu 13 and Gentoo 64 users,
  
  another beta of the upcoming v5.3 is available here:
  
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz
  
  this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
  who wished to test that the segfault problem in v5.2 and the prior beta
  v5.3 is fixed.  Your help in testing this release is appreciated.
  
  Thanks,
  
  Nick
  
  
  
  
  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.
  
 
 
 -- 
 Joerg Pfannmoeller pfannmo...@uni-greifswald.de
 ___
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-- 
pfannmo...@uni-greifswald.de
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Re: [Freesurfer] beta v5.3 for fedora 18 and ubuntu 13

[Daniel Haehn]

Hi Nick,

I installed it on Ubuntu 13.04 and all tools seem to work. I didn't test
recon-all yet.

Cheers,
Daniel


On Sun, May 12, 2013 at 10:41 PM, Nick Schmansky
ni...@nmr.mgh.harvard.eduwrote:

 Fedora 18, Ubuntu 13 and Gentoo 64 users,

 another beta of the upcoming v5.3 is available here:


 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz

 this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users
 who wished to test that the segfault problem in v5.2 and the prior beta
 v5.3 is fixed.  Your help in testing this release is appreciated.

 Thanks,

 Nick


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


 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
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 dispose of the e-mail.




-- 
Daniel Haehn
FNNDSC / BCH
+1.857.218.5140
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Re: [Freesurfer] beta

[Irwin, William]

Hi Bruce-

The teams at UCSF and the SFVAMC would be more than willing to provide letters 
of support.

Regards,
Wil

───
William Irwin | Imaging Core Supervisor
University of California | Mission Bay
Sandler Neurosciences Building
Memory and Aging Center |  MC: 1207
675 Nelson Rising Lane | Suite 190
San Francisco | CA | 94158
wirwin |at| memory.ucsf.edu
p: 415-502-7146 | f: 415-476-1816



-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Wednesday, January 30, 2013 9:43 AM
To: Joshua Lee
Cc: freesurfer@nmr.mgh.harvard.edu; Ed Gronenschild
Subject: Re: [Freesurfer] beta

thanks Joshua

I wish study sections agreed with you. We will probably put in another support 
grant in the next year when I work up the energy to write one (they are quite 
dull). I'll probably request support letters at that time.

cheers
Bruce


On Wed, 30 Jan 2013, Joshua Lee
wrote:

 This news is most unfortunate. We all appreciate the Freesurfer team's 
 work. Freesurfer, and project's like these, provide a substantial 
 multiplier effect to the productivity of the neuroscience community. There 
 should be more funding for these types of neuroscience research 
 infrastructure.
 -
 Joshua
 
 
 On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
 wrote:
   Hi Ed

   I mean that the grant funding FreeSurfer maintainance didn't get 
 renewed. We certainly will
   continue support and development, but it does have a substantial 
 negative impact on the
   engineering we can do, such as getting rid of the 1mm restrictions.

   cheers
   Bruce
 

   On Wed, 30 Jan 2013, Ed Gronenschild wrote:

 Hi Bruce,
 What do you mean: no support anymore or no new development?

 Cheers,
 Ed

 On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

       Message: 7
       Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
       From: Bruce Fischl fis...@nmr.mgh.harvard.edu
       Subject: Re: [Freesurfer] beta
       To: Colin Reveley reve...@gmail.com
       Cc: Joshua Lee
       jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
          Nick Schmansky ni...@nmr.mgh.harvard.edu
       Message-ID:
          
 alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
       Content-Type: text/plain; charset=iso-8859-1

       Hi Colin

       yes, but we simply don't have the person power to do it at 
 the
       moment. Our
       FS support grant ends in a month and is not going to get
       renewed, so it's
       going to be hard to do anytime soon.

       sorry
       Bruce
 
 
 
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 The information in this e-mail is intended only for the person to whom 
 it is addressed. If you believe this e-mail was sent to you in error 
 and the e-mail contains patient information, please contact the 
 Partners Compliance HelpLine at http://www.partners.org/complianceline 
 . If the e-mail was sent to you in error but does not contain patient 
 information, please contact the sender and properly dispose of the e-mail.
 
 
 



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Re: [Freesurfer] beta

[Bruce Fischl]

thanks Wil
Bruce
On Thu, 31 Jan 2013, Irwin, William wrote:


Hi Bruce-

The teams at UCSF and the SFVAMC would be more than willing to provide letters 
of support.

Regards,
Wil

???
William Irwin | Imaging Core Supervisor
University of California | Mission Bay
Sandler Neurosciences Building
Memory and Aging Center |  MC: 1207
675 Nelson Rising Lane | Suite 190
San Francisco | CA | 94158
wirwin |at| memory.ucsf.edu
p: 415-502-7146 | f: 415-476-1816



-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, January 30, 2013 9:43 AM
To: Joshua Lee
Cc: freesurfer@nmr.mgh.harvard.edu; Ed Gronenschild
Subject: Re: [Freesurfer] beta

thanks Joshua

I wish study sections agreed with you. We will probably put in another support 
grant in the next year when I work up the energy to write one (they are quite 
dull). I'll probably request support letters at that time.

cheers
Bruce


On Wed, 30 Jan 2013, Joshua Lee
wrote:


This news is most unfortunate. We all appreciate the Freesurfer team's
work. Freesurfer, and project's like these, provide a substantial
multiplier effect to the productivity of the neuroscience community. There 
should be more funding for these types of neuroscience research infrastructure.
-
Joshua


On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
wrote:
  Hi Ed

  I mean that the grant funding FreeSurfer maintainance didn't get renewed. 
We certainly will
  continue support and development, but it does have a substantial negative 
impact on the
  engineering we can do, such as getting rid of the 1mm restrictions.

  cheers
  Bruce


  On Wed, 30 Jan 2013, Ed Gronenschild wrote:

Hi Bruce,
What do you mean: no support anymore or no new development?

Cheers,
Ed

On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

      Message: 7
      Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
      From: Bruce Fischl fis...@nmr.mgh.harvard.edu
      Subject: Re: [Freesurfer] beta
      To: Colin Reveley reve...@gmail.com
      Cc: Joshua Lee
      jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
         Nick Schmansky ni...@nmr.mgh.harvard.edu
      Message-ID:
         
alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
      Content-Type: text/plain; charset=iso-8859-1

      Hi Colin

      yes, but we simply don't have the person power to do it at the
      moment. Our
      FS support grant ends in a month and is not going to get
      renewed, so it's
      going to be hard to do anytime soon.

      sorry
      Bruce




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it is addressed. If you believe this e-mail was sent to you in error
and the e-mail contains patient information, please contact the
Partners Compliance HelpLine at http://www.partners.org/complianceline
. If the e-mail was sent to you in error but does not contain patient
information, please contact the sender and properly dispose of the e-mail.








