[Freesurfer] FDR correction

[stdp82]

Hi list,
I would like to ask you a number of questions regarding the FDR which is 
performed following seed-based fcMRI using FS-FAST.1-In the previous mail you 
have suggested me to use mir_fdr command line (version 6.0). Because I have 
some problem with new version license (as reported in previous mail) and, 
overall I have run my data using version 5.3, I would ask you whether FDR 
integrated in tksurfer (version 5.3) is however reliable as the FDR included in 
6.0?
2-Becouse the FDR analysis was performed separately for the right and left 
hemispheres and the subcortical structures, should I set the FDR threshold to 
0.05/3 in order to correct for multiple comparison? (I have one group)
3- Is easy for me to follow the guidelines and visualize the cortical areas 
which are functionally connected with the omolateral seed. How can I do to 
visualize also the the cortical areas which are functionally connected with the 
controlateral seed? If change only the rh/lh in command line the visualization 
of the results is wrong.
4- I'd like to perform mri_surfcluster on a group to eliminate cluster < 5 
voxels from sig.nii.gz after FDR correction. I'm running mri_surfcluster --in 
sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum summaryfile --ocn 
ocnid but --subject ... must be included.How should do I do? I would like to 
run my analysis on group results, not on a single subject.
Thanks for your work.Regards,

Stefano
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[Freesurfer] output from mri_glmfit

[Peggy Skelly]

Hello Freesurfer statistical experts,

I need some assistance in explaining the output generated by mri_glmfit
(then followed by correction for multiple comparisions, mri_glmfit-sim). We
fit one model and got some statistically significant clusters. Then, we ran
another model, the same plus an additional nuisance variable. It had
similar significant clusters. How do we compare the results from the 2
different models? Which model is better?

In other statistic programs, we could examine an R^2 value, which can be
interpreted as the percent of the response variable variation that is
explained by the model. The model with the higher R^2 would be considered
better since it fits the data better. But the output from mri_glmfit has
rvar.mgh -  the sum of the squares of the residual error divided by the
DOF. So it would seem that a lower rvar would indicate a better fit. Can
rvar.mgh be used to compute an R^2, because the R^2 concept is more widely
understood. Or, is there a way to explain rvar in lay terms similar to R^2?

Thanks,
Peggy
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Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

[Douglas N Greve]

First, look in the qdec output folder to determine the FWHM in the 
fwhm.dat file. Assuming the value is 10, you are looking at the left 
hemisphere, you used a positive tail, and the voxel-wise threshold was 
1.3 (p<.05), then you would find the following file

$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf

This will have 8 columns, but you will be interested in columns 2 and 4 
(MaxClustBin and MaxClustCDF). The MaxClustCDF is the p-value for the 
given cluster size MaxClustBin. Eg, on line 25:

   25  473.758087   0.021000 0.169000  0.045775 11.261296  
0.002800  0.325000

indicates that the clustersize must be at least 473.758 to have a 
cluster p-value of .045775

clear?

doug



On 01/05/2016 08:35 PM, Tara Miskovich wrote:
> Hello Freesurfer experts,
>
> I need help me finding how to get the minimum number of vertices 
> required to pass the cluster-corrected threshold with monte carlo 
> simulations used in qdec for a surface based analysis?
>
> This is per a reviewer request, but I cannot find anything on the wiki 
> or in the mail archives on how to get this value.
>
> Can someone please help me with this issue?
>
> -- 
> Thank you,
>
> Tara
>
>
> ___
> 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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Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

[Tara Miskovich]

Thank you so much, this is incredibly helpful. And just to be clear is this
the minimum area or vertices?

