Re: [Freesurfer] extract lgi

2019-11-26 Thread Greve, Douglas N.,Ph.D. 
yes, see
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI

On 11/26/2019 2:07 AM, An Lijun wrote:

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Dear Yanyan,
Actually you could refer to the freesurfer tutorial firstly.

Best Regards,
An Lijun


Lin Yanyan mailto:linyan...@outlook.com>> 于2019年11月26日周二 
下午12:49写道：

External Email - Use Caution

Hello, I have a question about lgi computing and extracting. I had run 
recon-all -s  -all, and there are lh.pail/rh.pail under each subject, 
then what should I do?





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Re: [Freesurfer] extract lgi

2019-11-25 Thread An Lijun 
External Email - Use Caution

Dear Yanyan,
Actually you could refer to the freesurfer tutorial firstly.

Best Regards,
An Lijun


Lin Yanyan mailto:linyan...@outlook.com>> 于2019年11月26日周二 
下午12:49写道：

External Email - Use Caution

Hello, I have a question about lgi computing and extracting. I had run 
recon-all -s  -all, and there are lh.pail/rh.pail under each subject, 
then what should I do?





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[Freesurfer] extract lgi

2019-11-25 Thread Lin Yanyan 
External Email - Use Caution

Hello, I have a question about lgi computing and extracting. I had run 
recon-all -s  -all, and there are lh.pail/rh.pail under each subject, 
then what should I do?





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Re: [Freesurfer] Extract LGI at MaxVertex and extract effect-sizes in table format

2016-03-03 Thread Douglas N Greve 


On 02/29/2016 02:38 AM, Bittner, Nora wrote:
>
> Dear FreeSurfer Experts,
>
> Sorry for reposting this massage again, but I still have two 
> questions, which you can hopefully answer to:
>
> 1)
>
> I calculated several analyses with LGI as my dependent variable, 
> resulting in several significant clusters.
>
> Now, I would like to extract the individual LGI value at the *maximum 
> vertex* of each significant cluster to plot it against my experimental 
> variables (instead of working with the mean LGI values of the clusters).
>
> What I tried so far is to use mri_segstats to extract the LGI at the 
> maximum vertex:
>
> mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 
> --avgwf vertexno84367.dat
>
> where y.mgh is my input file from the glm and vertexno 84367 is the 
> maximum vertex of the cluster as reported in the cluster.summary-file.
>
> I found the command in the FS helpline documentation 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), 
> but regrettably 
> 
>  
> I get the following error message:
> “ERROR: Option –-crs unkown”
> In the fswiki I also couldn´t find the “mri_segstats - - crs option” 
> in the user description.
> Is there any other option or argument I can use in mri_segstats (or in 
> any other command) to extract the LGI value per person at the given 
> vertex?
Remember, you can always run commands with --help to get more info. If 
you run this command with --help, you will see:
--vox C R S
 replace seg with all 0s except at CRS

So use --vox, not --crs.
>
> 2)
>
> I would like to calculate effect sizes of my results. Therefore I used 
> fscalc:
>
> fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div 
> $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ 
> glm/contrast/effectsize.mgh
> This worked fine and resulted in a surface overlay displaying the 
> effect sizes. Now, I would like to extract these effect sizes in 
> 'table' format. I tried to use mri-segstats:
>
> mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf 
> effectsize.dat
>
> I am not sure, if this gives me the correct results. Is this the right 
> command?
>
> I would really appreciate 
> 
>  
> your help.
>
Yes, that will give you the effect size averaged over each annotation
>
> Thank you in advance,
>
> Nora
>
>
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Extract LGI at MaxVertex and extract effect-sizes in table format

2016-02-28 Thread Bittner, Nora 
Dear FreeSurfer Experts,

Sorry for reposting this massage again, but I still have two questions, which 
you can hopefully answer to:

1)
I calculated several analyses with LGI as my dependent variable, resulting in 
several significant clusters.
Now, I would like to extract the individual LGI value at the maximum vertex of 
each significant cluster to plot it against my experimental variables (instead 
of working with the mean LGI values of the clusters).
What I tried so far is to use mri_segstats to extract the LGI at the maximum 
vertex:


mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 --avgwf 
vertexno84367.dat


where y.mgh is my input file from the glm and vertexno 84367 is the maximum 
vertex of the cluster as reported in the cluster.summary-file.