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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] beta

[Ed Gronenschild]

Hi Bruce,

What do you mean: no support anymore or no new development?

Cheers,
Ed

On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

 Message: 7
 Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
 From: Bruce Fischl fis...@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] beta
 To: Colin Reveley reve...@gmail.com
 Cc: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
Nick Schmansky ni...@nmr.mgh.harvard.edu
 Message-ID:
alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
 Content-Type: text/plain; charset=iso-8859-1
 
 Hi Colin
 
 yes, but we simply don't have the person power to do it at the moment. Our
 FS support grant ends in a month and is not going to get renewed, so it's
 going to be hard to do anytime soon.
 
 sorry
 Bruce

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Re: [Freesurfer] beta

[Bruce Fischl]

Hi Ed

I mean that the grant funding FreeSurfer maintainance didn't get renewed. 
We certainly will continue support and development, but it does have a 
substantial negative impact on the engineering we can do, such as getting 
rid of the 1mm restrictions.


cheers
Bruce


On 
Wed, 30 Jan 2013, Ed Gronenschild wrote:



Hi Bruce,
What do you mean: no support anymore or no new development?

Cheers,
Ed

On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

  Message: 7
  Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
  From: Bruce Fischl fis...@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] beta
  To: Colin Reveley reve...@gmail.com
  Cc: Joshua Lee
  jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
     Nick Schmansky ni...@nmr.mgh.harvard.edu
  Message-ID:
     alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
  Content-Type: text/plain; charset=iso-8859-1

  Hi Colin

  yes, but we simply don't have the person power to do it at the
  moment. Our
  FS support grant ends in a month and is not going to get
  renewed, so it's
  going to be hard to do anytime soon.

  sorry
  Bruce



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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] beta

[Joshua Lee]

This news is most unfortunate. We all appreciate the Freesurfer team's
work. Freesurfer, and project's like these, provide a substantial
multiplier effect to the productivity of the neuroscience community. There
should be more funding for these types of neuroscience research
infrastructure.
-
Joshua


On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 Hi Ed

 I mean that the grant funding FreeSurfer maintainance didn't get renewed.
 We certainly will continue support and development, but it does have a
 substantial negative impact on the engineering we can do, such as getting
 rid of the 1mm restrictions.

 cheers
 Bruce



 On Wed, 30 Jan 2013, Ed Gronenschild wrote:

  Hi Bruce,
 What do you mean: no support anymore or no new development?

 Cheers,
 Ed

 On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

   Message: 7
   Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
   From: Bruce Fischl fis...@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] beta
   To: Colin Reveley reve...@gmail.com
   Cc: Joshua Lee
   jki...@ucdavis.edu, 
 freesurf**e...@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu
 ,
  Nick Schmansky ni...@nmr.mgh.harvard.edu
   Message-ID:
  alpine.LRH.2.00.**1301211918340.29...@entry.nmr.**
 mgh.harvard.edualpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
 
   Content-Type: text/plain; charset=iso-8859-1

   Hi Colin

   yes, but we simply don't have the person power to do it at the
   moment. Our
   FS support grant ends in a month and is not going to get
   renewed, so it's
   going to be hard to do anytime soon.

   sorry
   Bruce




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


 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.


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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] beta

[Bruce Fischl]

thanks Joshua

I wish study sections agreed with you. We will probably put in another 
support grant in the next year when I work up the energy to write one (they 
are quite dull). I'll probably request support letters at that time.


cheers
Bruce


On Wed, 30 Jan 2013, Joshua Lee 
wrote:



This news is most unfortunate. We all appreciate the Freesurfer team's work. 
Freesurfer, and project's like
these, provide a substantial multiplier effect to the productivity of the 
neuroscience community. There
should be more funding for these types of neuroscience research infrastructure.
-
Joshua


On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
wrote:
  Hi Ed

  I mean that the grant funding FreeSurfer maintainance didn't get renewed. 
We certainly will
  continue support and development, but it does have a substantial negative 
impact on the
  engineering we can do, such as getting rid of the 1mm restrictions.

  cheers
  Bruce


  On Wed, 30 Jan 2013, Ed Gronenschild wrote:

Hi Bruce,
What do you mean: no support anymore or no new development?

Cheers,
Ed

On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

      Message: 7
      Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
      From: Bruce Fischl fis...@nmr.mgh.harvard.edu
      Subject: Re: [Freesurfer] beta
      To: Colin Reveley reve...@gmail.com
      Cc: Joshua Lee
      jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
         Nick Schmansky ni...@nmr.mgh.harvard.edu
      Message-ID:
         
alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
      Content-Type: text/plain; charset=iso-8859-1

      Hi Colin

      yes, but we simply don't have the person power to do it at the
      moment. Our
      FS support grant ends in a month and is not going to get
      renewed, so it's
      going to be hard to do anytime soon.

      sorry
      Bruce




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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] beta

[Bruce Fischl]

thanks Fidel

we will certainly take you up on it in the next submission
Bruce
On Wed, 30 Jan 
2013, Fidel Vila wrote:

 Sorry to hear about this. If there is anything it can be done at a 
 FS-virtual-community level that could support the funding request, I'd be 
 supportive of it.

 Fidel
 On 2013-01-30, at 9:43, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 thanks Joshua

 I wish study sections agreed with you. We will probably put in another 
 support grant in the next year when I work up the energy to write one (they 
 are quite dull). I'll probably request support letters at that time.

 cheers
 Bruce


 On Wed, 30 Jan 2013, Joshua Lee wrote:

 This news is most unfortunate. We all appreciate the Freesurfer team's 
 work. Freesurfer, and project's like
 these, provide a substantial multiplier effect to the productivity of the 
 neuroscience community. There
 should be more funding for these types of neuroscience research 
 infrastructure.
 -
 Joshua
 On Wed, Jan 30, 2013 at 7:50 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
 wrote:
  Hi Ed

  I mean that the grant funding FreeSurfer maintainance didn't get 
 renewed. We certainly will
  continue support and development, but it does have a substantial 
 negative impact on the
  engineering we can do, such as getting rid of the 1mm restrictions.

  cheers
  Bruce

  On Wed, 30 Jan 2013, Ed Gronenschild wrote:

Hi Bruce,
What do you mean: no support anymore or no new development?