Tara

On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve 
wrote:

>
> First, look in the qdec output folder to determine the FWHM in the
> fwhm.dat file. Assuming the value is 10, you are looking at the left
> hemisphere, you used a positive tail, and the voxel-wise threshold was
> 1.3 (p<.05), then you would find the following file
>
>
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf
>
> This will have 8 columns, but you will be interested in columns 2 and 4
> (MaxClustBin and MaxClustCDF). The MaxClustCDF is the p-value for the
> given cluster size MaxClustBin. Eg, on line 25:
>
>25  473.758087   0.021000 0.169000  0.045775 11.261296
> 0.002800  0.325000
>
> indicates that the clustersize must be at least 473.758 to have a
> cluster p-value of .045775
>
> clear?
>
> doug
>
>
>
> On 01/05/2016 08:35 PM, Tara Miskovich wrote:
> > Hello Freesurfer experts,
> >
> > I need help me finding how to get the minimum number of vertices
> > required to pass the cluster-corrected threshold with monte carlo
> > simulations used in qdec for a surface based analysis?
> >
> > This is per a reviewer request, but I cannot find anything on the wiki
> > or in the mail archives on how to get this value.
> >
> > Can someone please help me with this issue?
> >
> > --
> > Thank you,
> >
> > Tara
> >
> >
> > ___
> > 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.
>
>


-- 
Thank you,

Tara A. Miskovich, M.S.
Affective Neuroscience Laboratory
Department of Psychology
University of Wisconsin-Milwaukee
334 Garland Hall
misko...@uwm.edu
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Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

[Douglas N Greve]

Area in mm^2

On 01/06/2016 01:16 PM, Tara Miskovich wrote:
> Thank you so much, this is incredibly helpful. And just to be clear is 
> this the minimum area or vertices?
>
> Tara
>
> On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> First, look in the qdec output folder to determine the FWHM in the
> fwhm.dat file. Assuming the value is 10, you are looking at the left
> hemisphere, you used a positive tail, and the voxel-wise threshold was
> 1.3 (p<.05), then you would find the following file
>
> 
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf
>
> This will have 8 columns, but you will be interested in columns 2
> and 4
> (MaxClustBin and MaxClustCDF). The MaxClustCDF is the p-value for the
> given cluster size MaxClustBin. Eg, on line 25:
>
>25  473.758087   0.021000 0.169000  0.045775 11.261296
> 0.002800  0.325000
>
> indicates that the clustersize must be at least 473.758 to have a
> cluster p-value of .045775
>
> clear?
>
> doug
>
>
>
> On 01/05/2016 08:35 PM, Tara Miskovich wrote:
> > Hello Freesurfer experts,
> >
> > I need help me finding how to get the minimum number of vertices
> > required to pass the cluster-corrected threshold with monte carlo
> > simulations used in qdec for a surface based analysis?
> >
> > This is per a reviewer request, but I cannot find anything on
> the wiki
> > or in the mail archives on how to get this value.
> >
> > Can someone please help me with this issue?
> >
> > --
> > Thank you,
> >
> > Tara
> >
> >
> > ___
> > 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.
>
>
>
>
> -- 
> Thank you,
>
> Tara A. Miskovich, M.S.
> Affective Neuroscience Laboratory
> Department of Psychology
> University of Wisconsin-Milwaukee
> 334 Garland Hall
> misko...@uwm.edu 
>
>
> ___
> 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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Re: [Freesurfer] output from mri_glmfit

[Douglas N Greve]

You can get the SSE from rvar*DOF (eg, fscalc rvar.mgh mul 100 -o 
sse.mgh). You can get the SST using
fscalc y.mgh sqr -o sst.mgh
mri_concat sst.mgh --sum --o sst.mgh
Then the unadjusted r-squared as
fscalc sse.mgh div sst.mgh sub 1 mul -1 -o rsquared.mgh
The final calculation is a  little obtuse but it realizes r2 = 1 - sse/sst

For judging the model, you can compare the rvars.  I think you can also 
test the significance of the regressor you added.

doug


On 01/06/2016 01:00 PM, Peggy Skelly wrote:
> Hello Freesurfer statistical experts,
>
> I need some assistance in explaining the output generated by 
> mri_glmfit (then followed by correction for multiple 
> comparisions, mri_glmfit-sim). We fit one model and got some 
> statistically significant clusters. Then, we ran another model, the 
> same plus an additional nuisance variable. It had similar significant 
> clusters. How do we compare the results from the 2 different models? 
> Which model is better?
>
> In other statistic programs, we could examine an R^2 value, which can 
> be interpreted as the percent of the response variable variation that 
> is explained by the model. The model with the higher R^2 would be 
> considered better since it fits the data better. But the output from 
> mri_glmfit has rvar.mgh -  the sum of the squares of the residual 
> error divided by the DOF. So it would seem that a lower rvar would 
> indicate a better fit. Can rvar.mgh be used to compute an R^2, because 
> the R^2 concept is more widely understood. Or, is there a way to 
> explain rvar in lay terms similar to R^2?
>
> Thanks,
> Peggy
>
>
> ___
> 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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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
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Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

[Tara Miskovich]

Thank you for the clarification. So even though it is a vertex-wise
threshold, there is no minimum amount of vertices, it goes by area?

