Re: [Freesurfer] Hippocampal subfields

[_andreia_]

Hi,

Will it be possible to incorporate the new hippo subfields atlas and stats
generation in the 5.3 recon-all without having to process everything from
scratch with 6.0?

Thank you,
Andreia

 Citando Eugenio Iglesias :


Dear Erik / Angela,
the atlas in 5.3 was derived from manual annotations on in vivo images
that relied largely on geometric rules, and led to volume estimates that
did not agree well with histology studies. The new atlas is based on ex
vivo MRI and agrees better with histology. Moreover, it also has the
option to input higher resolution images (in addition to the standard 1
mm T1), which yield a much better fit of the internal structure of the
hippocampus.
That said, IMHO you can still publish papers with the old tool; you just
need to be careful with the interpretation of the results, and discuss
these issues in the submission.
Kind regards,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com[1]
www.bcbl.eu[2]

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer[3]

- Original Message -
From: "Erik O'Hanlon" 
To: "Freesurfer support list" 
Sent: Tuesday, December 2, 2014 11:20:35 PM
Subject: Re: [Freesurfer] Hippocampal subfields

Hi FS experts,

Yes, I'm in the same position and have been trying to do it
longitudinally. Does this mean that the outputs are completely
unreliable and unstable? Should it be parked until the release of
version 6?

Thanks

Erik

Erik O'Hanlon
Postdoctoral researcher

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie  W: www.rcsi.ie[4]

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
angela.fav...@unipd.it [angela.fav...@unipd.it]
Sent: 02 December 2014 21:53
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields

Hi all, this is really a terrible news!
I am writing a paper using hippocampal subfields (ver 5.3). What is the
problem with segmentation using this tool? Is it reliable at least on

some

of the subfield?
When will Freesurfer 6 be released?

Thank you

Angela


Hi Georg,
we will be releasing with FreeSurfer 6 a new hippocampal subfield module
based on a more accurate atlas built upon ex vivo MRI scans. However, if
what you are interested in is the whole hippocampal volume, the results
from the new module won't be too different.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com[1]
www.bcbl.eu[2]

Legal disclaimer/Aviso legal/Lege-oharra:

www.bcbl.eu/legal-disclaimer[3]


- Original Message -
From: "Georg Ferdinand Anto von Polier" 
To: "Freesurfer support list" 
Sent: Tuesday, December 2, 2014 2:46:40 PM
Subject: [Freesurfer] Hippocampal subfields

Dear FreeSurfers,

I am just finishing a paper using output from Hippocampal subfields and
recognized that the current version has been deprecated. I am interested
in volumes of the whole hippocampus.

Are these volumes still valid and can you estimate when a new version
will
be available? Can you provide maybe a brief comment on the decision to
deprecate the current version?

Best regards,

Georg

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[Freesurfer] Brodmann area thickness, surface area and volume

[_andreia_]

Hi all,

I'm using FS 5.0 and some time ago I was told by Bruce that I had to  
threshold the BA in order to have an approximate area when overlaying  
in the inflated surface. To get surface area values I also need to use  
the label_area and put a threshold
having the possibility to choose the surface that I want, either white  
or pial.

But I can also get the BA stats in a table for all subjects and areas  
using either mris_anatomical_stats (on each label) or usinga script by  
Jamaan to get the table (since I already have the ?.BA.stats files),  
right?

My question is, which is the better/correct way to get the thickness  
and surface area values of the BA to export for statistical analysis  
since there are the thresolds issue.

I want to study mainly cortical thickness and surface area but also  
look also at the volume (which is surface-based, thus  
thickness*surface are will not be = volume since they are an average  
from each label, right?).

I' not sure of which approach to follow now... Does it depend on the  
measure I'll be using?

Thank you!

Andreia


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Re: [Freesurfer] Brodmann area thickness, surface area and volume

[_andreia_]

Hi Bruce,

Thank you for the quick response!

In the meanwhile, does that also apply to cortical thickness and volume?

Thank you!

Andreia

Quoting Bruce Fischl :

> Hi Andreia
>
> the issue is that the BA labels contain every point that has any non-zero
> probability (no matter how small!) of being in that label. So the total
> label area is almost certainly always bigger than the actual BA. Anastasia
> has some scripts for automatically computing the correct threshold, and I
> believe she and Nick integrated them into 5.2 so that the stats are
> computed both thresholded and unthresholded, hopefully they can comment.
> Bruce
>
>
>
> On Fri, 22 Mar 2013, _andre...@sapo.pt
> wrote:
>
>> Hi all,
>>
>> I'm using FS 5.0 and some time ago I was told by Bruce that I had to
>> threshold the BA in order to have an approximate area when overlaying
>> in the inflated surface. To get surface area values I also need to use
>> the label_area and put a threshold
>> having the possibility to choose the surface that I want, either white
>> or pial.
>>
>> But I can also get the BA stats in a table for all subjects and areas
>> using either mris_anatomical_stats (on each label) or usinga script by
>> Jamaan to get the table (since I already have the ?.BA.stats files),
>> right?
>>
>> My question is, which is the better/correct way to get the thickness
>> and surface area values of the BA to export for statistical analysis
>> since there are the thresolds issue.
>>
>> I want to study mainly cortical thickness and surface area but also
>> look also at the volume (which is surface-based, thus
>> thickness*surface are will not be = volume since they are an average
>> from each label, right?).
>>
>> I' not sure of which approach to follow now... Does it depend on the
>> measure I'll be using?
>>
>> Thank you!
>>
>> Andreia
>>
>>
>> ___
>> Freesurfer mailing list
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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
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[Freesurfer] Talairach manual correction

[_andreia_]

Hello!

After completing the talairach correction in tkregister2 (saving the  
changes with the SAVEREG button), I am running recon-all -all -s subj.  
But now I'm wondering if by doing it this way the changes will be  
incorporated or the process will start from the beggining leaving  
everything as before the manual corrections...

Is there any flag needed?

Thank you,
Andreia



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Re: [Freesurfer] Brodmann area thickness, surface area and volume

[_andreia_]

Ok, that was my guess... I am running against a deadline, any news on  
automatically computing the correct threshold script? Will I be able  
to use it in 5.0?

Thanks you!

Andreia


Quoting Bruce Fischl :

> yes. Surface area will be the affected much more than thickness (and  
> volume of course scales with area)
>
> On Fri, 22 Mar 2013, _andre...@sapo.pt wrote:
>
>> Hi Bruce,
>>
>> Thank you for the quick response!
>>
>> In the meanwhile, does that also apply to cortical thickness and volume?
>>
>> Thank you!
>>
>> Andreia
>>
>> Quoting Bruce Fischl :
>>
>>> Hi Andreia
>>>
>>> the issue is that the BA labels contain every point that has any non-zero
>>> probability (no matter how small!) of being in that label. So the total
>>> label area is almost certainly always bigger than the actual BA. Anastasia
>>> has some scripts for automatically computing the correct threshold, and I
>>> believe she and Nick integrated them into 5.2 so that the stats are
>>> computed both thresholded and unthresholded, hopefully they can comment.
>>> Bruce
>>>
>>>
>>>
>>> On Fri, 22 Mar 2013, _andre...@sapo.pt
>>> wrote:
>>>
 Hi all,

 I'm using FS 5.0 and some time ago I was told by Bruce that I had to
 threshold the BA in order to have an approximate area when overlaying
 in the inflated surface. To get surface area values I also need to use
 the label_area and put a threshold
 having the possibility to choose the surface that I want, either white
 or pial.

 But I can also get the BA stats in a table for all subjects and areas
 using either mris_anatomical_stats (on each label) or usinga script by
 Jamaan to get the table (since I already have the ?.BA.stats files),
 right?

 My question is, which is the better/correct way to get the thickness
 and surface area values of the BA to export for statistical analysis
 since there are the thresolds issue.

 I want to study mainly cortical thickness and surface area but also
 look also at the volume (which is surface-based, thus
 thickness*surface are will not be = volume since they are an average
 from each label, right?).

 I' not sure of which approach to follow now... Does it depend on the
 measure I'll be using?

 Thank you!

 Andreia


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 Freesurfer@nmr.mgh.harvard.edu
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>>> ___
>>> 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] Brodmann area thickness, surface area and volume

[_andreia_]

Hi all,

I want to study Brodmann Areas cortical thickness, surface area and  
volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage  
and run the recon-all BA labels command. Now I run aparcstats2table  
and get a table with the values but they are the same as before  
running the BAxxx.threshold.label.

So, everything is working but the values haven't changed. Am I missing  
something? Do I need to run any other command so to the threshold have  
effect?

Andreia


Quoting Anastasia Yendiki :

> Sounds like centos4 is probably the safest bet for you, although you  
> should ask the list this question.
>
> Sorry, I don't know what values you want to get in a table.
>
> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ah ok! Anyway, I'm thinking of working with 5.2, should I download  
>> the version for centOS 4 then?
>>
>> After running the new BAxxx.thresh.label files how can I get the  
>> values in a table?
>>
>>
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> It doesn't matter. You just need to use those .label files from  
>>> the fsaverage directory in the 5.2 distritbution. You don't need  
>>> to run any of the executables from the 5.2 distribution.
>>>
>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>>>
 I'm using Centos5, which file should I download? The one for  
 CentOS 6 or > 4?
 > > Quoting Anastasia Yendiki :
 > > You'll need to go to the section of recon-all.log under the  
 heading "BA > > labels". You'll need to rerun the commands in  
 that section, but instead > > of using the BAxxx.label files, us  
 the BAxxx.thresh.label files, which > > you'll find in the  
 fsaverage subject dir in the 5.2 distribution.
 > > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 > > > > Hello Anastasia,
 > > >  How should I proceed to get the different BAs measures  
 output with > > > >  FS > 5.0?
 > > >  Thank you very much!
 > > >  Andreia
 > > > >  Quoting Anastasia Yendiki :
 > > > >  The thresholded labels are in the 5.2 version of  
 fsaverage > > > > >  under:
 > > >  $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label
 > > > > >  On Sat, 23 Mar 2013, Bruce Fischl wrote:
 > > > > > >  Anastasia?
 > > > >  On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 > > > > > >   Ok, that was my guess... I am running against a  
 deadline, > > > > > > >   any > > > > >  news on
 > > > > >   automatically computing the correct threshold script?  
 Will I > > > > > >   be > > > >  able to
 > > > > >   use it in 5.0?
 > > > > > > >   Thanks you!
 > > > > > > >   Andreia
 > > > > > > > > >   Quoting Bruce Fischl :
 > > > > > > > >yes. Surface area will be the affected much  
 more than > > > > > > > > >> > > > > > >   thickness (and > >  
 >  >  volume of > > > > > > > > >course scales with area)
 > > > > > > > On Fri, 22 Mar 2013, _andre...@sapo.pt wrote:
 > > > > > > > > Hi Bruce,
 > > > > > > > > > Thank you for the quick response!
 > > > > > > > > > In the meanwhile, does that also apply to  
 cortical > > > > > > > > > > > > > > > > > >thickness > >  
 > > > >   and > > > > > > > > > > > > volume?
 > > > > > > > > > Thank you!
 > > > > > > > > > Andreia
 > > > > > > > > > Quoting Bruce Fischl :
 > > > > > > > > > > Hi Andreia
 > > > > > > > > > > > the issue is that the BA labels contain  
 every > > > > > > > > > > > > point > > > > > > > > > > 
 that > > > > > > > > > > > > > > > > > > > >   has any > > >   
 non-zero
 > > > > > > > > probability (no matter how small!) of being  
 in that > > > > > > > > > label. > > > > > > >So > > > >  
 >   the > > > > > > > > > > > > total
 > > > > > > > > label area is almost certainly always bigger  
 than the > > > > > > > > > > > > > > > >actual > > > > >   
  BA. > > > > > > > > > > > > Anastasia
 > > > > > > > > has some scripts for automatically computing  
 the > > > > > > > > > correct > > > > > > > >> > > >
 threshold, > > > > > > > > > > > > and I
 > > > > > > > > believe she and Nick integrated them into 5.2  
 so that > > > > > > > > > the > > > > > > >stats > > > >  
 >   are
 > > > > > > > > computed both thresholded and unthresholded,  
 > > > > > > > > > hopefully > > > > > > >they can > > > >  
 >   > > > > > > > > > > > > comment.
 > > > > > > > > Bruce
 > > > > > > > > > > > > > > > > > On Fri, 22 Mar 2013, > > >  
 > > > > > > > > > > > > > > > _andre...@sapo.pt
 > > > > > > > > wrote:
 > > > > > > > > > > > > Hi all,
 > > > > > > > > > > > > > I'm using FS 5.0 and some time ago  
 I was > > > > > > > > > > > > > > told by > > > > > > > > > >  
 > >> > > > > > > > > > > > > > 

[Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

Hello list!

Any suggestions on what I may be doing wrong?