Cheers,
Ed

On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote:

  Message: 7
  Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
  From: Bruce Fischl fis...@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] beta
  To: Colin Reveley reve...@gmail.com
  Cc: Joshua Lee
  jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu,
 Nick Schmansky ni...@nmr.mgh.harvard.edu
  Message-ID:
 
 alpine.lrh.2.00.1301211918340.29...@entry.nmr.mgh.harvard.edu
  Content-Type: text/plain; charset=iso-8859-1

  Hi Colin

  yes, but we simply don't have the person power to do it at 
 the
  moment. Our
  FS support grant ends in a month and is not going to get
  renewed, so it's
  going to be hard to do anytime soon.

  sorry
  Bruce
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Re: [Freesurfer] beta

[Falk Lüsebrink]

Hi Colin,

actually there is no hard limit for the size of your input data, except for the 
subcortical segmentation which behaves quite strange.

What I currently do is to run recon-all on the hires data normally conforming 
the data. Then I use the upsampled brainmask as a mask to skullstrip my hires 
data and the upsampled aseg stuff to feed the upcoming stages of the recon-all 
pipeline. The -fix stage takes incredibly long that is why I'm trying to find a 
suitable work-around here. All other stages are being run normally.

Although isotropic data and the -noconform flag are mandatory.

Best,
Falk

 
 Original-Nachricht 
 Datum: Mon, 21 Jan 2013 19:19:25 -0500 (EST)
 Von: Bruce Fischl fis...@nmr.mgh.harvard.edu
 An: Colin Reveley reve...@gmail.com
 CC: Joshua Lee jki...@ucdavis.edu, freesurfer@nmr.mgh.harvard.edu, Nick 
 Schmansky ni...@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] beta

 Hi Colin
 
 yes, but we simply don't have the person power to do it at the moment. Our
 FS support grant ends in a month and is not going to get renewed, so it's 
 going to be hard to do anytime soon.
 
 sorry
 Bruce
 
 
 On 
 Mon, 21 Jan 2013, Colin Reveley wrote:
 
  do you plan to support data that is more that 256^3, ever?
   
  just, do you plan to support that
  
  On 21 January 2013 22:17, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
no, it won't change anything on the subcortical side yet
On Mon, 21 Jan 2013, Joshua Lee wrote:
  
 
  Thanks Bruce. That sounds great. Will subcortical
 segmentations also benefit yet. I remember that you once
  told me that there were
  some problems with it.
  -
  Josh
  
 
  On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:
        Hi Josh
 
        the way we are handling sub-mm data is to run it
 through the standard recon-all, then run a
  postprocessing surface
        deformation on the higher res data. Our preliminary
 results are pretty encouraging on T1s, T2s and
  FLAIRs.
 
        cheers
        Bruce
  
 
        On Mon, 21 Jan 2013, Joshua Lee wrote:
 
              Does this mean that using Freesurfer at
 sub-1mm isotropic resolutions will not be possible next
  version?
              Josh
  
 
              On Sun, Jan 20, 2013 at 8:07 AM, Nick
 Schmansky ni...@nmr.mgh.harvard.edu wrote:
                    Colin,
 
                    It will still error if any
 dimension is greater than 256, which then means
                    the flag -cw256 must be added to
 recon-all.  This flag chops dimensions
                    greater than 256 down to 256.
  The reason it doesnt do it automatically is
                    that with this chopping, its not
 certain that it isnt removing into the
                    head, so the user needs to be
 aware of this, so that they can inspect
                    orig.mgz with freeview to make
 sure the head is fully visible.
 
                    Nick
 
                     Does the beta permit volumes
 bigger than 256^3 voxels? just askingand
                     just asking about raw
 dimensions in unit-voxels at the start of pipeline
                    
                     cheers
                    
                     Colin
                    
                     On 18 January 2013 17:00,
 freesurfer-requ...@nmr.mgh.harvard.edu wrote:
                    
                     Send Freesurfer mailing list
 submissions to
                            
 freesurfer@nmr.mgh.harvard.edu
                    
                     To subscribe or unsubscribe
 via the World Wide Web, visit
                            
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
                     or, via email, send a message
 with subject or body 'help' to
                            
 freesurfer-requ...@nmr.mgh.harvard.edu
                    
                     You can reach the person
 managing the list at
                            
 freesurfer-ow...@nmr.mgh.harvard.edu
                    
                     When replying, please edit
 your Subject line so it is more specific
                     than Re: Contents of
 Freesurfer digest...
                    
                     Today's Topics:
                    
                        1. v5.2.0 beta, round two
 (Nick Schmansky)
                        2. Re: pial

Re: [Freesurfer] beta

[Joshua Lee]

Does this mean that using Freesurfer at sub-1mm isotropic resolutions will
not be possible next version?
Josh


On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky
ni...@nmr.mgh.harvard.eduwrote:

 Colin,

 It will still error if any dimension is greater than 256, which then means
 the flag -cw256 must be added to recon-all.  This flag chops dimensions
 greater than 256 down to 256.  The reason it doesnt do it automatically is
 that with this chopping, its not certain that it isnt removing into the
 head, so the user needs to be aware of this, so that they can inspect
 orig.mgz with freeview to make sure the head is fully visible.

 Nick

  Does the beta permit volumes bigger than 256^3 voxels? just askingand
  just asking about raw dimensions in unit-voxels at the start of pipeline
 
  cheers
 
  Colin
 
  On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.harvard.edu
 wrote:
 
  Send Freesurfer mailing list submissions to
  freesurfer@nmr.mgh.harvard.edu
 
  To subscribe or unsubscribe via the World Wide Web, visit
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  or, via email, send a message with subject or body 'help' to
  freesurfer-requ...@nmr.mgh.harvard.edu
 
  You can reach the person managing the list at
  freesurfer-ow...@nmr.mgh.harvard.edu
 
  When replying, please edit your Subject line so it is more specific
  than Re: Contents of Freesurfer digest...
 