Tara

On Wed, Jan 6, 2016 at 12:21 PM, Douglas N Greve 
wrote:

> Area in mm^2
>
> On 01/06/2016 01:16 PM, Tara Miskovich wrote:
> > Thank you so much, this is incredibly helpful. And just to be clear is
> > this the minimum area or vertices?
> >
> > Tara
> >
> > On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > First, look in the qdec output folder to determine the FWHM in the
> > fwhm.dat file. Assuming the value is 10, you are looking at the left
> > hemisphere, you used a positive tail, and the voxel-wise threshold
> was
> > 1.3 (p<.05), then you would find the following file
> >
> >
>  
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf
> >
> > This will have 8 columns, but you will be interested in columns 2
> > and 4
> > (MaxClustBin and MaxClustCDF). The MaxClustCDF is the p-value for the
> > given cluster size MaxClustBin. Eg, on line 25:
> >
> >25  473.758087   0.021000 0.169000  0.045775 11.261296
> > 0.002800  0.325000
> >
> > indicates that the clustersize must be at least 473.758 to have a
> > cluster p-value of .045775
> >
> > clear?
> >
> > doug
> >
> >
> >
> > On 01/05/2016 08:35 PM, Tara Miskovich wrote:
> > > Hello Freesurfer experts,
> > >
> > > I need help me finding how to get the minimum number of vertices
> > > required to pass the cluster-corrected threshold with monte carlo
> > > simulations used in qdec for a surface based analysis?
> > >
> > > This is per a reviewer request, but I cannot find anything on
> > the wiki
> > > or in the mail archives on how to get this value.
> > >
> > > Can someone please help me with this issue?
> > >
> > > --
> > > Thank you,
> > >
> > > Tara
> > >
> > >
> > > ___
> > > 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  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.
> >
> >
> >
> >
> > --
> > Thank you,
> >
> > Tara A. Miskovich, M.S.
> > Affective Neuroscience Laboratory
> > Department of Psychology
> > University of Wisconsin-Milwaukee
> > 334 Garland Hall
> > misko...@uwm.edu 
> >
> >
> > ___
> > 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
>



-- 
Thank you,

Tara A. Miskovich, M.S.
Affective Neuroscience Laboratory
Department of Psychology
University of Wisconsin-Milwaukee
334 Garland Hall
misko...@uwm.edu
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The information in this e-mail is intended only for the per

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

[Douglas N Greve]

Yes. In theory you can compute the number of vertices by dividing by the 
average vertex area

On 01/06/2016 01:34 PM, Tara Miskovich wrote:
> Thank you for the clarification. So even though it is a vertex-wise 
> threshold, there is no minimum amount of vertices, it goes by area?
>
> Tara
>
> On Wed, Jan 6, 2016 at 12:21 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Area in mm^2
>
> On 01/06/2016 01:16 PM, Tara Miskovich wrote:
> > Thank you so much, this is incredibly helpful. And just to be
> clear is
> > this the minimum area or vertices?
> >
> > Tara
> >
> > On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > First, look in the qdec output folder to determine the FWHM
> in the
> > fwhm.dat file. Assuming the value is 10, you are looking at
> the left
> > hemisphere, you used a positive tail, and the voxel-wise
> threshold was
> > 1.3 (p<.05), then you would find the following file
> >
> >
>  
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf
> >
> > This will have 8 columns, but you will be interested in
> columns 2
> > and 4
> > (MaxClustBin and MaxClustCDF). The MaxClustCDF is the
> p-value for the
> > given cluster size MaxClustBin. Eg, on line 25:
> >
> >25  473.758087   0.021000 0.169000 0.045775 11.261296
> > 0.002800  0.325000
> >
> > indicates that the clustersize must be at least 473.758 to
> have a
> > cluster p-value of .045775
> >
> > clear?
> >
> > doug
> >
> >
> >
> > On 01/05/2016 08:35 PM, Tara Miskovich wrote:
> > > Hello Freesurfer experts,
> > >
> > > I need help me finding how to get the minimum number of
> vertices
> > > required to pass the cluster-corrected threshold with
> monte carlo
> > > simulations used in qdec for a surface based analysis?
> > >
> > > This is per a reviewer request, but I cannot find anything on
> > the wiki
> > > or in the mail archives on how to get this value.
> > >
> > > Can someone please help me with this issue?
> > >
> > > --
> > > Thank you,
> > >
> > > Tara
> > >
> > >
> > > ___
> > > 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.
> >
> >
> >
> >
> > --
> > Thank you,
> >
> > Tara A. Miskovich, M.S.
> > Affective Neuroscience Laboratory
> > Department of Psychology
> > University of Wisconsin-Milwaukee
> > 334 Garland Hall
> > misko...@uwm.edu 