Thanks!
Andreia



- Mensagem encaminhada de _andre...@sapo.pt -
Data: Sun, 24 Mar 2013 19:11:13 +
  De: _andre...@sapo.pt
Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume
Para: Anastasia Yendiki , freesurfer  

  Cc: Bruce Fischl 

Hi all,

I want to study Brodmann Areas cortical thickness, surface area and  
volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage  
and run the recon-all BA labels command. Now I run aparcstats2table  
and get a table with the values but they are the same as before  
running the BAxxx.threshold.label.

So, everything is working but the values haven't changed. Am I missing  
something? Do I need to run any other command so to the threshold have  
effect?

Andreia


Quoting Anastasia Yendiki :

> Sounds like centos4 is probably the safest bet for you, although you  
> should ask the list this question.
>
> Sorry, I don't know what values you want to get in a table.
>
> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ah ok! Anyway, I'm thinking of working with 5.2, should I download  
>> the version for centOS 4 then?
>>
>> After running the new BAxxx.thresh.label files how can I get the  
>> values in a table?
>>
>>
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> It doesn't matter. You just need to use those .label files from  
>>> the fsaverage directory in the 5.2 distritbution. You don't need  
>>> to run any of the executables from the 5.2 distribution.
>>>
>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>>>
 I'm using Centos5, which file should I download? The one for  
 CentOS 6 or > 4?
> > Quoting Anastasia Yendiki :
> > You'll need to go to the section of recon-all.log under the  
> heading "BA > > labels". You'll need to rerun the commands in  
> that section, but instead > > of using the BAxxx.label files, us  
> the BAxxx.thresh.label files, which > > you'll find in the  
> fsaverage subject dir in the 5.2 distribution.
> > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
> > > > Hello Anastasia,
> > >  How should I proceed to get the different BAs measures  
> output with > > > >  FS > 5.0?
> > >  Thank you very much!
> > >  Andreia
> > > >  Quoting Anastasia Yendiki :
> > > >  The thresholded labels are in the 5.2 version of  
> fsaverage > > > > >  under:
> > >  $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label
> > > > >  On Sat, 23 Mar 2013, Bruce Fischl wrote:
> > > > > >  Anastasia?
> > > >  On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
> > > > > >   Ok, that was my guess... I am running against a  
> deadline, > > > > > > >   any > > > > >  news on
> > > > >   automatically computing the correct threshold script?  
> Will I > > > > > >   be > > > >  able to
> > > > >   use it in 5.0?
> > > > > > >   Thanks you!
> > > > > > >   Andreia
> > > > > > > > >   Quoting Bruce Fischl :
> > > > > > > >yes. Surface area will be the affected much  
> more than > > > > > > > > >> > > > > > >   thickness (and >  
> > >  >  volume of > > > > > > > > >course scales with area)
> > > > > > > On Fri, 22 Mar 2013, _andre...@sapo.pt wrote:
> > > > > > > > Hi Bruce,
> > > > > > > > > Thank you for the quick response!
> > > > > > > > > In the meanwhile, does that also apply to  
> cortical > > > > > > > > > > > > > > > > > >thickness >  
> > > > > >   and > > > > > > > > > > > > volume?
> > > > > > > > > Thank you!
> > > > > > > > > Andreia
> > > > > > > > > Quoting Bruce Fischl :
> > > > > > > > > > Hi Andreia
> > > > > > > > > > > the issue is that the BA labels contain  
> every > > > > > > > > > > > > point > > > > > > > > > > 
> that > > > > > > > > > > > > > > > > > > > >   has any > > >  
>  non-zero
> > > > > > > > probability (no matter how small!) of being in  
> that > > > > > > > > > label. > > > > > > >So > > > > >   
>  the > > > > > > > > > > > > total
> > > > > > > > label area is almost certainly always bigger  
> than the > > > > > > > > > > > > > > > >actual > > > > >  
>   BA. > > > > > > > > > > > > Anastasia
> > > > > > > > has some scripts for automatically computing  
> the > > > > > > > > > correct > > > > > > > >> > > >
> threshold, > > > > > > > > > > > > and I
> > > > > > > > believe she and Nick integrated them into 5.2  
> so that > > > > > > > > > the > > > > > > >stats > > > >  
> >   are
> > > > > > > > computed both thresholded and unthresholded, >  
> > > > > > > > > hopefully > > > > > > >they can > > > >  
> >   > > > > > > > > > > > > comment.
> > > > > > > > Bruce
> > > > > > > > > > > > > > > > > On Fri, 

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

Hi Anastasia!

 The command in the recon-all.log is this one:

 mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject
SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface

 And I tried substituing BAxxx.label by BAxxx.thresh.label like this:

 mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/_lh.BA1.threshold.label_--trgsubject
SUSANAFERREIRA --trglabel ._/lh.BA1.thresolh.label_ --hemi lh --regmethod
surface

 gave an error :

 SUBJECTS_DIR    /home/user/visao/Freesurfer/
 FREESURFER_HOME /usr/local/freesurfer
 Loading source label.
 No such file or directory
 mri_label2label: could not open label file
/home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 Illegal seek
 ERROR reading
/home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label

 Thus, I substitued only in the second BAxxx.label and it worked. I thought
that was it, but then the values were the same. I'm sorry, I'm not sure
what is missing.

 Thank you!

 Andreia

 Quoting Anastasia Yendiki :

 > Hi Andreia - What you're rerunning is using BAxxx.label instead of
 > BAxxx.thresh.label. So of course the results will be the same as before
 > you copied over the BAxxx.thresh.label files, b/c these new files aren't
 > being used in 5.0.
 >
 > You'll need to find the "BA labels" section in recon-all.log and rerun
 > those commands yourself, changing every BAxxx.label to
BAxxx.thresh.label.
 >
 > Hope this helps,
 > a.y
 >
 > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
 >
 >> Hello list!
 >>
 >> Any suggestions on what I may be doing wrong?
 >>
 >> Thanks!
 >> Andreia
 >>
 >>
 >>
 >> - Mensagem encaminhada de _andre...@sapo.pt -
 >>    Data: Sun, 24 Mar 2013 19:11:13 +
 >>      De: _andre...@sapo.pt
 >> Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and
volume
 >>    Para: Anastasia Yendiki , freesurfer
 >> 
 >>      Cc: Bruce Fischl 
 >>
 >> Hi all,
 >>
 >> I want to study Brodmann Areas cortical thickness, surface area and
 >> volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage
 >> and run the recon-all BA labels command. Now I run aparcstats2table
 >> and get a table with the values but they are the same as before
 >> running the BAxxx.threshold.label.
 >>
 >> So, everything is working but the values haven't changed. Am I missing
 >> something? Do I need to run any other command so to the threshold have
 >> effect?
 >>
 >> Andreia
 >>
 >>
 >> Quoting Anastasia Yendiki :
 >>
 >>> Sounds like centos4 is probably the safest bet for you, although you
 >>> should ask the list this question.
 >>>
 >>> Sorry, I don't know what values you want to get in a table.
 >>>
 >>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 >>>
  Ah ok! Anyway, I'm thinking of working with 5.2, should I download
  the version for centOS 4 then?
 
  After running the new BAxxx.thresh.label files how can I get the
  values in a table?
 
 
 
 
  Quoting Anastasia Yendiki :
 
 > It doesn't matter. You just need to use those .label files from
 > the fsaverage directory in the 5.2 distritbution. You don't need
 > to run any of the executables from the 5.2 distribution.
 >
 > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 >
 >> I'm using Centos5, which file should I download? The one for
 >> CentOS 6 or > 4?
  Quoting Anastasia Yendiki :
  You'll need to go to the section of recon-all.log under the
 >>> heading "BA > > labels". You'll need to rerun the commands in
 >>> that section, but instead > > of using the BAxxx.label files, us
 >>> the BAxxx.thresh.label files, which > > you'll find in the
 >>> fsaverage subject dir in the 5.2 distribution.
 > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 >> Hello Anastasia,
 >  How should I proceed to get the different BAs measures
 >>> output with > > > >  FS > 5.0?
 >  Thank you very much!
 >  Andreia
 >>  Quoting Anastasia Yendiki :
 >>  The thresholded labels are in the 5.2 version of
 >>> fsaverage > > > > >  under:
 >  $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label
 >>>  On Sat, 23 Mar 2013, Bruce Fischl wrote:
   Anastasia?
 >>  On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
    Ok, that was my guess... I am running against a
 >>> deadline, > > > > > > >   any > > > > >  news on
 >>>   automatically computing the correct threshold script?
 >>> Will I > > > > > >   be > > > >  able to
 >>>   use it in 5.0?
 >   Thanks you!
 >   Andreia
 >>>   Quoting Bruce Fischl :
 >>    yes. Surface area will be the affected much
 >>> more than > > > > > > > > >    > > > > > > >   thickness (and >
 > >  volume of > > > > > > > > >    course scales w

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

Ah ok! Sorry... In both places?


Quoting Anastasia Yendiki :

> It's .thresh.label, not .threshold.label.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>>
>> Hi Anastasia!
>>
>> The command in the recon-all.log is this one:
>>
>> mri_label2label --srcsubject fsaverage --srclabel  
>> /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
>> --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh  
>> --regmethod surface
>>
>> And I tried substituing BAxxx.label by BAxxx.thresh.label like this:
>>
>> mri_label2label --srcsubject fsaverage --srclabel
>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label  
>> --trgsubject SUSANAFERREIRA --trglabel
>> ./lh.BA1.thresolh.label --hemi lh --regmethod surface
>>
>> gave an error :
>>
>> SUBJECTS_DIR    /home/user/visao/Freesurfer/
>> FREESURFER_HOME /usr/local/freesurfer
>> Loading source label.
>> No such file or directory
>> mri_label2label: could not open label file  
>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
>> Illegal seek
>> ERROR reading  
>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
>>
>> Thus, I substitued only in the second BAxxx.label and it worked. I  
>> thought that was it, but then the values
>> were the same. I'm sorry, I'm not sure what is missing.
>>
>> Thank you!
>>
>> Andreia
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> Hi Andreia - What you're rerunning is using BAxxx.label instead of
>>> BAxxx.thresh.label. So of course the results will be the same as before
>>> you copied over the BAxxx.thresh.label files, b/c these new files aren't
>>> being used in 5.0.
>>>
>>> You'll need to find the "BA labels" section in recon-all.log and rerun
>>> those commands yourself, changing every BAxxx.label to BAxxx.thresh.label.
>>>
>>> Hope this helps,
>>> a.y
>>>
>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>>>
 Hello list!

 Any suggestions on what I may be doing wrong?

 Thanks!
 Andreia



 - Mensagem encaminhada de _andre...@sapo.pt -
     Data: Sun, 24 Mar 2013 19:11:13 +
       De: _andre...@sapo.pt
 Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume
     Para: Anastasia Yendiki , freesurfer
 
       Cc: Bruce Fischl 

 Hi all,

 I want to study Brodmann Areas cortical thickness, surface area and
 volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage
 and run the recon-all BA labels command. Now I run aparcstats2table
 and get a table with the values but they are the same as before
 running the BAxxx.threshold.label.

 So, everything is working but the values haven't changed. Am I missing
 something? Do I need to run any other command so to the threshold have
 effect?

 Andreia


 Quoting Anastasia Yendiki :

> Sounds like centos4 is probably the safest bet for you, although you
> should ask the list this question.
>
> Sorry, I don't know what values you want to get in a table.
>
> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ah ok! Anyway, I'm thinking of working with 5.2, should I download
>> the version for centOS 4 then?
>>
>> After running the new BAxxx.thresh.label files how can I get the
>> values in a table?
>>
>>
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> It doesn't matter. You just need to use those .label files from
>>> the fsaverage directory in the 5.2 distritbution. You don't need
>>> to run any of the executables from the 5.2 distribution.
>>>
>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>>>
 I'm using Centos5, which file should I download? The one for
 CentOS 6 or > 4?
>> Quoting Anastasia Yendiki :
>> You'll need to go to the section of recon-all.log under the
> heading "BA > > labels". You'll need to rerun the commands in
> that section, but instead > > of using the BAxxx.label files, us
> the BAxxx.thresh.label files, which > > you'll find in the
> fsaverage subject dir in the 5.2 distribution.
>>> On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 Hello Anastasia,
>>>   How should I proceed to get the different BAs measures
> output with > > > >  FS > 5.0?
>>>   Thank you very much!
>>>   Andreia
   Quoting Anastasia Yendiki :
   The thresholded labels are in the 5.2 version of
> fsaverage > > > > >  under:
>>>   $FREESURFER_HOME/subjects/fsaverage/label/*.thresh.label
>   On Sat, 23 Mar 2013, Bruce Fischl wrote:
>>   Anastasia?
   On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
>>    Ok, that was my guess... I am running against a
> deadline, > > > > > > >   any > > > > >  news on
>    automatically computing the corr

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

Ok. So the first is the input and the second is the output, correct?  
So I'll have a different file for each out put? Is it possible to have  
a table with the different measures after the threshold?

Thank you very much and I apologize for the naive questions...

