[Freesurfer] Possible to Specify Default Version of MATLAB for selxavg3-sess?

2021-12-25 Thread Yadav, Shrikanth Muralidhar 


Hello Freesurfer Developers,

I am having trouble with my first level analysis using selxavg3-sess. I passed 
the -debug flag in my command and noticed that MATLAB 2021a was being used. 
However, the command worked as expected before MATLAB was updated from 2020b. 
Is there a way I can specify freesurfer (v6.0.0) to use a specific version of 
MATLAB?

I tried passing the -octave flag but got the following error

ERROR: cannot find /usr/local/freesurfer/stable5_1_0/matlab/

The full command:

selxavg3-sess -s 002_S_0413_V1_fMRI -overwrite -a lh-FastADNI12state1 
-no-preproc -force -debug

Thank you
Shrikanth
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Re: [Freesurfer] Cohen´s D effect size

2021-12-25 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Sorry, I wrote this previous email from a different adress because I did
not receive emails from the freesurfer's support list 😅

Thank you!

El sáb., 25 dic. 2021 17:01, Miguel Ángel Rivas Fernández <
miguelrivasf...@gmail.com> escribió:

> Dear Tim,
>
>
> Thank you for your reply. I used these two commands and now it seems that
> everything worked fine:
>
>
> 1) cd glmdir/contrast  fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh
>
> 2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
> --sum test.output
>
>
> After using the second command, I can open the test.output file and see
> the mean Cohen's D of each significant cluster. Is correct the second
> command?
>
> mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
> --sum test.output
>
> Thank you very much.
>
>
> Best regards,
>
> Steve.
>
> El sáb., 25 dic. 2021 15:57, Tim Schäfer  escribió:
>
>> External Email - Use Caution
>>
>> Hi Steve,
>>
>> what exactly do you mean by unable to open? What happens if you try to
>> load it as an overlay for fsaverage in FreeView? Is there any error message
>> if you try to open it?
>>
>> Best,
>>
>> Tim
>>
>>
>> --
>> Dr. Tim Schäfer
>> Postdoc Computational Neuroimaging
>> Department of Child and Adolescent Psychiatry, Psychosomatics and
>> Psychotherapy
>> University Hospital Frankfurt, Goethe University Frankfurt am Main,
>> Germany
>>
>> > On 12/22/2021 5:02 PM Steve Petersen  wrote:
>> >
>> >
>> > External Email - Use Caution
>> >
>> > Dear Freesurfer experts,
>> >
>> > I would really appreciate it if anyone can give me some guidance about
>> this
>> > question that I posted a few days ago. I conducted a One-way ANOVA and
>> now
>> > I would to report the Cohen's D effect size for each pairwise comparison
>> > (t-tests). For that purpose, I estimated the Cohen's D effect size of
>> > significant clusters using the suggested command
>> > <
>> https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html
>> >:
>> >
>> >
>> > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
>> >
>> > Now, I get the cohensd.mgh file but I am not able to open this file. How
>> > can I see the particular effect size of each significant cluster
>> included
>> > in the sig.cluster.summary file?.
>> >
>> > Thank you very much in advance for your time!
>> >
>> > Best regards,
>> >
>> > Steve,
>> >
>> > El mié, 15 dic 2021 a las 19:14, Steve Petersen ()
>> > escribió:
>> >
>> > > Dear Freesurfer experts,
>> > >
>> > > I am attempting to estimate the Cohen's D effect size of significant
>> > > clusters using the suggested command
>> > > <
>> https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html
>> >:
>> > >
>> > >
>> > > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
>> > >
>> > > Now, I get the cohensd.mgh file but I am not able to open this file.
>> How
>> > > can I see the particular effect size of each significant cluster
>> included
>> > > in the sig.cluster.summary file?.
>> > >
>> > > Thank you very much for your help!
>> > >
>> > > Best regards,
>> > >
>> > >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> >
>> https://secure-web.cisco.com/1DzWVfD7aS3RdSncH3YwQ3Gj-hgoNwquNSuAofwpNP31cDynL2xd2pSKjoIWA3ul3pF2QUWS6xwforZUGNvOjq0gUlXCH6YrmQRhFgDbwqvGLGkgks3D45HwD1Po5jsnZ1OHc0htwaNGHlWqDQjBHeVHR7zpgg_q9kZUMq2IfIpGOGpChoPxaP2lTUlFlS8fouQ8AxcY2OTE-EHQWovNIEEhrP1UZNN8ZEVIMdouf_bzoVo26YAp7GqmlDMniaa43UJSAaycNU-0ViAu1_MStJj5i17R-hj6bP9xQpxkw2zgZ2Xuepc0ZONsZrxf9TnTACRZ_KrPDHhrs769GH_cyKA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>
>> ___
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Re: [Freesurfer] Cohen´s D effect size

2021-12-25 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Dear Tim,


Thank you for your reply. I used these two commands and now it seems that
everything worked fine:


1) cd glmdir/contrast  fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh

2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
--sum test.output


After using the second command, I can open the test.output file and see the
mean Cohen's D of each significant cluster. Is correct the second command?

mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0
--sum test.output

Thank you very much.


Best regards,

Steve.