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

[Tara Miskovich]

Great! Thank you for all the help.

On Wed, Jan 6, 2016 at 12:38 PM, Douglas N Greve 
wrote:

> Yes. In theory you can compute the number of vertices by dividing by the
> average vertex area
>
> On 01/06/2016 01:34 PM, Tara Miskovich wrote:
> > Thank you for the clarification. So even though it is a vertex-wise
> > threshold, there is no minimum amount of vertices, it goes by area?
> >
> > Tara
> >
> > On Wed, Jan 6, 2016 at 12:21 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Area in mm^2
> >
> > On 01/06/2016 01:16 PM, Tara Miskovich wrote:
> > > Thank you so much, this is incredibly helpful. And just to be
> > clear is
> > > this the minimum area or vertices?
> > >
> > > Tara
> > >
> > > On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > >
> > > First, look in the qdec output folder to determine the FWHM
> > in the
> > > fwhm.dat file. Assuming the value is 10, you are looking at
> > the left
> > > hemisphere, you used a positive tail, and the voxel-wise
> > threshold was
> > > 1.3 (p<.05), then you would find the following file
> > >
> > >
> >
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/pos/th13/mc-z.cdf
> > >
> > > This will have 8 columns, but you will be interested in
> > columns 2
> > > and 4
> > > (MaxClustBin and MaxClustCDF). The MaxClustCDF is the
> > p-value for the
> > > given cluster size MaxClustBin. Eg, on line 25:
> > >
> > >25  473.758087   0.021000 0.169000 0.045775
> 11.261296
> > > 0.002800  0.325000
> > >
> > > indicates that the clustersize must be at least 473.758 to
> > have a
> > > cluster p-value of .045775
> > >
> > > clear?
> > >
> > > doug
> > >
> > >
> > >
> > > On 01/05/2016 08:35 PM, Tara Miskovich wrote:
> > > > Hello Freesurfer experts,
> > > >
> > > > I need help me finding how to get the minimum number of
> > vertices
> > > > required to pass the cluster-corrected threshold with
> > monte carlo
> > > > simulations used in qdec for a surface based analysis?
> > > >
> > > > This is per a reviewer request, but I cannot find anything on
> > > the wiki
> > > > or in the mail archives on how to get this value.
> > > >
> > > > Can someone please help me with this issue?
> > > >
> > > > --
> > > > Thank you,
> > > >
> > > > Tara
> > > >
> > > >
> > > > ___
> > > > 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 

Re: [Freesurfer] hello freesurfer developer~

[Bruce Fischl]

Hi A-reum

did you talk to the Wash U group? If you have nifti files they can be 
processed using recon-all (i.e. recon-all -i  -s 
 -sd  -all)


cheers
Bruce


On Tue, 29 Dec 2015, A-reum Min 
wrote:



hello experts!my name is areum.
i have some question to you.i have never seen before these NIFTI
format(fig.1.png)
I want to see these data subjects's cortical thickness using qdec.
how can i to do? plz answer me  

2015-12-25 2:16 GMT+09:00 Bruce Fischl :
  Hi A-reum

  you should probably ask the Wash U HCP group. I'll cc Matt
  Glasser who might be able to answer your question
  cheers
  Bruce

  On Thu, 24 Dec 2015, A-reum Min wrote:

hello experts!my name is areum.
i have some question to you.
a few days ago i was down load HCP(human connectom
project) data.
but.. how can i use these HCP format.
i have never seen before these format(fig.1.png)
I want to see HCP data subjects's cortical thickness
using qdec.
how can i to do? 
plz answer me  

2015-11-10 7:49 GMT+09:00 A-reum Min
:
      Hello experts!
I have some question to you..