Andreia


Quoting Anastasia Yendiki :

> What you call the output label is up to you. What you call the input  
> label is more important - it has to be a file that actually exists.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ah ok! Sorry... In both places?
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> It's .thresh.label, not .threshold.label.
>>>
>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>>>
 > Hi Anastasia!
 > The command in the recon-all.log is this one:
 > mri_label2label --srcsubject fsaverage --srclabel >  
 /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
 --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh >  
 --regmethod surface
 > And I tried substituing BAxxx.label by BAxxx.thresh.label like this:
 > mri_label2label --srcsubject fsaverage --srclabel
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >  
 --trgsubject SUSANAFERREIRA --trglabel
 ./lh.BA1.thresolh.label --hemi lh --regmethod surface
 > gave an error :
 > SUBJECTS_DIR    /home/user/visao/Freesurfer/
 FREESURFER_HOME /usr/local/freesurfer
 Loading source label.
 No such file or directory
 mri_label2label: could not open label file >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 Illegal seek
 ERROR reading >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 > Thus, I substitued only in the second BAxxx.label and it  
 worked. I > thought that was it, but then the values
 were the same. I'm sorry, I'm not sure what is missing.
 > Thank you!
 > Andreia
 > > > > > > > > > > Quoting Anastasia Yendiki  
 :
 > > Hi Andreia - What you're rerunning is using BAxxx.label instead of
 > BAxxx.thresh.label. So of course the results will be the same as before
 > you copied over the BAxxx.thresh.label files, b/c these new  
 files > > aren't
 > being used in 5.0.
 > > > You'll need to find the "BA labels" section in  
 recon-all.log and rerun
 > those commands yourself, changing every BAxxx.label to > >  
 BAxxx.thresh.label.
 > > > Hope this helps,
 > a.y
 > > > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
 > > > > Hello list!
 > > > > > Any suggestions on what I may be doing wrong?
 > > > > > Thanks!
 > > Andreia
 > > > > > > > > > > > - Mensagem encaminhada de  
 _andre...@sapo.pt -
 > >     Data: Sun, 24 Mar 2013 19:11:13 +
 > >       De: _andre...@sapo.pt
 > > Assunto: Re: [Freesurfer] Brodmann area thickness, surface  
 area and > > > volume
 > >     Para: Anastasia Yendiki , >  
 > > freesurfer
 > > 
 > >       Cc: Bruce Fischl 
 > > > > > Hi all,
 > > > > > I want to study Brodmann Areas cortical thickness,  
 surface area and
 > > volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage
 > > and run the recon-all BA labels command. Now I run aparcstats2table
 > > and get a table with the values but they are the same as before
 > > running the BAxxx.threshold.label.
 > > > > > So, everything is working but the values haven't  
 changed. Am I > > > missing
 > > something? Do I need to run any other command so to the  
 threshold > > > have
 > > effect?
 > > > > > Andreia
 > > > > > > > > Quoting Anastasia Yendiki :
 > > > > > > Sounds like centos4 is probably the safest bet for  
 you, although > > > > you
 > > > should ask the list this question.
 > > > > > > > Sorry, I don't know what values you want to get in a table.
 > > > > > > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 > > > > > > > > Ah ok! Anyway, I'm thinking of working with 5.2,  
 should I > > > > > download
 > > > > the version for centOS 4 then?
 > > > > > > > > > After running the new BAxxx.thresh.label files  
 how can I get the
 > > > > values in a table?
 > > > > > > > > > > > > > > > > > > > > > > > > Quoting Anastasia  
 Yendiki :
 > > > > > > > > > > It doesn't matter. You just need to use those  
 .label files from
 > > > > > the fsaverage directory in the 5.2 distritbution. You  
 don't > > > > > > need
 > > > > > to run any of the executables from the 5.2 distribution.
 > > > > > > > > > > > On Sat, 23 Mar 2013, _andre...@sapo.pt wrote:
 > > > > > > > > > > > > I'm using Centos5, which file should I  
 download? The one for
 > > > > > > CentOS 6 or > 4?
 > > > > > > > > Quoting Anastasia Yendiki :
 > > > > > > > > You'll need to go to the section of recon-all.log  
 under > > > > > > > > > the
 > > > > > > > h

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

Hi,

I run the command for each BA labels of the right hemisphere and then run:

[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f  
../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT  
rh white

Which resulted in:

INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz...
reading input surface  
/home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
reading input pial surface  
/home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial...
reading input white surface  
/home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
could not read annot file ./rh.BA.annot
No such file or directory
mris_anatomical_stats:  could  not read annotation file ./rh.BA.annot
No such file or directory

What is wrong? Is there a way to run everything that is needed to get  
the BA stats at once using the BAxxx.thresh.label?

Thank you,
Andreia

Quoting Anastasia Yendiki :

> If you replace *every* occurence of BAxxx.label with  
> BAxxx.thresh.label, this will keep things simple and you won't have  
> to worry about which one is input and which one is output.
>
> Run *all* the commands from the "BA labels" section, all the way to  
> the end of that section, this will get you to the stats.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ok. So the first is the input and the second is the output,  
>> correct? So I'll have a different file for each out put? Is it  
>> possible to have a table with the different measures after the  
>> threshold?
>>
>> Thank you very much and I apologize for the naive questions...
>>
>> Andreia
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> What you call the output label is up to you. What you call the  
>>> input label is more important - it has to be a file that actually  
>>> exists.
>>>
>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>>>
 Ah ok! Sorry... In both places?
 > > Quoting Anastasia Yendiki :
 > > It's .thresh.label, not .threshold.label.
 > > > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
 > > > > >  Hi Anastasia!
 > > >  The command in the recon-all.log is this one:
 > > >  mri_label2label --srcsubject fsaverage --srclabel > > > >  
 >  /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
 > > --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi  
 rh > > > > --regmethod surface
 > > >  And I tried substituing BAxxx.label by BAxxx.thresh.label  
 like > > > >  this:
 > > >  mri_label2label --srcsubject fsaverage --srclabel
 > >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label > > >  
 > --trgsubject SUSANAFERREIRA --trglabel
 > > ./lh.BA1.thresolh.label --hemi lh --regmethod surface
 > > >  gave an error :
 > > >  SUBJECTS_DIR    /home/user/visao/Freesurfer/
 > > FREESURFER_HOME /usr/local/freesurfer
 > > Loading source label.
 > > No such file or directory
 > > mri_label2label: could not open label file > > > >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 > > Illegal seek
 > > ERROR reading > > > >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 > > >  Thus, I substitued only in the second BAxxx.label and it  
 worked. I > > > >  > thought that was it, but then the values
 > > were the same. I'm sorry, I'm not sure what is missing.
 > > >  Thank you!
 > > >  Andreia
 > > > > > > > > > > > >  Quoting Anastasia Yendiki > > > > > > >  
 > > > > > >  :
 > > > >  Hi Andreia - What you're rerunning is using BAxxx.label  
 instead > > > > >  of
 > > >  BAxxx.thresh.label. So of course the results will be the  
 same as > > > >  before
 > > >  you copied over the BAxxx.thresh.label files, b/c these  
 new files > > > >  > > aren't
 > > >  being used in 5.0.
 > > > > >  You'll need to find the "BA labels" section in  
 recon-all.log > > > > > >  and rerun
 > > >  those commands yourself, changing every BAxxx.label to > >  
 > > > >  BAxxx.thresh.label.
 > > > > >  Hope this helps,
 > > >  a.y
 > > > > >  On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
 > > > > > >  Hello list!
 > > > > > > >  Any suggestions on what I may be doing wrong?
 > > > > > > >  Thanks!
 > > > >  Andreia
 > > > > > > > > > > > > >  - Mensagem encaminhada de > > > >  
 > > > > > > > > > >  _andre...@sapo.pt -
 > > > >      Data: Sun, 24 Mar 2013 19:11:13 +
 > > > >        De: _andre...@sapo.pt
 > > > >  Assunto: Re: [Freesurfer] Brodmann area thickness,  
 surface area > > > > >  and > > > volume
 > > > >      Para: Anastasia Yendiki  
 , > > > > > > >  > freesurfer
 > > > >  
 > > > >        Cc: Bruce Fischl 
 > > > > > > >  Hi all,
 > > > > > > >  I want to study Brodmann Areas cortical thickness,  
 surface > >

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

Nevermind the last email... If I change the output (wich is the second  
place where BAxx.label appears, right?) file name and give the subjs  
id this won't be a problem... Anyway, what are these files for? Will I  
need to use them somehow?

Thanks
Andreia


Quoting _andre...@sapo.pt:

> Addicionaly, this approach is creating an individual file for each  
> BAxxx.thresh.label (see atchment) and I think that if I run these  
> commands for another subject these outputs will be replaced since  
> the name of the files has no info relating to the subject who it  
> belongs.
>
> I'm kind of lost here...
>
>
>
>
>
> Quoting _andre...@sapo.pt:
>
>> Hi,
>>
>> I run the command for each BA labels of the right hemisphere and then run:
>>
>> [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f  
>> ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab  
>> SUBJECT rh white
>>
>> Which resulted in:
>>
>> INFO: assuming MGZ format for volumes.
>> computing statistics for each annotation in ./rh.BA.annot.
>> reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz...
>> reading input surface  
>> /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
>> reading input pial surface  
>> /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial...
>> reading input white surface  
>> /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
>> could not read annot file ./rh.BA.annot
>> No such file or directory
>> mris_anatomical_stats:  could  not read annotation file ./rh.BA.annot
>> No such file or directory
>>
>> What is wrong? Is there a way to run everything that is needed to  
>> get the BA stats at once using the BAxxx.thresh.label?
>>
>> Thank you,
>> Andreia
>>
>> Quoting Anastasia Yendiki :
>>
>>> If you replace *every* occurence of BAxxx.label with  
>>> BAxxx.thresh.label, this will keep things simple and you won't  
>>> have to worry about which one is input and which one is output.
>>>
>>> Run *all* the commands from the "BA labels" section, all the way  
>>> to the end of that section, this will get you to the stats.
>>>
>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>>>
 Ok. So the first is the input and the second is the output,  
 correct? So I'll have a different file for each out put? Is it  
 possible to have a table with the different measures after the  
 threshold?

 Thank you very much and I apologize for the naive questions...

 Andreia


 Quoting Anastasia Yendiki :

> What you call the output label is up to you. What you call the  
> input label is more important - it has to be a file that  
> actually exists.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ah ok! Sorry... In both places?
 Quoting Anastasia Yendiki :
 It's .thresh.label, not .threshold.label.
 > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
 > > >  Hi Anastasia!
 >  The command in the recon-all.log is this one:
 >  mri_label2label --srcsubject fsaverage --srclabel > > > >  
 >  /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
 --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi  
 rh > > > > --regmethod surface
 >  And I tried substituing BAxxx.label by BAxxx.thresh.label  
 like > > > >  this:
 >  mri_label2label --srcsubject fsaverage --srclabel
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label >  
 > > > --trgsubject SUSANAFERREIRA --trglabel
 ./lh.BA1.thresolh.label --hemi lh --regmethod surface
 >  gave an error :
 >  SUBJECTS_DIR    /home/user/visao/Freesurfer/
 FREESURFER_HOME /usr/local/freesurfer
 Loading source label.
 No such file or directory
 mri_label2label: could not open label file > > > >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 Illegal seek
 ERROR reading > > > >  
 /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label
 >  Thus, I substitued only in the second BAxxx.label and it  
 worked. I > > > >  > thought that was it, but then the values
 were the same. I'm sorry, I'm not sure what is missing.
 >  Thank you!
 >  Andreia
 > > > > > > > > > >  Quoting Anastasia Yendiki > > > > > > >  
 > > > > > >  :
 > >  Hi Andreia - What you're rerunning is using BAxxx.label  
 instead > > > > >  of
 >  BAxxx.thresh.label. So of course the results will be the  
 same as > > > >  before
 >  you copied over the BAxxx.thresh.label files, b/c these  
 new files > > > >  > > aren't
 >  being used in 5.0.
 > > >  You'll need to find the "BA labels" section in  
 recon-all.log > > > > > >  and rerun
 >  those commands yourself, changing every BAxxx.label to > >  
 > > > >  BAxxx.thresh.label.

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

After running the mri_label2label and mris_label2annot a new  
rh.BA.annot file was created  (I had to remove the old one since it  
doesn't overwritte) but when running

[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f  
../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white

It says that can't read annotation file:

INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/user/visao/Freesurfer//SUBJECT/mri/wm.mgz...
reading input surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white...
reading input pial surface  
/home/user/visao/Freesurfer//SUBJECT/surf/rh.pial...
reading input white surface  
/home/user/visao/Freesurfer//SUBJECT/surf/rh.white...
could not read annot file ./rh.BA.annot
No such file or directory
mris_anatomical_stats:  could  not read annotation file ./rh.BA.annot
No such file or directory

I only tried with rh, but I don't think that's a problem is it?

Thank you!