  Today's Topics:
 
 1. v5.2.0 beta, round two (Nick Schmansky)
 2. Re: pial not computing (Borzello, Mia)
 3. Re: pial not computing (Bruce Fischl)
 4. Re: FW:  longitudinal analysis (Alex Hanganu)
 
 
  -- Forwarded message --
  From: Nick Schmansky ni...@nmr.mgh.harvard.edu
  To: freesurfer@nmr.mgh.harvard.edu
  Cc:
  Date: Fri, 18 Jan 2013 11:20:43 -0500
  Subject: [Freesurfer] v5.2.0 beta, round two
  For those willing and brave enough, another beta of v5.2.0 has been
  posted
  here for you to download and test:
 
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
 
  The Mac builds should work (note: the lion build is 64b, snow-leopard is
  32b).
 
  The final release still awaits some critical improvements to the Tracula
  stream, but the main recon-all stream with this beta is final.  The
  final
  release is expected the first week of February.
 
  Freesurfer team
 
 
 
 
 
  -- Forwarded message --
  From: Borzello, Mia mborze...@partners.org
  To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
  Cc:
  Date: Fri, 18 Jan 2013 16:25:40 +
  Subject: Re: [Freesurfer] pial not computing
  great. is there a freesurfer page on mris_topo_fixer? I'm not sure
  how/where to run this and I don't see a page on the freesurfer site.
 
  Thanks so much,
  m
  
  From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
  Sent: Thursday, January 17, 2013 1:30 PM
  To: Borzello, Mia
  Cc: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] pial not computing
 
  Hi Mia
 
  this is fixed in the newest version. You can grab a new mris_topo_fixer
  and you rerun and it should be all set. You probably should take a look
  at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
  or skull attached, and the hemispherees successfully separated)
 
  cheers
  Bruce
  On Thu, 17
  Jan 2013, Borzello, Mia wrote:
 
   Okay, so it didn't complete without error. I've attached the
  recon-all.log. Also, I was using another post op patient's MRI scans.
  
   thanks so much,
   m
   
   From: freesurfer-boun...@nmr.mgh.harvard.edu [
  freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
  fis...@nmr.mgh.harvard.edu]
   Sent: Thursday, January 17, 2013 11:22 AM
   To: Borzello, Mia
   Cc: freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] pial not computing
  
   Hi Mia
  
   we need to see the recon-all.log. Did it end with an error?
   Bruce
   On Thu, 17 Jan
   2013, Borzello, Mia wrote:
  
   Hi Freesurfers,
  
   I just ran a recon, and it seems that only  the lh.pial computed, but
  not the rh.pial. What would be the cause of this?
   Thanks,
   m
  
   ___
   Freesurfer mailing list
   Freesurfer@nmr.mgh.harvard.edu
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  
  
  
   ___
   Freesurfer mailing list
   Freesurfer@nmr.mgh.harvard.edu
   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
 
  -- Forwarded message --
  From: Bruce Fischl fis...@nmr.mgh.harvard.edu
  To: Borzello, Mia mborze...@partners.org
  Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
  Date: Fri, 18 Jan 2013 11:28:00 -0500
  Subject: Re: [Freesurfer] pial not computing
  it's run as part of recon-all. If you grab a new one and run
 
  recon-all -make all ...
 
  you should be all set
  

Re: [Freesurfer] beta

[Colin Reveley]

just to be clear:

my question is indeed about very high resoliution data. but it is at
present possible to use freesurfer with any resolution you like; you simply
fake nifti-headers or do whatever you need to do such that the data appears
1mm, and then you can rescale meshes if you need to afterwards. and so on.

You can't do with with just recon-all you need to look things up and
write your own recon-all with FS components for your data.

however there is still a hard limit on 256 voxels. it doesn't matter what
size you call them, that's the limit.

if you have more there is no trick way around it (if you want a dense, well
fitted mesh commensurate with the MRI data, obviously you can downsample
the MRI data).

Whether recon-all and FS in general will deal excplicitly with sub 1mm, or
with 256^3 data I do not know.

I'd suspect that it will and will be called freesufer V6.0.

I was jusk asking if this beta 5.2 happens to do 256 in a raw sense for
e.g. mri-tesselate

On 21 January 2013 19:59, Joshua Lee jki...@ucdavis.edu wrote:

 Does this mean that using Freesurfer at sub-1mm isotropic resolutions will
 not be possible next version?
 Josh


 On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu
  wrote:

 Colin,

 It will still error if any dimension is greater than 256, which then means
 the flag -cw256 must be added to recon-all.  This flag chops dimensions
 greater than 256 down to 256.  The reason it doesnt do it automatically is
 that with this chopping, its not certain that it isnt removing into the
 head, so the user needs to be aware of this, so that they can inspect
 orig.mgz with freeview to make sure the head is fully visible.

 Nick

  Does the beta permit volumes bigger than 256^3 voxels? just
 askingand
  just asking about raw dimensions in unit-voxels at the start of pipeline
 
  cheers
 
  Colin
 
  On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.harvard.edu
 wrote:
 
  Send Freesurfer mailing list submissions to
  freesurfer@nmr.mgh.harvard.edu
 
  To subscribe or unsubscribe via the World Wide Web, visit
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  or, via email, send a message with subject or body 'help' to
  freesurfer-requ...@nmr.mgh.harvard.edu
 
  You can reach the person managing the list at
  freesurfer-ow...@nmr.mgh.harvard.edu
 
  When replying, please edit your Subject line so it is more specific
  than Re: Contents of Freesurfer digest...
 
  Today's Topics:
 
 1. v5.2.0 beta, round two (Nick Schmansky)
 2. Re: pial not computing (Borzello, Mia)
 3. Re: pial not computing (Bruce Fischl)
 4. Re: FW:  longitudinal analysis (Alex Hanganu)
 
 
  -- Forwarded message --
  From: Nick Schmansky ni...@nmr.mgh.harvard.edu
  To: freesurfer@nmr.mgh.harvard.edu
  Cc:
  Date: Fri, 18 Jan 2013 11:20:43 -0500
  Subject: [Freesurfer] v5.2.0 beta, round two
  For those willing and brave enough, another beta of v5.2.0 has been
  posted
  here for you to download and test:
 
  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
 
  The Mac builds should work (note: the lion build is 64b, snow-leopard
 is
  32b).
 
  The final release still awaits some critical improvements to the
 Tracula
  stream, but the main recon-all stream with this beta is final.  The
  final
  release is expected the first week of February.
 