I don't need to show up so small blue regions(fig.1
blue region)

How can i control these? 

2015-11-10 7:41 GMT+09:00 Douglas N Greve
:
      Hi, please create a new thread since this is a
new topic.
      Also, I don't
      understand your question so please elaborate.

      On 11/09/2015 05:34 AM, A-reum Min wrote:
      > Hello experts!
      >
      > i have some question to you..
      >
      > How can i control the cluster size?
      >
      > My cluster threshold is 1.
      >
      > then, too many blue regions (as shown
fig.1).
      >
      > so, i want to control cluster threshold 1-->
cluster
      threshold 5.
      >
      > 2015-11-08 20:44 GMT+09:00 A-reum Min
       >:
      >
      >     Hello bruce!
      >
      >     I solve the problem for your answer.
      >
      >     And.. i have some question to you..
      >
      >     How can i control the cluster size?
      >
      >     My cluster threshold is 1.
      >
      >     then, too many blue regions (as shown
fig.1).
      >
      >     so, i want to control cluster threshold
1--> cluster
      threshold 5.
      >
      >     How can i to do?
      >
      >
      >
      >
      >
      >     2015-11-05 22:22 GMT+09:00 Bruce Fischl
      >     mailto:fis...@nmr.mgh.harvard.edu>>:
      >
      >         are
     
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
      >         and
     
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
      >         images from *different* series or
from the
      *same* series? If
      >         they are in the same series than
that explains
      what is
      >         happening. You should only give
recon-all a
      single file from
      >         any one acquisition - it will figure
out the
      rest of the files
      >         that are part of it.
      >
      >         cheers
      >         Bruce
      >
      >
      >         On Thu, 5 Nov 2015, A-reum Min
wrote:
      >
      >             hello experts.
      >             i have some question to  you...
      >
      >             when i enter the recon-all -i
/paht~
      >
      >             error showed up like below
one..
      >
      >             how can i to fix it?
      >
      >             [areum@localhost 0165766_1]#
recon-all -i
      >           
     
 /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
      -i
      >           
     
 /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
      >             -all -s sub002
  

Re: [Freesurfer] Recon-all Run Time

[Bruce Fischl]

Hi Marissa

we can't help unless you give us more details. What processors/memory was 
there on the old computers? What is on the new one? Have you tried 
running the same data on each to get comparable timings?


cheers
Bruce
On Mon, 28 Dec 
2015, Marissa Pifer wrote:



Hi Freesurfers,

I've recently downloaded free surfer onto a new computer. It's working
correctly, but the running time for the recon-all -all command is 30-50
hours. This is in contrast to when I've used free surfer on previous
computers where the run time was 6-12 hours. I'm wondering why this would be
the case and if anyone else has run into this problem.

Marissa 

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Re: [Freesurfer] Recon-all Run Time

[Marissa Pifer]

Sure, sorry I should've put all of the information on here originally. We
bought a new MacBook Pro. The version of FS (5.3.0) is the same on both
computers, and the machines are the same in terms of RAM (the new one
actually has a faster processor), the only difference is the older machine
has OS 10.9.5 and the new one has 10.11.1. We ran the same subject on the
different machines and got the differences in time (the older one took
about 6 hours, and the new one taking 30+ hours). It is not a bad brain
that we processed, a little older but in pretty good shape and it is a 1mm
isovoxel scan with good resolution etc.