Andreia



Quoting Anastasia Yendiki :

> In the "BA label" section there are:
> - Several mri_label2label commands that map each label from  
> fsaverage space to your indidvidual's space
> - One mris_label2annot command that combines the mapped label into  
> an annotation file.
> - One mris_anatomical_stats command that gets stats for that annotation.
>
> For each of these commands you can run them with --help to see what  
> the inputs and outputs are, or look them up on the wiki.
>
> On Tue, 26 Mar 2013, _andre...@sapo.pt wrote:
>
>> Nevermind the last email... If I change the output (wich is the second
>> place where BAxx.label appears, right?) file name and give the subjs
>> id this won't be a problem... Anyway, what are these files for? Will I
>> need to use them somehow?
>>
>> Thanks
>> Andreia
>>
>>
>> Quoting _andre...@sapo.pt:
>>
>>> Addicionaly, this approach is creating an individual file for each
>>> BAxxx.thresh.label (see atchment) and I think that if I run these
>>> commands for another subject these outputs will be replaced since
>>> the name of the files has no info relating to the subject who it
>>> belongs.
>>>
>>> I'm kind of lost here...
>>>
>>>
>>>
>>>
>>>
>>> Quoting _andre...@sapo.pt:
>>>
 Hi,

 I run the command for each BA labels of the right hemisphere and then run:

 [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
 ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab
 SUBJECT rh white

 Which resulted in:

 INFO: assuming MGZ format for volumes.
 computing statistics for each annotation in ./rh.BA.annot.
 reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz...
 reading input surface
 /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
 reading input pial surface
 /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial...
 reading input white surface
 /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
 could not read annot file ./rh.BA.annot
 No such file or directory
 mris_anatomical_stats:  could  not read annotation file ./rh.BA.annot
 No such file or directory

 What is wrong? Is there a way to run everything that is needed to
 get the BA stats at once using the BAxxx.thresh.label?

 Thank you,
 Andreia

 Quoting Anastasia Yendiki :

> If you replace *every* occurence of BAxxx.label with
> BAxxx.thresh.label, this will keep things simple and you won't
> have to worry about which one is input and which one is output.
>
> Run *all* the commands from the "BA labels" section, all the way
> to the end of that section, this will get you to the stats.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>> Ok. So the first is the input and the second is the output,
>> correct? So I'll have a different file for each out put? Is it
>> possible to have a table with the different measures after the
>> threshold?
>>
>> Thank you very much and I apologize for the naive questions...
>>
>> Andreia
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> What you call the output label is up to you. What you call the
>>> input label is more important - it has to be a file that
>>> actually exists.
>>>
>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>>>
 Ah ok! Sorry... In both places?
>> Quoting Anastasia Yendiki :
>> It's .thresh.label, not .threshold.label.
>>> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
> Hi Anastasia!
>>> The command in the recon-all.log is this one:
>>> mri_label2label --srcsubject fsaverage --srclabel > > > >
>>> /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
>> --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi
>> rh > > > > --regmethod surface
>>> And I tried substituing BAxxx.label by BAxxx.thresh.label
>>>

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

It was automatically created in the same folder of the old one -> label

However, inside this folder there are the old rh.BAxxx.label. The new  
ones (BAxxx.thresh.label) were created inside the Freesurfer folder,  
could it be related to that?




Quoting Anastasia Yendiki :

> What's the location of the new rh.BA.annot that was created by  
> mris_label2annot? You need to pass that same file to  
> mris_anatomical_stats with the -a option.
>
> On Tue, 26 Mar 2013, _andre...@sapo.pt wrote:
>
>> After running the mri_label2label and mris_label2annot a new  
>> rh.BA.annot file was created  (I had to remove the old one since it  
>> doesn't overwritte) but when running
>>
>> [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f  
>> ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh  
>> white
>>
>> It says that can't read annotation file:
>>
>> INFO: assuming MGZ format for volumes.
>> computing statistics for each annotation in ./rh.BA.annot.
>> reading volume /home/user/visao/Freesurfer//SUBJECT/mri/wm.mgz...
>> reading input surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white...
>> reading input pial surface  
>> /home/user/visao/Freesurfer//SUBJECT/surf/rh.pial...
>> reading input white surface  
>> /home/user/visao/Freesurfer//SUBJECT/surf/rh.white...
>> could not read annot file ./rh.BA.annot
>> No such file or directory
>> mris_anatomical_stats:  could  not read annotation file ./rh.BA.annot
>> No such file or directory
>>
>> I only tried with rh, but I don't think that's a problem is it?
>>
>> Thank you!
>>
>> Andreia
>>
>>
>>
>> Quoting Anastasia Yendiki :
>>
>>> In the "BA label" section there are:
>>> - Several mri_label2label commands that map each label from  
>>> fsaverage space to your indidvidual's space
>>> - One mris_label2annot command that combines the mapped label into  
>>> an annotation file.
>>> - One mris_anatomical_stats command that gets stats for that annotation.
>>>
>>> For each of these commands you can run them with --help to see  
>>> what the inputs and outputs are, or look them up on the wiki.
>>>
>>> On Tue, 26 Mar 2013, _andre...@sapo.pt wrote:
>>>
 Nevermind the last email... If I change the output (wich is the second
 place where BAxx.label appears, right?) file name and give the subjs
 id this won't be a problem... Anyway, what are these files for? Will I
 need to use them somehow?
 > Thanks
 Andreia
 > > Quoting _andre...@sapo.pt:
 > > Addicionaly, this approach is creating an individual file for each
 > BAxxx.thresh.label (see atchment) and I think that if I run these
 > commands for another subject these outputs will be replaced since
 > the name of the files has no info relating to the subject who it
 > belongs.
 > > > I'm kind of lost here...
 > > > > > > > > > > > Quoting _andre...@sapo.pt:
 > > > > Hi,
 > > > > > I run the command for each BA labels of the right  
 hemisphere and then > > > run:
 > > > > > [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
 > > ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab
 > > SUBJECT rh white
 > > > > > Which resulted in:
 > > > > > INFO: assuming MGZ format for volumes.
 > > computing statistics for each annotation in ./rh.BA.annot.
 > > reading volume > > >  
 /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz...
 > > reading input surface
 > > /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
 > > reading input pial surface
 > > /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial...
 > > reading input white surface
 > > /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white...
 > > could not read annot file ./rh.BA.annot
 > > No such file or directory
 > > mris_anatomical_stats:  could  not read annotation file ./rh.BA.annot
 > > No such file or directory
 > > > > > What is wrong? Is there a way to run everything that is  
 needed to
 > > get the BA stats at once using the BAxxx.thresh.label?
 > > > > > Thank you,
 > > Andreia
 > > > > > Quoting Anastasia Yendiki :
 > > > > > > If you replace *every* occurence of BAxxx.label with
 > > > BAxxx.thresh.label, this will keep things simple and you won't
 > > > have to worry about which one is input and which one is output.
 > > > > > > > Run *all* the commands from the "BA labels"  
 section, all the way
 > > > to the end of that section, this will get you to the stats.
 > > > > > > > On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
 > > > > > > > > Ok. So the first is the input and the second is  
 the output,
 > > > > correct? So I'll have a different file for each out put? Is it
 > > > > possible to have a table with the different measures after the
 > > > > threshold?
 > > > > > > > > > Thank you very much and I apologize for the  
 naive questions...
 > > > > > > > > > Andreia
 > > >

Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume

[_andreia_]

I'll bear that in mind next time!

Thank you!!
Andreia


Quoting Anastasia Yendiki :

> No problem, you can usually find the answers to most of these types  
> of questions in the help text of the commands. For example if you  
> run "mris_label2annot --help" you'll see:
>
> [...]
>
> --a annotname
>
> Name of the annotation to create. The actual file will be called
> hemi.annotname.annot, and it will be created in subject/label.
> If this file exists, then mris_label2annot exits immediately
> with an error message. It is then up to the user to manually
> delete this file (this is so annotations are not accidentally
> deleted, which could be a huge inconvenience).
>
> [...]
>
> On Tue, 26 Mar 2013, _andre...@sapo.pt wrote:
>
>> Oh so that was it... I've cd to the dir where the annot file is and now
>> everything worked just fine... I checked the values in the stats file
>> and they are smaller now.
>>
>> So I must do that when running the label2label so the files are  
>> created in the label dir and not in Freesurfer dir...
>>
>> By the way, why did the command label2annot created the file in the  
>> right dir?
>>
>>
>> As you're noticing I'm not very familiar with Unix and while using>  
>> Freesurfer I never had to use the cd command to work...
>>
>> Thank you very much Anastasia!
>
>
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[Freesurfer] Different MPRAGE sequences

[_andreia_]

Hello list,

I have a group of subjects (4 patients  and 8 controls) in which one  
MPRAGE sequence was used and another group of subjects (2 patients and  
2 controls) where a diffent MPRAGE was used. Both groups were acquired  
in the same scanner. For each subject I have two anatomical sequences  
and I'm working with the average dataset. My question is can I put  
both groups together for comparision?

I've thought about this and I can't really be sure... I was thinking  
that since for group 2 the number of acquisitions is balanced maybe  
the overall impact of different sequences won't be significative...  
Patients and subjects are age-matched in both groups.

Please, any advice will be greatly appreciated!

Thank you!
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Re: [Freesurfer] Different MPRAGE sequences

[_andreia_]

Hi Bruce,

I did that test some time ago (each sequence alone or averaged) but  
only with one control subject. I then checked the values of different  
measures and the cortical thickness maps for each situation and they  
were very similar indeed. I did it only with one subject because the  
point was to choose one of the MPRAGEs. But now that I need to drag  
conclusions I wasn't sure if the different sequences would be a major  
problem and would invalidate the conclusions.

I'll match the number of subjects for each sequence but bearing in  
mind that I have two different sequences anyway.


Thank you for the help!

Andreia


Quoting Bruce Fischl :

> p.s. you would be better off if you had the same proportion of  
> patients and controls with each sequence. Matching the numbers  
> within one sequence and not the other doesn't really help
>
> On Thu, 28 Mar 2013, _andre...@sapo.pt wrote:
>
>> Hello list,
>>
>> I have a group of subjects (4 patients  and 8 controls) in which one
>> MPRAGE sequence was used and another group of subjects (2 patients and
>> 2 controls) where a diffent MPRAGE was used. Both groups were acquired
>> in the same scanner. For each subject I have two anatomical sequences
>> and I'm working with the average dataset. My question is can I put
>> both groups together for comparision?
>>
>> I've thought about this and I can't really be sure... I was thinking
>> that since for group 2 the number of acquisitions is balanced maybe
>> the overall impact of different sequences won't be significative...
>> Patients and subjects are age-matched in both groups.
>>
>> Please, any advice will be greatly appreciated!
>>
>> Thank you!
>> ___
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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  
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[Freesurfer] Overlay thickness for BA areas

[_andreia_]

Hello list!

Is there a way to display the thickness of individual Bordmann areas  
in the inflated surface using tksurfer?


I'm able to show surface area with File-> Label -> Load label and  
choosing the thresholded label. Now, I qould like to do the same but  
with cortical thickness, is this possible?

I'm using FS 5.0.

Thank you in advance,
Andreia

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Re: [Freesurfer] Overlay thickness for BA areas

[_andreia_]

Hi Doug,

I would like to have the thickness map restricted to the BAs where the  
group differences showed up. Could it be possible to overlay the  
thickness map of an individual and then restrict it to the chosen BA,  
for example?

The ideia is to have two subjects with the thickness overlayed for  
display purposes.

If there would be a way to do this by groups it would also be nice!

Thank you!
Andreia



Quoting Douglas N Greve :

> Hi Andreia, do you mean that you want to display a constant value in
> each BA on the surface? We don't haveanything explicit to do that, but
> you could do it in matlab. Let me know if you need more info.
> doug
>
>
> On 05/21/2013 11:46 AM, _andre...@sapo.pt wrote:
>> Hello list!
>>
>> Is there a way to display the thickness of individual Bordmann areas
>> in the inflated surface using tksurfer?
>>
>>
>> I'm able to show surface area with File-> Label -> Load label and
>> choosing the thresholded label. Now, I qould like to do the same but
>> with cortical thickness, is this possible?
>>
>> I'm using FS 5.0.
>>
>> Thank you in advance,
>> Andreia
>>
>> ___
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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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>
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>
>
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[Freesurfer] cortex stats

[_andreia_]

Dear list,

To obtain the thickness, surface area and volume values for each  
hemisphere I ran the command line in the subjdir:

mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats subjid lh white

And did that with the pial surface too. However, the values I get from  
the generated cortex.stats do not match the ones in aparc.stats

How can I get the referred measures, which are in the aparc.stats but  
do not appear in the table when using aparcstats2table?

Thank you!

Andreia

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[Freesurfer] Error mri_label2label

[_andreia_]

Hello list,

 When running the following command :

 mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/lh.BA1.thresh.label
--trgsubject subjid --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod
surface

 I get the error

 "INFO: found  1014 nlabel points
 Performing mapping from target back to the source label
ERROR: SRCVTXNO = -1 < 0
 trgvtxno = 122050, dmin = 1000
 trgregxyz = 0, 0, 0
   This means that a vertex in the target surface could
   not be mapped to a vertex in the source surface
   because the xyz of the target is outside of the
   range of the hash table."