  Freesurfer team
 
 
 
 
 
  -- Forwarded message --
  From: Borzello, Mia mborze...@partners.org
  To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
  Cc:
  Date: Fri, 18 Jan 2013 16:25:40 +
  Subject: Re: [Freesurfer] pial not computing
  great. is there a freesurfer page on mris_topo_fixer? I'm not sure
  how/where to run this and I don't see a page on the freesurfer site.
 
  Thanks so much,
  m
  
  From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
  Sent: Thursday, January 17, 2013 1:30 PM
  To: Borzello, Mia
  Cc: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] pial not computing
 
  Hi Mia
 
  this is fixed in the newest version. You can grab a new mris_topo_fixer
  and you rerun and it should be all set. You probably should take a look
  at the ?h.orig.nofix to make sure it's reasonable (meaning no
 cerebellum
  or skull attached, and the hemispherees successfully separated)
 
  cheers
  Bruce
  On Thu, 17
  Jan 2013, Borzello, Mia wrote:
 
   Okay, so it didn't complete without error. I've attached the
  recon-all.log. Also, I was using another post op patient's MRI scans.
  
   thanks so much,
   m
   
   From: freesurfer-boun...@nmr.mgh.harvard.edu [
  freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
  fis...@nmr.mgh.harvard.edu]
   Sent: Thursday, January 17, 2013 11:22 AM
   To: Borzello, Mia
   Cc: freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] pial not computing
  
   Hi Mia
  
   we 

Re: [Freesurfer] beta

[Bruce Fischl]

Hi Josh

the way we are handling sub-mm data is to run it through the standard 
recon-all, then run a postprocessing surface deformation on the higher res 
data. Our preliminary results are pretty encouraging on T1s, T2s and 
FLAIRs.


cheers
Bruce


On Mon, 21 Jan 
2013, Joshua Lee wrote:



Does this mean that using Freesurfer at sub-1mm isotropic resolutions will not 
be possible next version?
Josh


On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu 
wrote:
  Colin,

  It will still error if any dimension is greater than 256, which then means
  the flag -cw256 must be added to recon-all.  This flag chops dimensions
  greater than 256 down to 256.  The reason it doesnt do it automatically is
  that with this chopping, its not certain that it isnt removing into the
  head, so the user needs to be aware of this, so that they can inspect
  orig.mgz with freeview to make sure the head is fully visible.

  Nick

   Does the beta permit volumes bigger than 256^3 voxels? just 
askingand
   just asking about raw dimensions in unit-voxels at the start of pipeline
  
   cheers
  
   Colin
  
   On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.harvard.edu 
wrote:
  
   Send Freesurfer mailing list submissions to
           freesurfer@nmr.mgh.harvard.edu
  
   To subscribe or unsubscribe via the World Wide Web, visit
           https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
   or, via email, send a message with subject or body 'help' to
           freesurfer-requ...@nmr.mgh.harvard.edu
  
   You can reach the person managing the list at
           freesurfer-ow...@nmr.mgh.harvard.edu
  
   When replying, please edit your Subject line so it is more specific
   than Re: Contents of Freesurfer digest...
  
   Today's Topics:
  
      1. v5.2.0 beta, round two (Nick Schmansky)
      2. Re: pial not computing (Borzello, Mia)
      3. Re: pial not computing (Bruce Fischl)
      4. Re: FW:  longitudinal analysis (Alex Hanganu)
  
  
   -- Forwarded message --
   From: Nick Schmansky ni...@nmr.mgh.harvard.edu
   To: freesurfer@nmr.mgh.harvard.edu
   Cc:
   Date: Fri, 18 Jan 2013 11:20:43 -0500
   Subject: [Freesurfer] v5.2.0 beta, round two
   For those willing and brave enough, another beta of v5.2.0 has been
   posted
   here for you to download and test:
  
   ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
  
   The Mac builds should work (note: the lion build is 64b, snow-leopard 
is
   32b).
  
   The final release still awaits some critical improvements to the 
Tracula
   stream, but the main recon-all stream with this beta is final.  The
   final
   release is expected the first week of February.
  
   Freesurfer team
  
  
  
  
  
   -- Forwarded message --
   From: Borzello, Mia mborze...@partners.org
   To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
   Cc:
   Date: Fri, 18 Jan 2013 16:25:40 +
   Subject: Re: [Freesurfer] pial not computing
   great. is there a freesurfer page on mris_topo_fixer? I'm not sure
   how/where to run this and I don't see a page on the freesurfer site.
  
   Thanks so much,
   m
   
   From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
   Sent: Thursday, January 17, 2013 1:30 PM
   To: Borzello, Mia
   Cc: freesurfer@nmr.mgh.harvard.edu
   Subject: Re: [Freesurfer] pial not computing
  
   Hi Mia
  
   this is fixed in the newest version. You can grab a new mris_topo_fixer
   and you rerun and it should be all set. You probably should take a look
   at the ?h.orig.nofix to make sure it's reasonable (meaning no 
cerebellum
   or skull attached, and the hemispherees successfully separated)
  
   cheers
   Bruce
   On Thu, 17
   Jan 2013, Borzello, Mia wrote:
  
Okay, so it didn't complete without error. I've attached the
   recon-all.log. Also, I was using another post op patient's MRI scans.
   
thanks so much,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu [
   freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
   fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 11:22 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
   
Hi Mia
   
we need to see the recon-all.log. Did it end with an error?
Bruce
On Thu, 17 Jan
2013, Borzello, Mia wrote:
   
Hi Freesurfers,
   
I just ran a recon, 

Re: [Freesurfer] beta

[Joshua Lee]

Thanks Bruce. That sounds great. Will subcortical segmentations also
benefit yet. I remember that you once told me that there were some problems
with it.
-
Josh


On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:

 Hi Josh

 the way we are handling sub-mm data is to run it through the standard
 recon-all, then run a postprocessing surface deformation on the higher res
 data. Our preliminary results are pretty encouraging on T1s, T2s and FLAIRs.

 cheers
 Bruce



 On Mon, 21 Jan 2013, Joshua Lee wrote:

  Does this mean that using Freesurfer at sub-1mm isotropic resolutions
 will not be possible next version?
 Josh


 On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky 
 ni...@nmr.mgh.harvard.edu wrote:
   Colin,

   It will still error if any dimension is greater than 256, which
 then means
   the flag -cw256 must be added to recon-all.  This flag chops
 dimensions
   greater than 256 down to 256.  The reason it doesnt do it
 automatically is
   that with this chopping, its not certain that it isnt removing into
 the
   head, so the user needs to be aware of this, so that they can
 inspect
   orig.mgz with freeview to make sure the head is fully visible.