I found the command in the FS helpline documentation 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), 
but 
regrettably
 I get the following error message:

"ERROR: Option --crs unkown"

In the fswiki I also couldn´t find the "mri_segstats - - crs option" in the 
user description.



Is there any other option or argument I can use in mri_segstats (or in any 
other command) to extract the LGI value per person at the given vertex?




2)
I would like to calculate effect sizes of my results. Therefore I used fscalc:


fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div 
$SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ 
glm/contrast/effectsize.mgh



This worked fine and resulted in a surface overlay displaying the effect sizes. 
Now, I would like to extract these effect sizes in 'table' format. I tried to 
use mri-segstats:


mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf 
effectsize.dat

I am not sure, if this gives me the correct results. Is this the right command?
I would really 
appreciate
 your help.


Thank you in advance,
Nora





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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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
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Re: [Freesurfer] Extract LGI at MaxVertex of a significant Cluster, Effect sizes

2016-02-16 Thread Douglas N Greve 


On 02/03/2016 08:20 AM, Bittner, Nora wrote:
>
> Dear FreeSurfer Experts,
>
> I have two questions, which you can hopefully answer to:
>
> 1)
>
> I calculated several analyses with LGI as my dependent variable, 
> resulting in several significant clusters.
>
> Now, I would like to extract the individual LGI value at the *maximum 
> vertex* of each significant cluster to plot it against my experimental 
> variables (instead of working with the mean LGI values of the clusters).
>
> What I tried so far is to use mri_segstats to extract the LGI at the 
> maximum vertex:
>
> mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 
> --avgwf vertexno84367.dat
>
> where y.mgh is my input file from the glm and vertexno 84367 is the 
> maximum vertex of the cluster as reported in the cluster.summary-file.
>
> I found the command in the FS helpline documentation 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), 
> but regrettably 
> 
>  
> I get the following error message:
> “ERROR: Option –-crs unkown”
> In the fswiki I also couldn´t find the “mri_segstats - - crs option” 
> in the user description.
> Is there any other option or argument I can use in mri_segstats (or in 
> any other command) to extract the LGI value per person at the given 
> vertex?
It should be --vox, not --crs. And don't include "vertexno", just use 
the 3 numbers.
>
> 2)
>
> I would like to calculate effect sizes of my results. Therefore I used 
> fscalc:
>
> fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div 
> $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ 
> glm/contrast/effectsize.mgh
>
> This worked fine and resulted in a surface overlay displaying the 
> effect sizes. Is there any way to convert this effectsize.mgh-file to 
> a table format? Such that I would get numerical values, let´s say, 
> vertexwise effect sizes or similar?
>
You can again use mri_segstats,passing it --annot to get a table of 
effect sizes averaged over each aparc annotation. Run mri_segstats with 
--help to get more info
>
> Thank you in advance,
>
> Nora Bittner
>
>
>
> 
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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
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dispose of the e-mail.

[Freesurfer] Extract LGI at MaxVertex of a significant Cluster, Effect sizes

2016-02-03 Thread Bittner, Nora 
Dear FreeSurfer Experts,

I have two questions, which you can hopefully answer to:

1)
I calculated several analyses with LGI as my dependent variable, resulting in 
several significant clusters.
Now, I would like to extract the individual LGI value at the maximum vertex of 
each significant cluster to plot it against my experimental variables (instead 
of working with the mean LGI values of the clusters).
What I tried so far is to use mri_segstats to extract the LGI at the maximum 
vertex:


mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 --avgwf 
vertexno84367.dat


where y.mgh is my input file from the glm and vertexno 84367 is the maximum 
vertex of the cluster as reported in the cluster.summary-file.

I found the command in the FS helpline documentation 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), 
but 
regrettably
 I get the following error message:

"ERROR: Option --crs unkown"

In the fswiki I also couldn´t find the "mri_segstats - - crs option" in the 
user description.



Is there any other option or argument I can use in mri_segstats (or in any 
other command) to extract the LGI value per person at the given vertex?




2)
I would like to calculate effect sizes of my results. Therefore I used fscalc:


fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div 
$SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ 
glm/contrast/effectsize.mgh


This worked fine and resulted in a surface overlay displaying the effect sizes. 
Is there any way to convert this effectsize.mgh-file to a table format? Such 
that I would get numerical values, let´s say, vertexwise effect sizes or 
similar?

Thank you in advance,
Nora Bittner




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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