 I have used this command in several subjects and never got this error.
What went wrong? As far as I'm aware I did all the processing in the same
way for every subject.

 How can I fix this this?

 Thank you!
 Andreia
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Re: [Freesurfer] Error mri_label2label

[_andreia_]

Hi Doug,

Thank you very much! It's working!

Andreia


Quoting Douglas N Greve :

> Not sure. Try running it with --nohash. It will probably take a lot longer
> doug
>
>
> On 03/12/2014 02:45 PM, _andre...@sapo.pt wrote:
>>
>> Hello list,
>>
>> When running the following command :
>>
>> mri_label2label --srcsubject fsaverage --srclabel
>> /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.thresh.label
>> --trgsubject subjid --trglabel ./lh.BA1.thresh.label --hemi lh
>> --regmethod surface
>>
>>
>> I get the error
>>
>> "INFO: found  1014 nlabel points
>> Performing mapping from target back to the source label
>> *ERROR: srcvtxno = -1 < 0*
>> trgvtxno = 122050, dmin = 1000
>> trgregxyz = 0, 0, 0
>>   This means that a vertex in the target surface could
>>   not be mapped to a vertex in the source surface
>>   because the xyz of the target is outside of the
>>   range of the hash table."
>>
>>
>> I have used this command in several subjects and never got this error.
>> What went wrong? As far as I'm aware I did all the processing in the
>> same way for every subject.
>>
>> How can I fix this this?
>>
>> Thank you!
>> Andreia
>>
>>
>>
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate

[_andreia_]

Hi all,

just two quick questions: to what FS version is this related? And what  
is wrong to do if one does not have the fix? Using what  
stats/procedures?

Thanks,
Andreia


Quoting Douglas N Greve :

>>> why would one control for total brain volume in doing vertex-based
> analyses when the vertex-based measures are computed in standard space?
>
> The vertex-based measures are computed in individual space, not standard
> space
> doug
>
>
> On 03/17/2014 05:12 PM, Narly Golestani wrote:
>> Dear Doug,
>>
>> Many thanks for your answers.
>>
>> > 3. The bug was related to how the measures were converted to standard
>> > space - I?d like to therefore confirm that when doing
>> > surface/vertex-based analyses, it is not necessary to use total brain
>> > volume as a covariate (whereas it is for ROI-based analyses).
>> >
>> This question has nothing to do with the bug. People generally use ICV
>> or total brain volume when exploring cortical volume or surface area,
>> but it is inappropriate for thicknss studies
>> doug
>> >
>>
>> Regarding the last point (which indeed has nothing to do with the bug,
>> sorry for having given the impression that I thought that it did), why
>> would one control for total brain volume in doing vertex-based
>> analyses when the vertex-based measures are computed in standard
>> space? I realize that this has to be done for ROI analyses since these
>> measures are in native space.
>>
>> Thanks again, and best,
>> Narly.
>>
>>
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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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>
>
> The information in this e-mail is intended only for the person to whom it is
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> HelpLine at
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[Freesurfer] Fwd: FW: bug in surface-based area and volume, and use of total brain volume as a covariate

[_andreia_]

Hi all,

just two quick questions: to what FS version is this related? And what
is wrong to do if one does not have the fix? Using what
stats/procedures?

Thanks,
Andreia


Quoting Douglas N Greve :

>>> why would one control for total brain volume in doing vertex-based
> analyses when the vertex-based measures are computed in standard space?
>
> The vertex-based measures are computed in individual space, not standard
> space
> doug
>
>
> On 03/17/2014 05:12 PM, Narly Golestani wrote:
>> Dear Doug,
>>
>> Many thanks for your answers.
>>
>> > 3. The bug was related to how the measures were converted to standard
>> > space - I?d like to therefore confirm that when doing
>> > surface/vertex-based analyses, it is not necessary to use total brain
>> > volume as a covariate (whereas it is for ROI-based analyses).
>> >
>> This question has nothing to do with the bug. People generally use ICV
>> or total brain volume when exploring cortical volume or surface area,
>> but it is inappropriate for thicknss studies
>> doug
>> >
>>
>> Regarding the last point (which indeed has nothing to do with the bug,
>> sorry for having given the impression that I thought that it did), why
>> would one control for total brain volume in doing vertex-based
>> analyses when the vertex-based measures are computed in standard
>> space? I realize that this has to be done for ROI analyses since these
>> measures are in native space.
>>
>> Thanks again, and best,
>> Narly.
>>
>>
>> ___
>> 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
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>
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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
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Re: [Freesurfer] FW: bug in surface-based area and volume, and use of total brain volume as a covariate

[_andreia_]

My apologies Doug... I thought that this email had all the history...

Narly, sorry for "invading" your discussion...

My questions came from the first email of Narly which referred to the  
bug in mris_preproc:

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html


This bug also exist in FS 5.0, right? I'm using 5.0 and until now I've  
used aparcstats2table to get Brodmann Area measures (CT and surface  
area of the thresholded labels) and total CT and surface area of each  
hemisphere. Does the bug also affect these measures or it is fine to  
use them?


Now I want to run a whole-brain analysis with qdec but to do so I'll  
have to run qcache with 5.3 which already has the bug fixed, correct?  
Is qcache equivalent to mris_preproc?

Hope I was more clear this time...

Thank you,
Andreia





Quoting Douglas N Greve :

> Sorry, the thread of the email that explains the problem and the fix are
> not included below. Can you re-explain? We get a lot of emails here and
> it is not possible to remember the context of each one.
> doug
>
>
>
>
>
>
> On 03/18/2014 11:32 AM, _andre...@sapo.pt wrote:
>> Hi all,
>>
>> just two quick questions: to what FS version is this related? And what
>> is wrong to do if one does not have the fix? Using what stats/procedures?
>>
>> Thanks,
>> Andreia
>>
>>
>> Quoting Douglas N Greve :
>>
> why would one control for total brain volume in doing vertex-based
>>> analyses when the vertex-based measures are computed in standard space?
>>>
>>> The vertex-based measures are computed in individual space, not standard
>>> space
>>> doug
>>>
>>>
>>> On 03/17/2014 05:12 PM, Narly Golestani wrote:
 Dear Doug,

 Many thanks for your answers.

> 3. The bug was related to how the measures were converted to standard
> space - I?d like to therefore confirm that when doing
> surface/vertex-based analyses, it is not necessary to use total brain
> volume as a covariate (whereas it is for ROI-based analyses).
>
 This question has nothing to do with the bug. People generally use ICV
 or total brain volume when exploring cortical volume or surface area,
 but it is inappropriate for thicknss studies
 doug
>

 Regarding the last point (which indeed has nothing to do with the bug,
 sorry for having given the impression that I thought that it did), why
 would one control for total brain volume in doing vertex-based
 analyses when the vertex-based measures are computed in standard
 space? I realize that this has to be done for ROI analyses since these
 measures are in native space.

 Thanks again, and best,
 Narly.


 ___
 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
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>>>
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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.
>>
>>
>>
>
> --
> 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
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[Freesurfer] Hemisphere stats question

[_andreia_]

Hello list,

I have a question regarding what stats are more correct to use to get  
whole hemisphere surface area and mean thickness.

The cortex.label values extracted using the two bottom command lines  
don't match aparc stats, however they match in the number of vertices  
between them, and using pial or white surface also results in values  
that make sense comparing each one (higher surface area using pial,  
same thickness, same volumes).

In the past I've been using the two first command lines (in which  
values agree in the same way as cortex.label between them but are also  
in agreement with aparc.stats), however now I'm having this question:  
which one is the correct one to use?

And why does this difference exists?


mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b  
SUBJ lh white (matches aparcstats)

mris_anatomical_stats -l ../label/lh.cortex.label -f  
lh.total_pial.stats -b SUBJ lh pial (matches aparcstats)


mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh  
pial (does not match aparcstats)

mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh  
white (does not match aparcstats)


Thank you in advance,
Andreia
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Re: [Freesurfer] Hemisphere stats question

[_andreia_]

I was also referring to the surface area and thickness (looking at the  
files originated from white matter, which is also the default for  
aparc I think):

For surface area
aparc= 72998.7
total= 72999
cortex=78090

For CT
aparc=  2.422
total=  2.422
cortex= 2.313


And also, which volume measure should I use to get total hemisphere  
gray volume?
Aseg lhCortexVol=196557.55 (is the surface-based estimation?)
Aparc (the sum of all labels)=199854
total.stats=199857
cortex= 204048

It seems that the value from total.stats is more approximated to the  
one from the sum of aparc.

I'm using F.S. 5.0.

Andreia


Quoting Douglas N Greve :

> Is this the difference you mean?
>
> [t:D:mri-> grep Cortex ~/tmp/lh.total.stats
> # Measure Cortex, NumVert, Number of Vertices, 118847, unitless
> # Measure Cortex, SurfArea, Surface Area, 78090, mm^2
>
> [t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats
> # Measure Cortex, NumVert, Number of Vertices, 111237, unitless
> # Measure Cortex, SurfArea, Surface Area, 72998.7, mm^2
>
> If so this is just the difference in the vertices coverted by
> cortex.label vs aparc
>
>
>
>
> On 03/24/2014 12:49 PM, _andre...@sapo.pt wrote:
>> Hi Doug,
>>
>> I've attached the files. To contextualize a little bit, I'm using
>> Brodmann Areas measures (CT, surface area and volume, thresholded to
>> the correct probability) and I'll be extracting the surface area using
>> pial and white surface. However, I'll be also analyzing whole brain
>> using the aparc stats (again, CT, surface area and volume) - should I
>> use the file that is in agreement with aparc?
>>
>> I don't understand why total.stats gives different values from
>> cortex.stats since I've created the total.stats file using the command:
>>
>> mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b
>> SUBJ lh white
>>
>>
>>
>> One more question: is the ?hCortexvol value from aseg that I should
>> use to get the total volume of each hemisphere?
>>
>> Sorry for so many questions...
>>
>> Thank you!
>>
>> Andreia
>>
>>
>> Quoting Douglas Greve :
>>
>>> How much of a difference is there? There should not be much, but there
>>> will be some because the aparc does not cover the exact same vertices as
>>> cortex.label
>>> doug
>>>
>>>
>>>
>>> On 3/24/14 8:04 AM, _andre...@sapo.pt wrote:
 Hello list,

 I have a question regarding what stats are more correct to use to get
 whole hemisphere surface area and mean thickness.

 The cortex.label values extracted using the two bottom command lines
 don't match aparc stats, however they match in the number of vertices
 between them, and using pial or white surface also results in values
 that make sense comparing each one (higher surface area using pial,
 same thickness, same volumes).

 In the past I've been using the two first command lines (in which
 values agree in the same way as cortex.label between them but are also
 in agreement with aparc.stats), however now I'm having this question:
 which one is the correct one to use?

 And why does this difference exists?


 mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b
 SUBJ lh white (matches aparcstats)

 mris_anatomical_stats -l ../label/lh.cortex.label -f
 lh.total_pial.stats -b SUBJ lh pial (matches aparcstats)


 mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh
 pial (does not match aparcstats)

 mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh
 white (does not match aparcstats)


 Thank you in advance,
 Andreia
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>>>
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>>>
>>>
>>> The information in this e-mail is intended only for the person to
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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 error
>>> but does not contain patient information, please contact the sender
>>> and properly
>>> dispose of the e-mail.
>>
>>
>
> --
> 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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[Freesurfer] Surface-based cortical volume calculation

[_andreia_]

Hello,

Recalling these emails:

"The methods are somewhat different. For the value in the aseg.stats
table, the method is to compute the total volume inside the pial surface
and subtract the total volume inside the white surface. For
mris_anatomical_stats, the method is to compute the thickness times area
of each vertex. This method will probably underestimate the total volume
because it uses the area of the white surface when it should use the
area of the surface in the middle between the white and pial surfaces.
I've added this to the list of known issues on our release page.

doug

Alexopoulos, Dimitrios wrote:
> I have generated surfaces using the the centos4 build (version 5.0)
> and want to confirm that my surface-based GM and WM volumes are correct.
> For the surface-based GM calculation I originally used  
> 'mris_anatomical_stats -l lh.cortex.label subjectID hemi'
> (run from within the 'label' subdirectory) and for WM i used  
> 'mris_wm_volume subjectID hemi' (run from within
> the 'surf' subdirectory).
> When I add the calculated left/right cortical volumes, I get a total  
> that is different from what is output in
> the 'aseg.stats' file, which in version 5.0 is noted to contain  
> total surface-based GM volume
> (Cortex, CortexVol: Total cortical gray matter volume (based on  
> surface-stream).
>  What are the correct GM and WM surface-based volumes?
> Thanks. Jim"


I question came up to me:

The surfaces in the hippocampus/amygdala are inaccurate and should be  
ignored. However, in version 5.0 the cortical volume is surface-based,  
thus it takes into account the surfaces in the hippocampus/amygdala,  
is this correct?