   Nick

Does the beta permit volumes bigger than 256^3 voxels? just
 askingand
just asking about raw dimensions in unit-voxels at the start of
 pipeline
   
cheers
   
Colin
   
On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.**
 harvard.edu freesurfer-requ...@nmr.mgh.harvard.edu wrote:
   
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
   
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
 freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to

 freesurfer-requ...@nmr.mgh.**harvard.edufreesurfer-requ...@nmr.mgh.harvard.edu
   
You can reach the person managing the list at

 freesurfer-ow...@nmr.mgh.**harvard.edufreesurfer-ow...@nmr.mgh.harvard.edu
   
When replying, please edit your Subject line so it is more
 specific
than Re: Contents of Freesurfer digest...
   
Today's Topics:
   
   1. v5.2.0 beta, round two (Nick Schmansky)
   2. Re: pial not computing (Borzello, Mia)
   3. Re: pial not computing (Bruce Fischl)
   4. Re: FW:  longitudinal analysis (Alex Hanganu)
   
   
-- Forwarded message --
From: Nick Schmansky ni...@nmr.mgh.harvard.edu
To: 
 freesur...@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu
 
Cc:
Date: Fri, 18 Jan 2013 11:20:43 -0500
Subject: [Freesurfer] v5.2.0 beta, round two
For those willing and brave enough, another beta of v5.2.0 has
 been
posted
here for you to download and test:
   
ftp://surfer.nmr.mgh.harvard.**edu/pub/dist/freesurfer/5.2.0-**
 BETA/ ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
   
The Mac builds should work (note: the lion build is 64b,
 snow-leopard is
32b).
   
The final release still awaits some critical improvements to the
 Tracula
stream, but the main recon-all stream with this beta is final.
  The
final
release is expected the first week of February.
   
Freesurfer team
   
   
   
   
   
-- Forwarded message --
From: Borzello, Mia mborze...@partners.org
To: 
 freesur...@nmr.mgh.harvard.**edufreesurfer@nmr.mgh.harvard.edu
 freesur...@nmr.mgh.harvard.**edu freesurfer@nmr.mgh.harvard.edu
Cc:
Date: Fri, 18 Jan 2013 16:25:40 +
Subject: Re: [Freesurfer] pial not computing
great. is there a freesurfer page on mris_topo_fixer? I'm not
 sure
how/where to run this and I don't see a page on the freesurfer
 site.
   
Thanks so much,
m
__**__
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 1:30 PM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
   
Hi Mia
   
this is fixed in the newest version. You can grab a new
 mris_topo_fixer
and you rerun and it should be all set. You probably should take
 a look
at the ?h.orig.nofix to make sure it's reasonable (meaning no
 cerebellum
or skull attached, and the hemispherees successfully separated)
   
cheers
Bruce
On Thu, 17
Jan 2013, Borzello, Mia wrote:
   
 Okay, so it didn't complete without error. I've attached the

Re: [Freesurfer] beta

[Bruce Fischl]

no, it won't change anything on the subcortical side yet
On Mon, 21 Jan 
2013, Joshua Lee wrote:




Thanks Bruce. That sounds great. Will subcortical segmentations also benefit 
yet. I remember that you once told me that there were
some problems with it.
-
Josh


On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
wrote:
  Hi Josh

  the way we are handling sub-mm data is to run it through the standard 
recon-all, then run a postprocessing surface
  deformation on the higher res data. Our preliminary results are pretty 
encouraging on T1s, T2s and FLAIRs.

  cheers
  Bruce


  On Mon, 21 Jan 2013, Joshua Lee wrote:

Does this mean that using Freesurfer at sub-1mm isotropic 
resolutions will not be possible next version?
Josh


On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky 
ni...@nmr.mgh.harvard.edu wrote:
      Colin,

      It will still error if any dimension is greater than 256, 
which then means
      the flag -cw256 must be added to recon-all.  This flag chops 
dimensions
      greater than 256 down to 256.  The reason it doesnt do it 
automatically is
      that with this chopping, its not certain that it isnt 
removing into the
      head, so the user needs to be aware of this, so that they can 
inspect
      orig.mgz with freeview to make sure the head is fully visible.

      Nick

       Does the beta permit volumes bigger than 256^3 voxels? just 
askingand
       just asking about raw dimensions in unit-voxels at the 
start of pipeline
      
       cheers
      
       Colin
      
       On 18 January 2013 17:00, 
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
      
       Send Freesurfer mailing list submissions to
               freesurfer@nmr.mgh.harvard.edu
      
       To subscribe or unsubscribe via the World Wide Web, visit
               
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
       or, via email, send a message with subject or body 'help' 
to
               freesurfer-requ...@nmr.mgh.harvard.edu
      
       You can reach the person managing the list at
               freesurfer-ow...@nmr.mgh.harvard.edu
      
       When replying, please edit your Subject line so it is more 
specific
       than Re: Contents of Freesurfer digest...
      
       Today's Topics:
      
          1. v5.2.0 beta, round two (Nick Schmansky)
          2. Re: pial not computing (Borzello, Mia)
          3. Re: pial not computing (Bruce Fischl)
          4. Re: FW:  longitudinal analysis (Alex Hanganu)
      
      
       -- Forwarded message --
       From: Nick Schmansky ni...@nmr.mgh.harvard.edu
       To: freesurfer@nmr.mgh.harvard.edu
       Cc:
       Date: Fri, 18 Jan 2013 11:20:43 -0500
       Subject: [Freesurfer] v5.2.0 beta, round two
       For those willing and brave enough, another beta of v5.2.0 
has been
       posted
       here for you to download and test:
      
       
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
      
       The Mac builds should work (note: the lion build is 64b, 
snow-leopard is
       32b).
      
       The final release still awaits some critical improvements 
to the Tracula
       stream, but the main recon-all stream with this beta is 
final.  The
       final
       release is expected the first week of February.
      
       Freesurfer team
      
      
      
      
      
       -- Forwarded message --
       From: Borzello, Mia mborze...@partners.org
       To: freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edu
       Cc:
       Date: Fri, 18 Jan 2013 16:25:40 +
       Subject: Re: [Freesurfer] pial not computing
       great. is there a freesurfer page on mris_topo_fixer? I'm 
not sure
       how/where to run this and I don't see a page on the 
freesurfer site.
      
