Re: [Freesurfer] [External] Freesurfer Digest, Vol 190, Issue 3

2019-12-03 Thread Greve, Douglas N.,Ph.D. 
Yes, that is the correct interpretation of the colors

On 12/3/2019 9:51 AM, Ferraro, Pilar wrote:
>  External Email - Use Caution
>
> Yes, absolutely, this should work! Many Thanks!
> I have just one last question concerning the colors in FreeView.
> I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) 
> after.
> The contrast matrix is 1 -1 0.
> Among the results I see blue and red regions in Freeview. Am I correct 
> assuming that blue regions are the ones where cortical thickness is reduced 
> in patients relative to HC (correcting for disease duration)?
> I just wanted to ask for a confirmation.
>
> Many thanks,
>
> Pilar
>> Message: 2
>> Date: Mon, 2 Dec 2019 16:06:54 +
>> From: "Greve, Douglas N.,Ph.D." 
>> Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one
>>  variable
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Message-ID: 
>> Content-Type: text/plain; charset="windows-1252"
>>
>> It sounds like it would be a one-group, two-variable situation, like this
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V
>> Is that not correct?
>>
>>
>> On 11/28/2019 5:24 AM, Ferraro, Pilar wrote:
>>
>> External Email - Use Caution
>>
>> Hi,
>>
>> I apologize if I did not explain my issue properly.
>> I'm interested in looking at age-related thickness reductions in 1 group 
>> (patients), but I'd like to also account for the effect of disease duration.
>> We can say that in my case disease duration is the nuisance factor.
>> Briefly, I have the same issue reported in here 
>> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html), 
>> but with only one group.
>> How would you recommend to proceed?
>>
>> Many  thanks,
>>
>> Pilar
>>
>> 
>> Message: 2
>> Date: Wed, 27 Nov 2019 16:56:20 +
>> From: "Greve, Douglas N.,Ph.D." 
>> 
>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>> 36
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> 
>> Message-ID: 
>> 
>> Content-Type: text/plain; charset="utf-8"
>>
>> what is the difference between and independent variable and a covariate?
>>
>> On 11/27/2019 6:57 AM, Ferraro, Pilar wrote:
>>>  External Email - Use Caution
>>>
>>> Yes, I did.
>>> But in this case I have two factors, not only one. In particular, I have an 
>>> independent variable X and a covariate I?d like to include in the model.
>>> How would you suggest to proceed?
>>>
>>>
>>> Thanks,
>>>
>>> Pilar
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>> URL: 
>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/cec9033a/attachment-0001.html
>>
>> --
>>
>> Message: 3
>> Date: Mon, 2 Dec 2019 16:08:08 +
>> From: "Greve, Douglas N.,Ph.D." 
>> Subject: Re: [Freesurfer] fsfast no run directories
>> To: "freesurfer@nmr.mgh.harvard.edu" 
>> Message-ID: <41b08316-678f-ff4e-aa09-86993b0c7...@mgh.harvard.edu>
>> Content-Type: text/plain; charset="utf-8"
>>
>> In the bold directory, it looks like you have one run directory called "1". 
>> Change this to "001"
>>
>> On 11/29/2019 1:48 AM, Renew Andrade wrote:
>>
>> External Email - Use Caution
>>
>> Dear FreeSurfer experts:
>> I have some issues with "preproc-sess" because I cannot seem to get the 
>> setup of the directory structure or files to connect different things(the T1 
>> subjects with functional bold or rest files). I have this output.
>>
>>
>> root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess 
>> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>> --
>> preproc-sess logfile is log/preproc-sess.sess1.log
>> --
>> $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
>> root
>> setenv FREESURFER_HOME /usr/local/freesurfer
>> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
>> Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 
>> 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
>> /home/andraderenew/Downloads/barrios/project
>> /usr/local/freesurfer/fsfast/bin/preproc-sess
>> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
>> vie nov 29 07:33:28 CET 2019
>> instem   f
>> mc   1 f fmcpr
>> stc  1fmcpr fmcpr.up
>> sm   0
>> mask 1   brain
>> sess1 Template -
>> mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project 
>> -fsd bold -update
>>
>> Session:

Re: [Freesurfer] [External] Freesurfer Digest, Vol 190, Issue 3

2019-12-03 Thread Ferraro, Pilar 
External Email - Use Caution

Yes, absolutely, this should work! Many Thanks!
I have just one last question concerning the colors in FreeView.
I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) 
after.
The contrast matrix is 1 -1 0.
Among the results I see blue and red regions in Freeview. Am I correct assuming 
that blue regions are the ones where cortical thickness is reduced in patients 
relative to HC (correcting for disease duration)?
I just wanted to ask for a confirmation.

Many thanks,

Pilar
> 
> Message: 2
> Date: Mon, 2 Dec 2019 16:06:54 +
> From: "Greve, Douglas N.,Ph.D." 
> Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one
>   variable
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID: 
> Content-Type: text/plain; charset="windows-1252"
> 
> It sounds like it would be a one-group, two-variable situation, like this
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V
> Is that not correct?
> 
> 
> On 11/28/2019 5:24 AM, Ferraro, Pilar wrote:
> 
>External Email - Use Caution
> 
> Hi,
> 
> I apologize if I did not explain my issue properly.
> I'm interested in looking at age-related thickness reductions in 1 group 
> (patients), but I'd like to also account for the effect of disease duration.
> We can say that in my case disease duration is the nuisance factor.
> Briefly, I have the same issue reported in here 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html), 
> but with only one group.
> How would you recommend to proceed?
> 
> Many  thanks,
> 
> Pilar
> 
> 
> Message: 2
> Date: Wed, 27 Nov 2019 16:56:20 +
> From: "Greve, Douglas N.,Ph.D." 
> 
> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue
>36
> To: "freesurfer@nmr.mgh.harvard.edu" 
> 
> Message-ID: 
> 
> Content-Type: text/plain; charset="utf-8"
> 
> what is the difference between and independent variable and a covariate?
> 
> On 11/27/2019 6:57 AM, Ferraro, Pilar wrote:
>> External Email - Use Caution
>> 
>> Yes, I did.
>> But in this case I have two factors, not only one. In particular, I have an 
>> independent variable X and a covariate I?d like to include in the model.
>> How would you suggest to proceed?
>> 
>> 
>> Thanks,
>> 
>> Pilar
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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> An HTML attachment was scrubbed...
> URL: 
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/cec9033a/attachment-0001.html
>  
> 
> --
> 
> Message: 3
> Date: Mon, 2 Dec 2019 16:08:08 +
> From: "Greve, Douglas N.,Ph.D." 
> Subject: Re: [Freesurfer] fsfast no run directories
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID: <41b08316-678f-ff4e-aa09-86993b0c7...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
> 
> In the bold directory, it looks like you have one run directory called "1". 
> Change this to "001"
> 
> On 11/29/2019 1:48 AM, Renew Andrade wrote:
> 
>External Email - Use Caution
> 
> Dear FreeSurfer experts:
> I have some issues with "preproc-sess" because I cannot seem to get the setup 
> of the directory structure or files to connect different things(the T1 
> subjects with functional bold or rest files). I have this output.
> 
> 
> root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess 
> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
> --
> preproc-sess logfile is log/preproc-sess.sess1.log
> --
> $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
> root
> setenv FREESURFER_HOME /usr/local/freesurfer
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
> Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 
> 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> /home/andraderenew/Downloads/barrios/project
> /usr/local/freesurfer/fsfast/bin/preproc-sess
> -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
> vie nov 29 07:33:28 CET 2019
> instem   f
> mc   1 f fmcpr
> stc  1fmcpr fmcpr.up
> sm   0
> mask 1   brain
> sess1 Template -
> mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project -fsd 
> bold -update
> 
> Session: /home/andraderenew/Downloads/barrios/project/sess1 
> vie nov 29 07:33:28 CET 2019
> ERROR: no run directories found
> 
> 
> 
> my working directory is
> 
>