If so, it is expected that an error is introduced in the surface-based  
calculation of cortical volume. Has anyone checked the influence of  
this error? Or FS compensates for the inaccuracy of the surface  
estimation of these regions somehow?

Thanks!

Andreia

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Re: [Freesurfer] Surface-based cortical volume calculation

[_andreia_]

Hi!

Ok! That would be a good improvement :)

Thanks to both!

Cheers,
Andreia





Citando Douglas N Greve :

> Actually, you are right! Most of the non-gray matter structures in the
> medial wall are zeroed out, but the part that goes through the hippo and
> amygdala are non-zero. As Mike points out, this is going to be a very
> small portion of the total cortical volume, but we'll find a way to
> remove it.
> doug
>
> _andre...@sapo.pt wrote:
>> Hi Michael and Doug,
>>
>> Michael:
>> "As you noted, the surfaces bisect the hippocampus and amygdala, so the
>> small amount of tissue outside the pial surface is not included in the
>> surface based measures of total GM volume.  Compared to the overall
>> variation in brain size, this should be inconsequential.
>>
>> cheers,
>> -MH"
>>
>> I got a little confused with your answer. The calculation is
>> everything inside the pial surface - everything inside the wm surface.
>> What is outside is half hippocampus/amygdala and is not included, ok.
>> But the other halves are inside the surfaces, being then included, right?
>>
>> Doug:
>>
>> If the thickness was 0 in those areas that would make sense. But do
>> the surfaces "have" the information that in those regions the
>> structures are hippocampus and amygdala?
>>
>> I checked if the thickness was 0 and from what I'm understanding it is
>> 5mm. What I did was to open tkmedit with aparc+aseg and open tksurfer
>> (for both hemispheres). Then, I used the buttons "Save point" and "Go
>> to saved point" to go from tkmedit to tksurfer. What happened was that
>> when the point was located in the hippocampus or amygdala in tkmedit
>> it had a correspondence in tksurfer in regions which have a thickness
>> value.
>>
>> Please see figures in attachement (green arrows are amygdala poinst
>> and blue arrows are hippocampus points)
>>
>> Am I missing something?
>>
>> Thank you,
>> Andreia
>>
>>
>>
>>
>> Citando Douglas N Greve :
>>
>>> Hi Andreia, I don't think this is a problem for the GM volume (ie, parts
>>> of the amyg or hippo getting counted twice). The thickness should be 0
>>> in those areas, so they should not contribute to GM volume. The
>>> computation of the WM volume is done in a different way (still surface
>>> based) but automatically excludes subcortical structures.
>>> doug
>>>
>>> _andre...@sapo.pt wrote:
 Hello,

 Recalling these emails:

 "The methods are somewhat different. For the value in the aseg.stats
 table, the method is to compute the total volume inside the pial
 surface
 and subtract the total volume inside the white surface. For
 mris_anatomical_stats, the method is to compute the thickness times
 area
 of each vertex. This method will probably underestimate the total
 volume
 because it uses the area of the white surface when it should use the
 area of the surface in the middle between the white and pial surfaces.
 I've added this to the list of known issues on our release page.

 doug

 Alexopoulos, Dimitrios wrote:

> I have generated surfaces using the the centos4 build (version 5.0)
> and want to confirm that my surface-based GM and WM volumes are
> correct.
> For the surface-based GM calculation I originally used
> 'mris_anatomical_stats -l lh.cortex.label subjectID hemi'
> (run from within the 'label' subdirectory) and for WM i used
> 'mris_wm_volume subjectID hemi' (run from within
> the 'surf' subdirectory).
> When I add the calculated left/right cortical volumes, I get a total
> that is different from what is output in
> the 'aseg.stats' file, which in version 5.0 is noted to contain
> total surface-based GM volume
> (Cortex, CortexVol: Total cortical gray matter volume (based on
> surface-stream).
>  What are the correct GM and WM surface-based volumes?
> Thanks. Jim"
>


 I question came up to me:

 The surfaces in the hippocampus/amygdala are inaccurate and should be
 ignored. However, in version 5.0 the cortical volume is surface-based,
 thus it takes into account the surfaces in the hippocampus/amygdala,
 is this correct?

 If so, it is expected that an error is introduced in the surface-based
 calculation of cortical volume. Has anyone checked the influence of
 this error? Or FS compensates for the inaccuracy of the surface
 estimation of these regions somehow?

 Thanks!

 Andreia

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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>
>>> _

[Freesurfer] Two FS versions in different user accounts

[_andreia_]

Hi everyone,

I'm sorry to bring this question up again, but I'm thinking to install  
version 5.1 in the same computer where version 5.0 is installed.  
However I'm thinking of installing the new one in another user account  
that I've created only for this porpuse. My question is, can I install  
and work in the new user independently? This way I won't need to be  
changing the subjects dir and the freesurfer environment each time I  
want to work with 5.0 or 5.1, right?

Advice needed =)

Thanks,
Andreia

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[Freesurfer] Two FS versions in different user accounts

[_andreia_]

Hi everyone,

I'm sorry to bring this question up again, but I'm thinking to install  
version 5.1 in the same computer where version 5.0 is installed.  
However I'm thinking of installing the new one in another user account  
that I've created only for this porpuse. My question is, can I install  
and work in the new user independently? This way I won't need to be  
changing the subjects dir and the freesurfer environment each time I  
want to work with 5.0 or 5.1, right?

Advice needed =)

Thanks,
Andreia

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[Freesurfer] Retinotopy

[_andreia_]

Hello!

I'm moving to FS 5.1 and I will be analysing retinotipic data (and the  
anatomical data bas well). I would like to know if there are any  
changes or issues while running this analysis in this new version  
before I move.

Thanks,
Andreia
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Re: [Freesurfer] optic nerve inlcuded as pial matter

[_andreia_]

Hi Julia,

I usually remove the voxels from brainmaks.mgz for the  pial edits but also 
from wm.mgz. If you deselect the button of the pial  surface in tkmedit, you 
will see that the white matter surface is  coincident with the pial, so you 
also need to correct that volume. With  wm.mgz as auxiliary volume you can 
erase the voxels from both volumes at  the same time, you only need to change 
the brush definitions in Tools  -> Configure brush info -> target main and aux 
volume. Don't forget to change back this definition if you want to make more 
corrections to only one volume.

After this I run recon-all -autorecon2-wm -autorecon3. 

Cheers,
Andreia

Citando Julia Hill : 

> Good morning,
> 
> I have a question about editing of the pial.  I have noticed that on every 
> single scan (so well over 100), the optic nerve has been included as pial 
> matter (see attached screenshot).  This occurs from between 5 and 10 slices 
> in length.  Will i need to remove the voxels from every scan, and do a 
> recon-all autorecon2-pial? 
> 
> Thank you kindly in advance,
> 
> Julia Hill
> 
>  
> 
> Julia Hill
> Research Assistant 
> 
> School of Psychiatry 
> 
> University of New South Wales  
> 
> Previously Prince of Wales Medical Research Institute 
> 
> www.NeuRA.edu.au
> Barker Street Randwick Sydney NSW 2031 Australia
> PO Box 1165 Randwick Sydney NSW 2031 Australia
> T +61 2 9399 1268   
>  
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Re: [Freesurfer] optic nerve inlcuded as pial matter

[_andreia_]

Ah ok! :)

So it won't affect any stats?

Anyway, not correcting this will make the inflated surface to have a  
prominence, right? In that case it will only look better for results'  
displaying.

Andreia


Citando Bruce Fischl :

> if they are coincident then it is accurately detected as  
> non-cortical and won't affect any thickness/volume corrections, so  
> fixing it is really just aesthetic.
>
> cheer
> Bruce
>
> On Thu, 16 Feb 2012, _andre...@sapo.pt wrote:
>
>>
>> Hi Julia,
>>
>> I usually remove the voxels from brainmaks.mgz for the pial edits but also
>> from wm.mgz. If you deselect the button of the pial surface in tkmedit, you
>> will see that the white matter surface is coincident with the pial, so you
>> also need to correct that volume. With wm.mgz as auxiliary volume you can
>> erase the voxels from both volumes at the same time, you only need to change
>> the brush definitions in Tools -> Configure brush info -> target main and
>> aux volume. Don't forget to change back this definition if you want to make
>> more corrections to only one volume.
>>
>> After this I run recon-all -autorecon2-wm -autorecon3.
>>
>> Cheers,
>> Andreia
>>
>>
>>
>>
>> Citando Julia Hill :
>>
>>  Good morning,
>>
>>  I have a question about editing of the pial.  I have noticed
>>  that on every single scan (so well over 100), the optic nerve
>>  has been included as pial matter (see attached screenshot). 
>>  This occurs from between 5 and 10 slices in length.  Will i need
>>  to remove the voxels from every scan, and do a recon-all
>>  autorecon2-pial? 
>>
>>  Thank you kindly in advance,
>>
>>  Julia Hill
>>
>>  Julia Hill
>>  Research Assistant
>>
>>  School of Psychiatry
>>
>>  University of New South Wales
>>
>> [IMAGE]
>>
>> Previously Prince of Wales Medical Research Institute
>>
>> www.NeuRA.edu.au
>> Barker Street Randwick Sydney NSW 2031 Australia
>> PO Box 1165 Randwick Sydney NSW 2031 Australia
>> T +61 2 9399 1268 
>>
>>
>>
>>
>
>
> 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] optic nerve inlcuded as pial matter

[_andreia_]

Since it is such a straightforward correction, I've been making it  
because I thought that it would have some effect (though tiny).

Thanks!
Andreia

Citando Bruce Fischl :

> yes, exactly. it will have a tiny effect on total surface area, but  
> that includes noncortical regions anyway
> On Thu, 16 Feb 2012, _andre...@sapo.pt wrote:
>
>> Ah ok! :)
>>
>> So it won't affect any stats?
>>
>> Anyway, not correcting this will make the inflated surface to have  
>> a prominence, right? In that case it will only look better for  
>> results' displaying.
>>
>> Andreia
>>
>>
>> Citando Bruce Fischl :
>>
>>> if they are coincident then it is accurately detected as  
>>> non-cortical and won't affect any thickness/volume corrections, so  
>>> fixing it is really just aesthetic.
>>>
>>> cheer
>>> Bruce
>>>
>>> On Thu, 16 Feb 2012, _andre...@sapo.pt wrote:
>>>

 Hi Julia,

 I usually remove the voxels from brainmaks.mgz for the pial edits but also
 from wm.mgz. If you deselect the button of the pial surface in  
 tkmedit, you
 will see that the white matter surface is coincident with the pial, so you
 also need to correct that volume. With wm.mgz as auxiliary volume you can
 erase the voxels from both volumes at the same time, you only  
 need to change
 the brush definitions in Tools -> Configure brush info -> target main and
 aux volume. Don't forget to change back this definition if you  
 want to make
 more corrections to only one volume.

 After this I run recon-all -autorecon2-wm -autorecon3.

 Cheers,
 Andreia




 Citando Julia Hill :

Good morning,

I have a question about editing of the pial.  I have noticed
that on every single scan (so well over 100), the optic nerve
has been included as pial matter (see attached screenshot). 
This occurs from between 5 and 10 slices in length.  Will i need
to remove the voxels from every scan, and do a recon-all
autorecon2-pial? 

Thank you kindly in advance,

Julia Hill

Julia Hill
Research Assistant

School of Psychiatry

University of New South Wales

 [IMAGE]

 Previously Prince of Wales Medical Research Institute

 www.NeuRA.edu.au
 Barker Street Randwick Sydney NSW 2031 Australia
 PO Box 1165 Randwick Sydney NSW 2031 Australia
 T +61 2 9399 1268 




>>>
>>>
>>> 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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[Freesurfer] Load Brodmann surface area into inflated surface

[_andreia_]

Hi all,

I'm sorry if these questions have already been covered here, but I've  
looked into the archives and still can't do what I need (and since I'm  
running out of time for this task I decided to post here):

I'm using version 5.0.0.

I want to show the resulting Brodmann area (only 3 BA) volume in the  
inflated surface of my subjects to show the differences between  
patients and controls (for visualization purpose only). I've managed  
to overlay the volume in the curvature menu but this is for the entire  
cortex and I can't show the values bar. How can I show the volume of  
only 3 BAs and have the scale bar?

Another question is, how is the volume of the BA calculated? Is it  
from the surface-based stream?

And, which surface area is the on in the output of the BA stats? Is it  
the pial or wm?