       Thanks so much,
       m
       
       From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
       Sent: Thursday, January 17, 2013 

Re: [Freesurfer] beta

[Bruce Fischl]

Hi Colin

yes, but we simply don't have the person power to do it at the moment. Our 
FS support grant ends in a month and is not going to get renewed, so it's 
going to be hard to do anytime soon.


sorry
Bruce


On 
Mon, 21 Jan 2013, Colin Reveley wrote:



do you plan to support data that is more that 256^3, ever?
 
just, do you plan to support that

On 21 January 2013 22:17, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
  no, it won't change anything on the subcortical side yet
  On Mon, 21 Jan 2013, Joshua Lee wrote:


Thanks Bruce. That sounds great. Will subcortical segmentations 
also benefit yet. I remember that you once
told me that there were
some problems with it.
-
Josh


On Mon, Jan 21, 2013 at 12:39 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edu wrote:
      Hi Josh

      the way we are handling sub-mm data is to run it through the 
standard recon-all, then run a
postprocessing surface
      deformation on the higher res data. Our preliminary results 
are pretty encouraging on T1s, T2s and
FLAIRs.

      cheers
      Bruce


      On Mon, 21 Jan 2013, Joshua Lee wrote:

            Does this mean that using Freesurfer at sub-1mm 
isotropic resolutions will not be possible next
version?
            Josh


            On Sun, Jan 20, 2013 at 8:07 AM, Nick Schmansky 
ni...@nmr.mgh.harvard.edu wrote:
                  Colin,

                  It will still error if any dimension is greater 
than 256, which then means
                  the flag -cw256 must be added to recon-all.  This 
flag chops dimensions
                  greater than 256 down to 256.  The reason it 
doesnt do it automatically is
                  that with this chopping, its not certain that it 
isnt removing into the
                  head, so the user needs to be aware of this, so 
that they can inspect
                  orig.mgz with freeview to make sure the head is 
fully visible.

                  Nick

                   Does the beta permit volumes bigger than 256^3 
voxels? just askingand
                   just asking about raw dimensions in unit-voxels 
at the start of pipeline
                  
                   cheers
                  
                   Colin
                  
                   On 18 January 2013 17:00, 
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
                  
                   Send Freesurfer mailing list submissions to
                           freesurfer@nmr.mgh.harvard.edu
                  
                   To subscribe or unsubscribe via the World Wide 
Web, visit
                           
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
                   or, via email, send a message with subject or 
body 'help' to
                           freesurfer-requ...@nmr.mgh.harvard.edu
                  
                   You can reach the person managing the list at
                           freesurfer-ow...@nmr.mgh.harvard.edu
                  
                   When replying, please edit your Subject line 
so it is more specific
                   than Re: Contents of Freesurfer digest...
                  
                   Today's Topics:
                  
                      1. v5.2.0 beta, round two (Nick Schmansky)
                      2. Re: pial not computing (Borzello, Mia)
                      3. Re: pial not computing (Bruce Fischl)
                      4. Re: FW:  longitudinal analysis (Alex 
Hanganu)
                  
                  
                   -- Forwarded message --
                   From: Nick Schmansky 
ni...@nmr.mgh.harvard.edu
                   To: freesurfer@nmr.mgh.harvard.edu
                   Cc:
                   Date: Fri, 18 Jan 2013 11:20:43 -0500
                   Subject: [Freesurfer] v5.2.0 beta, round two
                   For those willing and brave enough, another 
beta of v5.2.0 has been
                   posted
                   here for you to download and test:
                  
                   
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
                  
                   The Mac builds should work (note: the 

Re: [Freesurfer] beta

[Nick Schmansky]

Colin,

It will still error if any dimension is greater than 256, which then means
the flag -cw256 must be added to recon-all.  This flag chops dimensions
greater than 256 down to 256.  The reason it doesnt do it automatically is
that with this chopping, its not certain that it isnt removing into the
head, so the user needs to be aware of this, so that they can inspect
orig.mgz with freeview to make sure the head is fully visible.

Nick

 Does the beta permit volumes bigger than 256^3 voxels? just askingand
 just asking about raw dimensions in unit-voxels at the start of pipeline

 cheers

 Colin

 On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:

 Send Freesurfer mailing list submissions to
 freesurfer@nmr.mgh.harvard.edu

 To subscribe or unsubscribe via the World Wide Web, visit
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 or, via email, send a message with subject or body 'help' to
 freesurfer-requ...@nmr.mgh.harvard.edu

 You can reach the person managing the list at
 freesurfer-ow...@nmr.mgh.harvard.edu

 When replying, please edit your Subject line so it is more specific
 than Re: Contents of Freesurfer digest...

 Today's Topics:

1. v5.2.0 beta, round two (Nick Schmansky)
2. Re: pial not computing (Borzello, Mia)
3. Re: pial not computing (Bruce Fischl)
4. Re: FW:  longitudinal analysis (Alex Hanganu)


 -- Forwarded message --
 From: Nick Schmansky ni...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Cc:
 Date: Fri, 18 Jan 2013 11:20:43 -0500
 Subject: [Freesurfer] v5.2.0 beta, round two
 For those willing and brave enough, another beta of v5.2.0 has been
 posted
 here for you to download and test:

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/

 The Mac builds should work (note: the lion build is 64b, snow-leopard is
 32b).

 The final release still awaits some critical improvements to the Tracula
 stream, but the main recon-all stream with this beta is final.  The
 final
 release is expected the first week of February.

 Freesurfer team





 -- Forwarded message --
 From: Borzello, Mia mborze...@partners.org
 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Cc:
 Date: Fri, 18 Jan 2013 16:25:40 +
 Subject: Re: [Freesurfer] pial not computing
 great. is there a freesurfer page on mris_topo_fixer? I'm not sure
 how/where to run this and I don't see a page on the freesurfer site.