Please let me know if you have any information as to why this would be,

Thanks,

Marissa

On Wed, Jan 6, 2016 at 1:56 PM, Bruce Fischl 
wrote:

> Hi Marissa
>
> we can't help unless you give us more details. What processors/memory was
> there on the old computers? What is on the new one? Have you tried running
> the same data on each to get comparable timings?
>
> cheers
> Bruce
>
> On Mon, 28 Dec 2015, Marissa Pifer wrote:
>
> Hi Freesurfers,
>>
>> I've recently downloaded free surfer onto a new computer. It's working
>> correctly, but the running time for the recon-all -all command is 30-50
>> hours. This is in contrast to when I've used free surfer on previous
>> computers where the run time was 6-12 hours. I'm wondering why this would
>> be
>> the case and if anyone else has run into this problem.
>>
>> Marissa
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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> 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] .w file for freeview

[Bruce Fischl]

Hi Peng

you can use read_wfile to read it into matlab, then save_mgh or MRIwrite 
to save them in .mgz format. Note that you will need to make sure that the 
vector you are writing is the correct length. The w-files can be sparse 
(that is, every vertex doesn't have to have a  value), but the .mgz files 
cannot be, so you'll need to create a vector that is nvertices in length 
(the number of vertices in the surface you are using), then set the entries 
in the vertices given to you by read_wfile to the values it gives you


cheers
Bruce


On Tue, 29 Dec 
2015, peng wrote:



Hi Freesurfers,
   I tried to overlay .w file onto a surface, and failed. I dug the previous
posts and know this file format is obsolete now. However I wish to know in
which version of freeview can I still use this file format, if possible. It
will be great if you can provide the link for it. If this is not possible,
is there a matlab tool similar to 'write_file.m' so I can output my data in
matlab to the newer format (substitution of w-file)?
   Thanks in advance.

best
Peng

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Re: [Freesurfer] .w file for freeview

[Douglas N Greve]

You can also use mri_surf2surf to convert it to mgh or curv format

On 01/06/2016 02:03 PM, Bruce Fischl wrote:
> Hi Peng
>
> you can use read_wfile to read it into matlab, then save_mgh or 
> MRIwrite to save them in .mgz format. Note that you will need to make 
> sure that the vector you are writing is the correct length. The 
> w-files can be sparse (that is, every vertex doesn't have to have a  
> value), but the .mgz files cannot be, so you'll need to create a 
> vector that is nvertices in length (the number of vertices in the 
> surface you are using), then set the entries in the vertices given to 
> you by read_wfile to the values it gives you
>
> cheers
> Bruce
>
>
> On Tue, 29 Dec 2015, peng wrote:
>
>> Hi Freesurfers,
>>I tried to overlay .w file onto a surface, and failed. I dug the 
>> previous
>> posts and know this file format is obsolete now. However I wish to 
>> know in
>> which version of freeview can I still use this file format, if 
>> possible. It
>> will be great if you can provide the link for it. If this is not 
>> possible,
>> is there a matlab tool similar to 'write_file.m' so I can output my 
>> data in
>> matlab to the newer format (substitution of w-file)?
>>Thanks in advance.
>>
>> best
>> Peng
>>
>>
>
>
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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] .w file for freeview

[Bruce Fischl]

oh, much easier. I didn't realize mri_surf2surf supported .w format
Bruce
On Wed, 
6 Jan 2016, Douglas N Greve wrote:

> You can also use mri_surf2surf to convert it to mgh or curv format
>
> On 01/06/2016 02:03 PM, Bruce Fischl wrote:
>> Hi Peng
>>
>> you can use read_wfile to read it into matlab, then save_mgh or
>> MRIwrite to save them in .mgz format. Note that you will need to make
>> sure that the vector you are writing is the correct length. The
>> w-files can be sparse (that is, every vertex doesn't have to have a
>> value), but the .mgz files cannot be, so you'll need to create a
>> vector that is nvertices in length (the number of vertices in the
>> surface you are using), then set the entries in the vertices given to
>> you by read_wfile to the values it gives you
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 29 Dec 2015, peng wrote:
>>
>>> Hi Freesurfers,
>>>I tried to overlay .w file onto a surface, and failed. I dug the
>>> previous
>>> posts and know this file format is obsolete now. However I wish to
>>> know in
>>> which version of freeview can I still use this file format, if
>>> possible. It
>>> will be great if you can provide the link for it. If this is not
>>> possible,
>>> is there a matlab tool similar to 'write_file.m' so I can output my
>>> data in
>>> matlab to the newer format (substitution of w-file)?
>>>Thanks in advance.
>>>
>>> best
>>> Peng
>>>
>>>
>>
>>
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>
>
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Re: [Freesurfer] .w file for freeview

[peng]

Thank you Bruce!