Thanks in advance,
Andreia

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Re: [Freesurfer] Load Brodmann surface area into inflated surface

[_andreia_]

(forgot to do answer all, here it goes for the list too)


Citando _andre...@sapo.pt:

> Hi Bruce,
>
> The ideia is to show one control subject vs. one patient inflated  
> surface with BA surface (not volume, sorry) to show the difference  
> (reduced surface area in one patient). Loading the relevant labels  
> worked (I have the statistics shown in bar graphs, the images are  
> only for visualizing the difference between controls and patients).  
> When I threshold the labels in the subject's inflated surface they  
> shrink a lot, is this supposed to happen?
>
> The BA are V1, V2 and MT. What is the thresghold for V2?
>
> And is it correct to load ?h.sulc in a gray scale to have the usual  
> cortex representation, or I should do it other way?
>
>
> And getting back to my previous email:
>
> Another question is, how is the volume of the BA calculated? Is it
>>> from the surface-based stream?
>>>
>>> And, which surface area is the on in the output of the BA stats? Is it
>>> the pial or wm?
>
> Thanks,
> Andreia
>
>
> Citando Bruce Fischl :
>
>> Hi Andreia
>>
>> sorry, I don't understand. What do you mean when you say you want  
>> to " show the resulting Brodmann area (only 3 BA) volume in the  
>> inflated surface of my subjects". Do you mean just to show what  
>> portion of the surface is in each of 3 Brodmann areas? That you  
>> would do by loading the relevant labels, although you will probably  
>> want to threshold them differently (e.g. V1 you could threshold at  
>> .9 which is 90% and it would have about the surface area of an  
>> individual, while MT would need to be closer to .4 or .5). Or do  
>> you actually mean the volume of gray matter within each BA? If the  
>> latter, it's just 3 numbers/subject, so I would think you would  
>> want  a scatter plot or something, not a map on the surface.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote:
>>
>>> Hi all,
>>>
>>> I'm sorry if these questions have already been covered here, but I've
>>> looked into the archives and still can't do what I need (and since I'm
>>> running out of time for this task I decided to post here):
>>>
>>> I'm using version 5.0.0.
>>>
>>> I want to show the resulting Brodmann area (only 3 BA) volume in the
>>> inflated surface of my subjects to show the differences between
>>> patients and controls (for visualization purpose only). I've managed
>>> to overlay the volume in the curvature menu but this is for the entire
>>> cortex and I can't show the values bar. How can I show the volume of
>>> only 3 BAs and have the scale bar?
>>>
>>> Another question is, how is the volume of the BA calculated? Is it
>>> from the surface-based stream?
>>>
>>> And, which surface area is the on in the output of the BA stats? Is it
>>> the pial or wm?
>>>
>>> Thanks in advance,
>>> Andreia
>>>
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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  
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[Freesurfer] Fwd: Load Brodmann surface area into inflated surface

[_andreia_]

(sorry, here it is for the list again)



- Mensagem encaminhada de Bruce Fischl  -
Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT)
  De: Bruce Fischl 
Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface
Para: _andre...@sapo.pt

Hi Andreia,

can you cc the list so others can answer? I just took a look and  
label_area is so old that is uses ?h.smoothwm without any ability to  
change it. I think there are probably other tools around that will do  
it, but someone else will know. If not I'll fix label_area to be less  
obstinate.

cheers
Bruce


On Mon, 23 Apr 2012, _andre...@sapo.pt wrote:

> Hi Bruce,
>
> Thanks for the help! How do I know from which surface, i.e. pial or  
> wm is the command label_area getting the value? I compared V1  
> surface area given in the BA.stats and the one I get with the  
> command, and the late is higher (V1 from BA.stats= 2081 and from  
> label_area = 2592.272).
>
> Now, imagine the follwing: I have no differences in cortical  
> thickness (CT) and surface area of this BA but the volume is  
> different (with p values near 0.04...). Also, other BA shows no  
> differences in CT neither in volume, but with differences showing up  
> in the surface area (with lower p value here). Since the values for  
> volume and surface are computed in different ways, can this account  
> for these odd results?
>
> Thanks!
> Andreia
>
>
> Citando Bruce Fischl :
>
>> Hi Andreia,
>>
>> yes, they will always shrink since the label contains every point that
>> could possibly be in the BA, no matter how unlikely. I'll try to find time
>> to automatically threshold the BAs so that they have the average area of
>> the individual examples, but for now V2 is probably around .7 and MT around
>> .4 I think. And yes, I would use ?h.sulc as the background gray scale. The
>> volume of the BAs would be computed using both surfaces, but the surface
>> area can be from either one. I think we use the white by default, but you
>> can use label_area to measure on whatever surface you want.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 23 Apr 2012,
>> _andre...@sapo.pt wrote:
>>
>>> (forgot to do answer all, here it goes for the list too)
>>>
>>>
>>> Citando _andre...@sapo.pt:
>>>
 Hi Bruce,

 The ideia is to show one control subject vs. one patient inflated surface
 with BA surface (not volume, sorry) to show the difference  
 (reduced surface
 area in one patient). Loading the relevant labels worked (I have the
 statistics shown in bar graphs, the images are only for visualizing the
 difference between controls and patients). When I threshold the labels in
 the subject's inflated surface they shrink a lot, is this supposed to
 happen?

 The BA are V1, V2 and MT. What is the thresghold for V2?

 And is it correct to load ?h.sulc in a gray scale to have the usual cortex
 representation, or I should do it other way?


 And getting back to my previous email:

 Another question is, how is the volume of the BA calculated? Is it
>> from the surface-based stream?
>>
>> And, which surface area is the on in the output of the BA stats? Is it
>> the pial or wm?

 Thanks,
 Andreia


 Citando Bruce Fischl :

> Hi Andreia
>
> sorry, I don't understand. What do you mean when you say you want to "
> show the resulting Brodmann area (only 3 BA) volume in the inflated
> surface of my subjects". Do you mean just to show what portion of the
> surface is in each of 3 Brodmann areas? That you would do by loading the
> relevant labels, although you will probably want to threshold them
> differently (e.g. V1 you could threshold at .9 which is 90% and it would
> have about the surface area of an individual, while MT would need to be
> closer to .4 or .5). Or do you actually mean the volume of gray matter
> within each BA? If the latter, it's just 3 numbers/subject, so I would
> think you would want  a scatter plot or something, not a map on the
> surface.
>
> cheers
> Bruce
>
>
> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote:
>
>> Hi all,
>>
>> I'm sorry if these questions have already been covered here, but I've
>> looked into the archives and still can't do what I need (and since I'm
>> running out of time for this task I decided to post here):
>>
>> I'm using version 5.0.0.
>>
>> I want to show the resulting Brodmann area (only 3 BA) volume in the
>> inflated surface of my subjects to show the differences between
>> patients and controls (for visualization purpose only). I've managed
>> to overlay the volume in the curvature menu but this is for the entire
>> cortex and I can't show the values bar. How can I show the volume of
>> only 3 BAs and have the scale bar?
>>
>> Another question is, how is the volume of the BA calculated? Is i

Re: [Freesurfer] Fwd: Load Brodmann surface area into inflated surface

[_andreia_]

Hi Bruce,

I'm using freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0.
I will also be using FS 5.1 paralelly.

Thank you very much!!

Andreia


Citando Bruce Fischl :

> Hi Andreia
>
> I just modified label_area to allow the specification of a threshold  
> (with -t ) and a surface (with -s ), and to  
> use white by default. If you let us know what hardware/software  
> platform you are running on we can send you an updated binary
>
> cheers
> Bruce
> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote:
>
>> (sorry, here it is for the list again)
>>
>>
>>
>> - Mensagem encaminhada de Bruce Fischl  
>>  -
>>   Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT)
>> De: Bruce Fischl 
>> Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface
>>   Para: _andre...@sapo.pt
>>
>> Hi Andreia,
>>
>> can you cc the list so others can answer? I just took a look and
>> label_area is so old that is uses ?h.smoothwm without any ability to
>> change it. I think there are probably other tools around that will do
>> it, but someone else will know. If not I'll fix label_area to be less
>> obstinate.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks for the help! How do I know from which surface, i.e. pial or
>>> wm is the command label_area getting the value? I compared V1
>>> surface area given in the BA.stats and the one I get with the
>>> command, and the late is higher (V1 from BA.stats= 2081 and from
>>> label_area = 2592.272).
>>>
>>> Now, imagine the follwing: I have no differences in cortical
>>> thickness (CT) and surface area of this BA but the volume is
>>> different (with p values near 0.04...). Also, other BA shows no
>>> differences in CT neither in volume, but with differences showing up
>>> in the surface area (with lower p value here). Since the values for
>>> volume and surface are computed in different ways, can this account
>>> for these odd results?
>>>
>>> Thanks!
>>> Andreia
>>>
>>>
>>> Citando Bruce Fischl :
>>>
 Hi Andreia,

 yes, they will always shrink since the label contains every point that
 could possibly be in the BA, no matter how unlikely. I'll try to find time
 to automatically threshold the BAs so that they have the average area of
 the individual examples, but for now V2 is probably around .7 and  
 MT around
 .4 I think. And yes, I would use ?h.sulc as the background gray scale. The
 volume of the BAs would be computed using both surfaces, but the surface
 area can be from either one. I think we use the white by default, but you
 can use label_area to measure on whatever surface you want.

 cheers
 Bruce


 On Mon, 23 Apr 2012,
 _andre...@sapo.pt wrote:

> (forgot to do answer all, here it goes for the list too)
>
>
> Citando _andre...@sapo.pt:
>
>> Hi Bruce,
>>
>> The ideia is to show one control subject vs. one patient  
>> inflated surface
>> with BA surface (not volume, sorry) to show the difference
>> (reduced surface
>> area in one patient). Loading the relevant labels worked (I have the
>> statistics shown in bar graphs, the images are only for visualizing the
>> difference between controls and patients). When I threshold the  
>> labels in
>> the subject's inflated surface they shrink a lot, is this supposed to
>> happen?
>>
>> The BA are V1, V2 and MT. What is the thresghold for V2?
>>
>> And is it correct to load ?h.sulc in a gray scale to have the  
>> usual cortex
>> representation, or I should do it other way?
>>
>>
>> And getting back to my previous email:
>>
>> Another question is, how is the volume of the BA calculated? Is it
 from the surface-based stream?

 And, which surface area is the on in the output of the BA stats? Is it
 the pial or wm?
>>
>> Thanks,
>> Andreia
>>
>>
>> Citando Bruce Fischl :
>>
>>> Hi Andreia
>>>
>>> sorry, I don't understand. What do you mean when you say you want to "
>>> show the resulting Brodmann area (only 3 BA) volume in the inflated
>>> surface of my subjects". Do you mean just to show what portion of the
>>> surface is in each of 3 Brodmann areas? That you would do by  
>>> loading the
>>> relevant labels, although you will probably want to threshold them
>>> differently (e.g. V1 you could threshold at .9 which is 90%  
>>> and it would
>>> have about the surface area of an individual, while MT would need to be
>>> closer to .4 or .5). Or do you actually mean the volume of gray matter
>>> within each BA? If the latter, it's just 3 numbers/subject, so I would
>>> think you would want  a scatter plot or something, not a map on the
>>> surface.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 23 Apr 2012, _andre...@sapo.pt wrote:
>>>
>>>

Re: [Freesurfer] gzipRe: Fwd: Load Brodmann surface area into inflated surface

[_andreia_]

Thanks Bruce! Those are the main questions now (not only to V1, but  
also to the rest of the Brodmann areas). I really want to be sure  
where the measures come from. I want that the different measures (i.e.  
cortical thickness and area are really from the same region in the  
cortex), to know what should be exported to run the statistical  
analysis.

At some point the list email was not in Cc anymore... Here it goes to  
the list too.

Thank you so much for your help!

Andreia


Citando Bruce Fischl :

> where do the V1 stats in the stats dir come from? What binary and  
> what surface?
>
> On Wed, 16 May 2012, Douglas N Greve wrote:
>
>> sorry, what is the question?
>>
>> On 05/16/2012 11:23 AM, Bruce Fischl wrote:
>>> I'm not sure where the stats dir output comes from, Doug would  
>>> know. The others seem reasonable, and certainly the pial should be  
>>> bigger than the white. We also generate a couple of V1 labels, one  
>>> from the Hinds atlas and one from the Zilles labels I think,  
>>> although maybe the Hinds one isn't generated by default anymore.  
>>> Nick can answer that question.
>>>
>>> Also, please cc the list on these emails! You will get a faster  
>>> response time and the right people will be able to help you
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 May 2012, _andre...@sapo.pt wrote:
>>>
 Hi Bruce!

 Ok!

 In fact I've already tried to use 0 as threshold, here's what happens:

 surface area from
 - stats directory output: 2081
 - label_area -t 0 -s white rh S11 rh.V1: 2840.946
 - label_area -t 0 -s pial rh S11 rh.V1: 3509.024

 That's way too different. Using label_area  is given higher  
 values. Why? Could this have something to do with the  
 substitution of the label_area file? This would mean that at some  
 poit recon-all used the previous one to generate the output of  
 the stats directory?

 Since pial and white surfaces usually do not follow exactly the  
 same shape and, thus the same area (since there are different  
 thickness in between) , I'm antecipating reviwers questions of  
 things like "from what surface are you reporting the values?"