El sáb., 25 dic. 2021 15:57, Tim Schäfer  escribió:

> External Email - Use Caution
>
> Hi Steve,
>
> what exactly do you mean by unable to open? What happens if you try to
> load it as an overlay for fsaverage in FreeView? Is there any error message
> if you try to open it?
>
> Best,
>
> Tim
>
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
> > On 12/22/2021 5:02 PM Steve Petersen  wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> > I would really appreciate it if anyone can give me some guidance about
> this
> > question that I posted a few days ago. I conducted a One-way ANOVA and
> now
> > I would to report the Cohen's D effect size for each pairwise comparison
> > (t-tests). For that purpose, I estimated the Cohen's D effect size of
> > significant clusters using the suggested command
> > <
> https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html
> >:
> >
> >
> > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
> >
> > Now, I get the cohensd.mgh file but I am not able to open this file. How
> > can I see the particular effect size of each significant cluster included
> > in the sig.cluster.summary file?.
> >
> > Thank you very much in advance for your time!
> >
> > Best regards,
> >
> > Steve,
> >
> > El mié, 15 dic 2021 a las 19:14, Steve Petersen ()
> > escribió:
> >
> > > Dear Freesurfer experts,
> > >
> > > I am attempting to estimate the Cohen's D effect size of significant
> > > clusters using the suggested command
> > > <
> https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html
> >:
> > >
> > >
> > > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
> > >
> > > Now, I get the cohensd.mgh file but I am not able to open this file.
> How
> > > can I see the particular effect size of each significant cluster
> included
> > > in the sig.cluster.summary file?.
> > >
> > > Thank you very much for your help!
> > >
> > > Best regards,
> > >
> > >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://secure-web.cisco.com/1DzWVfD7aS3RdSncH3YwQ3Gj-hgoNwquNSuAofwpNP31cDynL2xd2pSKjoIWA3ul3pF2QUWS6xwforZUGNvOjq0gUlXCH6YrmQRhFgDbwqvGLGkgks3D45HwD1Po5jsnZ1OHc0htwaNGHlWqDQjBHeVHR7zpgg_q9kZUMq2IfIpGOGpChoPxaP2lTUlFlS8fouQ8AxcY2OTE-EHQWovNIEEhrP1UZNN8ZEVIMdouf_bzoVo26YAp7GqmlDMniaa43UJSAaycNU-0ViAu1_MStJj5i17R-hj6bP9xQpxkw2zgZ2Xuepc0ZONsZrxf9TnTACRZ_KrPDHhrs769GH_cyKA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
> ___
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Re: [Freesurfer] Cohen´s D effect size

2021-12-25 Thread Tim Schäfer 
External Email - Use Caution

Hi Steve,

what exactly do you mean by unable to open? What happens if you try to load it 
as an overlay for fsaverage in FreeView? Is there any error message if you try 
to open it?

Best,

Tim


--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On 12/22/2021 5:02 PM Steve Petersen  wrote:
> 
>  
> External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
> I would really appreciate it if anyone can give me some guidance about this
> question that I posted a few days ago. I conducted a One-way ANOVA and now
> I would to report the Cohen's D effect size for each pairwise comparison
> (t-tests). For that purpose, I estimated the Cohen's D effect size of
> significant clusters using the suggested command
> :
> 
> 
> fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
> 
> Now, I get the cohensd.mgh file but I am not able to open this file. How
> can I see the particular effect size of each significant cluster included
> in the sig.cluster.summary file?.
> 
> Thank you very much in advance for your time!
> 
> Best regards,
> 
> Steve,
> 
> El mié, 15 dic 2021 a las 19:14, Steve Petersen ()
> escribió:
> 
> > Dear Freesurfer experts,
> >
> > I am attempting to estimate the Cohen's D effect size of significant
> > clusters using the suggested command
> > :
> >
> >
> > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh
> >
> > Now, I get the cohensd.mgh file but I am not able to open this file. How
> > can I see the particular effect size of each significant cluster included
> > in the sig.cluster.summary file?.
> >
> > Thank you very much for your help!
> >
> > Best regards,
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Developer password for Ubuntu log in

2021-12-25 Thread Sang-Han Choi 
External Email - Use Caution

Dear FreeSurfer Manager

I am currently setting up FreeSurfer using the Ubuntu VM by following (
https://secure-web.cisco.com/146Qu5uXrq4DXeyoh_h2Rn9ul9DVRSvPNPQwb9piTjitrouZ-KMHv8-agmyj0OuD3oRQySl60b1B6JtppumYWZUgwV5dY2eLZbqhmzcZp9OlT2Yi5YdBSBzsiMArw6-ayC1C1twOSUF5R9W8dXykFdveYvTTzF8UqyVJDVqPMGGAGRkmZjv-MrtL_sHMsZE8N4Ei5PDwNZj4LMrEoGzyJqK4dWXE2lAxr00nNwh2iOEGtMMNiwDLuJWiVC2PkSgVekZ3UzQ856I0-_HyQS0KwEPiLKdo4jmHsMvCko0IMdUEmLp2t3qV3kTxUAC3MSTH4TcmKCdMlJAI2OGiuQ4mm0w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67_win),
But I can't log in because I don't have the developer password. Would it be
possible to provide me with the password?
Thank you!

sincerely yours,
 Sang-Han Choi
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