On Wed, Jan 6, 2016 at 8:03 PM, Bruce Fischl 
wrote:

> Hi Peng
>
> you can use read_wfile to read it into matlab, then save_mgh or MRIwrite
> to save them in .mgz format. Note that you will need to make sure that the
> vector you are writing is the correct length. The w-files can be sparse
> (that is, every vertex doesn't have to have a  value), but the .mgz files
> cannot be, so you'll need to create a vector that is nvertices in length
> (the number of vertices in the surface you are using), then set the entries
> in the vertices given to you by read_wfile to the values it gives you
>
> cheers
> Bruce
>
>
> On Tue, 29 Dec 2015, peng wrote:
>
> Hi Freesurfers,
>>I tried to overlay .w file onto a surface, and failed. I dug the
>> previous
>> posts and know this file format is obsolete now. However I wish to know in
>> which version of freeview can I still use this file format, if possible.
>> It
>> will be great if you can provide the link for it. If this is not possible,
>> is there a matlab tool similar to 'write_file.m' so I can output my data
>> in
>> matlab to the newer format (substitution of w-file)?
>>Thanks in advance.
>>
>> best
>> Peng
>>
>>
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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
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>
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Re: [Freesurfer] .w file for freeview

[peng]

Thank you Douglas!

On Wed, Jan 6, 2016 at 8:10 PM, Douglas N Greve 
wrote:

> You can also use mri_surf2surf to convert it to mgh or curv format
>
> On 01/06/2016 02:03 PM, Bruce Fischl wrote:
> > Hi Peng
> >
> > you can use read_wfile to read it into matlab, then save_mgh or
> > MRIwrite to save them in .mgz format. Note that you will need to make
> > sure that the vector you are writing is the correct length. The
> > w-files can be sparse (that is, every vertex doesn't have to have a
> > value), but the .mgz files cannot be, so you'll need to create a
> > vector that is nvertices in length (the number of vertices in the
> > surface you are using), then set the entries in the vertices given to
> > you by read_wfile to the values it gives you
> >
> > cheers
> > Bruce
> >
> >
> > On Tue, 29 Dec 2015, peng wrote:
> >
> >> Hi Freesurfers,
> >>I tried to overlay .w file onto a surface, and failed. I dug the
> >> previous
> >> posts and know this file format is obsolete now. However I wish to
> >> know in
> >> which version of freeview can I still use this file format, if
> >> possible. It
> >> will be great if you can provide the link for it. If this is not
> >> possible,
> >> is there a matlab tool similar to 'write_file.m' so I can output my
> >> data in
> >> matlab to the newer format (substitution of w-file)?
> >>Thanks in advance.
> >>
> >> best
> >> Peng
> >>
> >>
> >
> >
> > ___
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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
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] FDR correction

[Douglas N Greve]

On 01/06/2016 11:00 AM, std...@virgilio.it wrote:
> Hi list,
>
> I would like to ask you a number of questions regarding the FDR which 
> is performed following seed-based fcMRI using FS-FAST.
> 1-In the previous mail you have suggested me to use mir_fdr command 
> line (version 6.0). Because I have some problem with new version 
> license (as reported in previous mail) and, overall I have run my data 
> using version 5.3, I would ask you whether FDR integrated in tksurfer 
> (version 5.3) is however reliable as the FDR included in 6.0?
Yes, they call the same code.
>
> 2-Becouse the FDR analysis was performed separately for the right and 
> left hemispheres and the subcortical structures, should I set the FDR 
> threshold to 0.05/3 in order to correct for multiple comparison? (I 
> have one group)
I'm not sure. You can try to run both hemispheres in matlab, somethiing like
lh = MRIread('sig.lh.mgh');
lhp = 10^-abs(lh.vol);
rh = MRIread('sig.rh.mgh');
rlhp = 10^-abs(rh.vol);

p = [lhp rhp];
fdrthresh = fast_fdrthresh(p,fdr);