 Thanks so much,
 m
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, January 17, 2013 1:30 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] pial not computing

 Hi Mia

 this is fixed in the newest version. You can grab a new mris_topo_fixer
 and you rerun and it should be all set. You probably should take a look
 at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
 or skull attached, and the hemispherees successfully separated)

 cheers
 Bruce
 On Thu, 17
 Jan 2013, Borzello, Mia wrote:

  Okay, so it didn't complete without error. I've attached the
 recon-all.log. Also, I was using another post op patient's MRI scans.
 
  thanks so much,
  m
  
  From: freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
 fis...@nmr.mgh.harvard.edu]
  Sent: Thursday, January 17, 2013 11:22 AM
  To: Borzello, Mia
  Cc: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] pial not computing
 
  Hi Mia
 
  we need to see the recon-all.log. Did it end with an error?
  Bruce
  On Thu, 17 Jan
  2013, Borzello, Mia wrote:
 
  Hi Freesurfers,
 
  I just ran a recon, and it seems that only  the lh.pial computed, but
 not the rh.pial. What would be the cause of this?
  Thanks,
  m
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




 -- Forwarded message --
 From: Bruce Fischl fis...@nmr.mgh.harvard.edu
 To: Borzello, Mia mborze...@partners.org
 Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Date: Fri, 18 Jan 2013 11:28:00 -0500
 Subject: Re: [Freesurfer] pial not computing
 it's run as part of recon-all. If you grab a new one and run

 recon-all -make all ...

 you should be all set
 Bruce


 On Fri, 18 Jan 2013, Borzello, Mia wrote:

  great. is there a freesurfer page on mris_topo_fixer? I'm not sure
 how/where to run this and I don't see a page on the freesurfer site.

 Thanks so much,
 m
 __**__
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, January 17, 2013 1:30 

Re: [Freesurfer] beta

[Colin Reveley]

Does the beta permit volumes bigger than 256^3 voxels? just askingand
just asking about raw dimensions in unit-voxels at the start of pipeline

cheers

Colin

On 18 January 2013 17:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote:

 Send Freesurfer mailing list submissions to
 freesurfer@nmr.mgh.harvard.edu

 To subscribe or unsubscribe via the World Wide Web, visit
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 or, via email, send a message with subject or body 'help' to
 freesurfer-requ...@nmr.mgh.harvard.edu

 You can reach the person managing the list at
 freesurfer-ow...@nmr.mgh.harvard.edu

 When replying, please edit your Subject line so it is more specific
 than Re: Contents of Freesurfer digest...

 Today's Topics:

1. v5.2.0 beta, round two (Nick Schmansky)
2. Re: pial not computing (Borzello, Mia)
3. Re: pial not computing (Bruce Fischl)
4. Re: FW:  longitudinal analysis (Alex Hanganu)


 -- Forwarded message --
 From: Nick Schmansky ni...@nmr.mgh.harvard.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Cc:
 Date: Fri, 18 Jan 2013 11:20:43 -0500
 Subject: [Freesurfer] v5.2.0 beta, round two
 For those willing and brave enough, another beta of v5.2.0 has been posted
 here for you to download and test:

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/

 The Mac builds should work (note: the lion build is 64b, snow-leopard is
 32b).

 The final release still awaits some critical improvements to the Tracula
 stream, but the main recon-all stream with this beta is final.  The final
 release is expected the first week of February.

 Freesurfer team





 -- Forwarded message --
 From: Borzello, Mia mborze...@partners.org
 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Cc:
 Date: Fri, 18 Jan 2013 16:25:40 +
 Subject: Re: [Freesurfer] pial not computing
 great. is there a freesurfer page on mris_topo_fixer? I'm not sure
 how/where to run this and I don't see a page on the freesurfer site.

 Thanks so much,
 m
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, January 17, 2013 1:30 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] pial not computing

 Hi Mia

 this is fixed in the newest version. You can grab a new mris_topo_fixer
 and you rerun and it should be all set. You probably should take a look
 at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
 or skull attached, and the hemispherees successfully separated)

 cheers
 Bruce
 On Thu, 17
 Jan 2013, Borzello, Mia wrote:

  Okay, so it didn't complete without error. I've attached the
 recon-all.log. Also, I was using another post op patient's MRI scans.
 
  thanks so much,
  m
  
  From: freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [
 fis...@nmr.mgh.harvard.edu]
  Sent: Thursday, January 17, 2013 11:22 AM
  To: Borzello, Mia
  Cc: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] pial not computing
 
  Hi Mia
 
  we need to see the recon-all.log. Did it end with an error?
  Bruce
  On Thu, 17 Jan
  2013, Borzello, Mia wrote:
 
  Hi Freesurfers,
 
  I just ran a recon, and it seems that only  the lh.pial computed, but
 not the rh.pial. What would be the cause of this?
  Thanks,
  m
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




 -- Forwarded message --
 From: Bruce Fischl fis...@nmr.mgh.harvard.edu
 To: Borzello, Mia mborze...@partners.org
 Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Date: Fri, 18 Jan 2013 11:28:00 -0500
 Subject: Re: [Freesurfer] pial not computing
 it's run as part of recon-all. If you grab a new one and run

 recon-all -make all ...

 you should be all set
 Bruce


 On Fri, 18 Jan 2013, Borzello, Mia wrote:

  great. is there a freesurfer page on mris_topo_fixer? I'm not sure
 how/where to run this and I don't see a page on the freesurfer site.

 Thanks so much,
 m
 __**__
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, January 17, 2013 1:30 PM
 To: Borzello, Mia
 Cc: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] pial not computing

 Hi Mia

 this is fixed in the newest version. You can grab a new mris_topo_fixer
 and you rerun and it should be all set. You probably should take a look
 at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum
 or skull attached, and the hemispherees successfully separated)

 cheers
 Bruce
 On Thu, 17
 Jan 2013, Borzello, 

[Freesurfer] Beta maps

[Alex Hanganu]

Dear FreeSurfer List,

How can I visualise the beta maps ?

previously there is a mail about this: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html


The /average7/ subject is missing in FreeSurfer 5.1, so I guess using 
/fsaverage/ is the same, but that command shows no results.


The command:
/tksurfer fsaverage lh inflated -overlay beta.mgh -fthresh 0

/shows red areas on blue cortex. Is this correct ?

Thanks,

Alex.
___
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.

Re: [Freesurfer] Beta maps

[Douglas N Greve]

that command is correct. you might try adjusting the threshold
doug


On 12/14/2012 12:04 PM, Alex Hanganu wrote:
 Dear FreeSurfer List,

 How can I visualise the beta maps ?

 previously there is a mail about this: 
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html

 The /average7/ subject is missing in FreeSurfer 5.1, so I guess 
 using /fsaverage/ is the same, but that command shows no results.

 The command:
 /tksurfer fsaverage lh inflated -overlay beta.mgh -fthresh 0

 /shows red areas on blue cortex. Is this correct ?

 Thanks,

 Alex.


 ___
 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
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
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