>
> 3- Is easy for me to follow the guidelines and visualize the cortical 
> areas which are functionally connected with the omolateral seed. How 
> can I do to visualize also the the cortical areas which are 
> functionally connected with the controlateral seed? If change only the 
> rh/lh in command line the visualization of the results is wrong.
I don't understand.
>
> 4- I'd like to perform mri_surfcluster on a group to eliminate cluster 
> < 5
> voxels from sig.nii.gz after FDR correction. I'm running 
> mri_surfcluster --in
> sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum 
> summaryfile --ocn
> ocnid
> but --subject ... must be included.
> How should do I do? I would like to run my analysis on group results, 
> not on a single subject.
If this is from a group analysis, the subject is probablly fsaverage
>
> Thanks for your work.
> Regards,
>
>
> Stefano
>
>
>
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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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] P files

[John Anderson]

Dear Freesurfer experts,

I want to inquire if there is any tool in Freesurfer that can help to convert the p files ( raw data generated by GE scanner ) to DICOMs

 

 

Thanks for any advice!
 

Bests,
John 
 
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Re: [Freesurfer] P files

[Bruce Fischl]

Hi John

Luca Marinelli (ccd) might be able to help you.

cheers
Bruce

On Thu, 7 Jan 2016, John Anderson wrote:


Dear Freesurfer experts,
I want to inquire if there is any tool in Freesurfer that can help to
convert the p files ( raw data generated by GE scanner ) to DICOMs
 
 
Thanks for any advice!
 
Bests,
John 
 

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Re: [Freesurfer] P files

[Anthony Dick]

Another option is to open the files in OsiriX, and export to DICOM from 
there. This does not, to my knowledge, have a batch option though.


Anthony

On 1/6/16 9:35 PM, Bruce Fischl wrote:

Hi John

Luca Marinelli (ccd) might be able to help you.

cheers
Bruce

On Thu, 7 Jan 2016, John Anderson wrote:


Dear Freesurfer experts,
I want to inquire if there is any tool in Freesurfer that can help to
convert the p files ( raw data generated by GE scanner ) to DICOMs


Thanks for any advice!

Bests,
John






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--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick

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[Freesurfer] P files

[Bruce Fischl]

Begin forwarded message:

> From: "Marinelli, Luca (GE Global Research)" 
> Date: January 6, 2016 at 10:26:38 PM EST
> To: Bruce Fischl , Freesurfer support list 
> 
> Cc: "Marinelli, Luca (GE Global Research)" 
> Subject: Re: [Freesurfer] P files
> 
> Hi John,
> 
> Can you please reach out to me directly at marin...@research.ge.com so I
> can better understand your needs and see if there is anything I can do to
> help?
> 
> Best,
> 
> Luca
> 
> 
> 
> 
> 
> 
> 
> 
>> On 1/6/16, 9:35 PM, "Bruce Fischl"  wrote:
>> 
>> Hi John
>> 
>> Luca Marinelli (ccd) might be able to help you.
>> 
>> cheers
>> Bruce
>> 
>>> On Thu, 7 Jan 2016, John Anderson wrote:
>>> 
>>> Dear Freesurfer experts,
>>> I want to inquire if there is any tool in Freesurfer that can help to
>>> convert the p files ( raw data generated by GE scanner ) to DICOMs
>>> 
>>> 
>>> Thanks for any advice!
>>> 
>>> Bests,
>>> John
>> 
>> 
>> 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
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compl
>> ianceline&d=CwIGaQ&c=IV_clAzoPDE253xZdHuilRgztyh_RiV3wUrLrDQYWSI&r=eSTAoNl
>> ku4a3XnNWAquvb-o6CJqTPTXMUCt91ZS0mc8&m=wgtGJqDdB3Yobmvr8MXewimixBYbYOpxEkH
>> l8_Pac3I&s=RjenNXRWYQ_Xu93C2YeHP-fmxk1hQRnhVGVMd2Q9E3I&e=  . If the
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>> properly
>> dispose of the e-mail.
> 
> 
> 
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