 Cheers,
 Andreia


 Citando Bruce Fischl :

> Hi Andreia
>
> did I say use 1.1? If I did, I'm sorry and take it back. 0 would  
> give you all the vertices in the label (this is the default).  
> 1.1 would give you an empty label since nothing would pass that  
> threshold.
>
> I wouldn't worry about thresholding the aparc boundaries, as  
> there we want a complete parcellation of the cortex, so if you  
> took it out of one parcel you would have to give it to another  
> (less likely) one.
>
> cheers
> Bruce
>
>
> On Wed, 16 May 2012, _andre...@sapo.pt wrote:
>
>> Sorry now I'm confused. I understood you said that I should try  
>> 1.1 as threshold. Anyway, this means that the values in the  
>> outputs from the stats directory do not take into account any  
>> threshold. Thus, the surface area given is from the bigger  
>> probable area no matter how unlikely all the points belong to  
>> it, correct? Could this be a problem when interpreting results  
>> using cortical thickness, surface area and/or volume of the  
>> studied regions?
>>
>> And concerning the aparc areas, is the ideia the same?
>>
>> I'm sorry to be insisting on this but I need to know what is  
>> the meaning of the values I'm using, principally because when  
>> discussing measures like these one must be carefull, as you  
>> know :)
>>
>> Thanks!!
>> Andreia
>>
>>
>> Citando Bruce Fischl :
>>
>>> Hi Andreia
>>>
>>> the threshold should be in [0 1], as the label->stat is a  
>>> fraction not a pct. You should be able to run it for multiple  
>>> subjects. Nick or Doug might have some suggestions about how  
>>> to create a table of values. You can probably get something  
>>> similar out of other binaries.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 May 2012, _andre...@sapo.pt wrote:
>>>
 Hi Bruce,

 So if label_area is not used by recon-all when I run it I'll  
 just use it to obtain the area from the surface I specify,  
 that's ok. Is it possible to use it to get these measures  
 from multiple subjects and areas (areas from the aparc file  
 also) at once (and maybe to create an output where they all  
 come together?). However it would be good if one could be  
 sure of the surface that is being used to stats output in  
 fact. In fact, I was trying to know that by using the  
 label_area, but I cannot find a coincident value because I  
 can't use a threshold higher than 1.

 The rh.V1.label file

[Freesurfer] Command line to get BA stats with the thresholds

[_andreia_]

Hi!

Is there a command line to obtain the BA values with the recommended  
thresholds from all subjects at once?

Thank you,
Andreia Pereira

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[Freesurfer] Fwd: Command line to get BA stats with the thresholds

[_andreia_]

Hi!

I'm reposting my question:


Is there a command line to obtain the BA values with the recommended  
thresholds (e.g. 0.9 for V1) from all subjects at once? At least for  
each area at once for all subjects?

Thank you,
Andreia Pereira



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[Freesurfer] mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hello list,

I'm trying to get aparc surface area from the pial surface in a table  
using aparcstats2table but I'm not being able to...

I've already created the file aparc_pial.stats inside the stats dir  
running the following command line from the subjects's label dir:

mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a  
./rh.aparc.annot -c ./aparc.ctab subjectname rh pial

And if I open the aparc_pial.stats file the surfaces are bigger then  
in aparc (white matter).

But when I try to get the table using:

aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial  
--meas area -t rh_aparc_surface_pial.txt

I get the message:

Number of subjects : 1
Building the table..
ERROR: cannot find  
/home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats
Use --skip flag if you want to continue in such cases

What's wrong?

Thank you,
Andreia


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Re: [Freesurfer] mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hi Louis,

It didn't work either. This is what shows up in the terminal after  
running mris_anatomical_stats:

mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a  
./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.aparc.annot.
reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
reading input surface  
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
reading input pial surface  
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
reading input white surface  
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally  
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ./aparc.ctab

table columns are:
 number of vertices
 total surface area (mm^2)
 total gray matter volume (mm^3)
 average cortical thickness +- standard deviation (mm)
 integrated rectified mean curvature
 integrated rectified Gaussian curvature
 folding index
 intrinsic curvature index
 structure name

  1272793   2092  2.485 0.342 0.141 0.042   24 2.4  
  bankssts
  1184957   2200  2.419 0.757 0.226 0.187  24811.5  
  caudalanteriorcingulate
  3222   2408   5307  2.324 0.512 0.136 0.040   58 4.8  
  caudalmiddlefrontal
  2468   1735   2917  1.798 0.388 0.150 0.064   54 5.2  cuneus
   504582   1801  3.807 0.663 0.256 0.084   24 2.0  
  entorhinal
  4892   3757   9658  2.696 0.715 0.183 0.073  16715.0  
  fusiform
  8153   6383  13887  2.315 0.543 0.160 0.049  17916.6  
  inferiorparietal
  4885   3695  10298  2.929 0.668 0.171 0.069  18714.8  
  inferiortemporal
  1470   1045   2169  2.137 0.673 0.200 0.129  154 8.8  
  isthmuscingulate
  6612   4848  10068  2.208 0.530 0.161 0.058  21715.6  
  lateraloccipital
  3665   2871   6467  2.380 0.684 0.186 0.067  12311.1  
  lateralorbitofrontal
  4593   3224   5598  1.811 0.528 0.170 0.072  16513.4  lingual
  2623   2020   4262  2.290 0.776 0.191 0.072  179 8.1  
  medialorbitofrontal
  4570   3991  10068  2.785 0.605 0.169 0.052  15410.0  
  middletemporal
  1041802   1923  2.621 0.705 0.161 0.058   20 2.4  
  parahippocampal
  2067   1415   2808  2.156 0.580 0.115 0.024   20 2.1  
  paracentral
  1534   1130   2779  2.551 0.445 0.149 0.042   29 2.5  
  parsopercularis
  1366   1265   2718  2.458 0.607 0.184 0.049   23 2.9  
  parsorbitalis
  2166   1826   3699  2.258 0.484 0.166 0.048   34 4.8  
  parstriangularis
  2637   1647   2528  1.563 0.436 0.137 0.043   47 4.7  
  pericalcarine
  6180   4524   7746  1.879 0.596 0.122 0.030   62 7.3  
  postcentral
  1694   1270   2783  2.265 0.721 0.188 0.088   64 7.6  
  posteriorcingulate
  7118   5162  11283  2.336 0.590 0.115 0.027   67 8.4  
  precentral
  5554   4071   8657  2.206 0.527 0.149 0.051  10812.8  
  precuneus
   975856   2003  2.660 0.591 0.167 0.063   27 2.8  
  rostralanteriorcingulate
  8524   6942  13736  2.121 0.581 0.163 0.047  16816.2  
  rostralmiddlefrontal
  9820   7927  17866  2.426 0.605 0.150 0.043  14416.4  
  superiorfrontal
  8910   6920  12666  1.952 0.561 0.134 0.033  10211.5  
  superiorparietal
  5164   4064   9880  2.602 0.579 0.141 0.041  129 8.5  
  superiortemporal
  4538   3307   6832  2.129 0.591 0.140 0.035   63 6.4  
  supramarginal
   395426864  2.488 0.541 0.199 0.0576 0.9  
  frontalpole
   612699   2018  3.610 0.559 0.213 0.073   17 2.2  
  temporalpole
   479330680  2.330 0.353 0.110 0.0243 0.5  
  transversetemporal
  3442   1950   6183  2.886 0.890 0.376 1.131  154   291.0  insula
[user@localhost label]$ aparcstats2table --hemi rh --subjects  
FERNANDORODRIGUES --parc aparcpial --meas area -t  
rh_FERNANDORODRIGUES.aparc.surface.pial.txt
Number of subjects : 1
Building the table..
ERROR: cannot find  
/home/user/visao/Freesurfer/FERNANDORODRIGUES/stats/rh.aparcpial.stats
Use --skip flag if you want to continue in such cases


Maybe is the mris_anatomical_stats that has something wrong? I've been  
using the command for Brodmann Areas and just tried to adapt it to  
aparc. For BA I've also had to run label2label and had to create a new  
BA.annot but that was because I had to get the thresholded BA values,  
I think this doesn't apply to aparc. From aparc I only want to get  
surfa

[Freesurfer] mris_preproc patch download

[_andreia_]

Hello list,

I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit  
for whole brain analysis.

The link
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation

takes me to
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc

where a script appears. I thought that it would take me to a download  
page of some type of file that I would use to substitute the  
mrs_preproc I have now.

How should I proceed? Copy and the paste the script text in my current  
mris_preproc (deleting what is now written) and then save and run  
qcache.

Or, since I already have FS 5.3 installed in a different location, can  
I simply copy and paste the 5.3 mris_preproc file replacing the 5.0 one?

I predict that both approaches are equivalent but I want to be  
completely sure that I'll be doing it in the right way.

Thanks,
Andreia
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Re: [Freesurfer] mris_preproc patch download

[_andreia_]

Hi Doug,

I had to "Save file as"... So, that was the download... Backup made  
and mris_preproc replaced by the new one.

Thank you!

Andreia


Quoting Douglas N Greve :

> download the file and copy it into $FREESURFER_HOME/bin and make it
> executable (make a backup first)
>
>
> On 03/27/2014 09:37 AM, _andre...@sapo.pt wrote:
>> Hello list,
>>
>> I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit
>> for whole brain analysis.
>>
>> The link
>> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation
>>
>> takes me to
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc
>>
>> where a script appears. I thought that it would take me to a download
>> page of some type of file that I would use to substitute the
>> mrs_preproc I have now.
>>
>> How should I proceed? Copy and the paste the script text in my current
>> mris_preproc (deleting what is now written) and then save and run
>> qcache.
>>
>> Or, since I already have FS 5.3 installed in a different location, can
>> I simply copy and paste the 5.3 mris_preproc file replacing the 5.0 one?
>>
>> I predict that both approaches are equivalent but I want to be
>> completely sure that I'll be doing it in the right way.
>>
>> Thanks,
>> Andreia
>> ___
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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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>
>
> 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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[Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hello all,

How do I get aparc stats (area) using the pial surface, please?

Thanks,
Andreia



- Mensagem encaminhada de _andre...@sapo.pt -
   Data: Thu, 27 Mar 2014 11:31:13 +
 De: _andre...@sapo.pt
Responder Para: Freesurfer support list 
Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and  
aparcstats2table
   Para: freesurfer@nmr.mgh.harvard.edu, vi...@nmr.mgh.harvard.edu

Hi Louis,

It didn't work either. This is what shows up in the terminal after
running mris_anatomical_stats:

mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.aparc.annot.
reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
reading input surface
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
reading input pial surface
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
reading input white surface
/home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
reading colortable from annotation file...
colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ./aparc.ctab

table columns are:
  number of vertices
  total surface area (mm^2)
  total gray matter volume (mm^3)
  average cortical thickness +- standard deviation (mm)
  integrated rectified mean curvature
  integrated rectified Gaussian curvature
  folding index
  intrinsic curvature index
  structure name

   1272793   2092  2.485 0.342 0.141 0.042   24 2.4
   bankssts
   1184957   2200  2.419 0.757 0.226 0.187  24811.5
   caudalanteriorcingulate
   3222   2408   5307  2.324 0.512 0.136 0.040   58 4.8
   caudalmiddlefrontal
   2468   1735   2917  1.798 0.388 0.150 0.064   54 5.2  cuneus
504582   1801  3.807 0.663 0.256 0.084   24 2.0
   entorhinal
   4892   3757   9658  2.696 0.715 0.183 0.073  16715.0
   fusiform
   8153   6383  13887  2.315 0.543 0.160 0.049  17916.6
   inferiorparietal
   4885   3695  10298  2.929 0.668 0.171 0.069  18714.8
   inferiortemporal
   1470   1045   2169  2.137 0.673 0.200 0.129  154 8.8
   isthmuscingulate
   6612   4848  10068  2.208 0.530 0.161 0.058  21715.6
   lateraloccipital
   3665   2871   6467  2.380 0.684 0.186 0.067  12311.1
   lateralorbitofrontal
   4593   3224   5598  1.811 0.528 0.170 0.072  165 
13.4  lingual
   2623   2020   4262  2.290 0.776 0.191 0.072  179 8.1
   medialorbitofrontal
   4570   3991  10068  2.785 0.605 0.169 0.052  15410.0
   middletemporal
   1041802   1923  2.621 0.705 0.161 0.058   20 2.4
   parahippocampal
   2067   1415   2808  2.156 0.580 0.115 0.024   20 2.1
   paracentral
   1534   1130   2779  2.551 0.445 0.149 0.042   29 2.5
   parsopercularis
   1366   1265   2718  2.458 0.607 0.184 0.049   23 2.9
   parsorbitalis
   2166   1826   3699  2.258 0.484 0.166 0.048   34 4.8
   parstriangularis
   2637   1647   2528  1.563 0.436 0.137 0.043   47 4.7
   pericalcarine
   6180   4524   7746  1.879 0.596 0.122 0.030   62 7.3
   postcentral
   1694   1270   2783  2.265 0.721 0.188 0.088   64 7.6
   posteriorcingulate
   7118   5162  11283  2.336 0.590 0.115 0.027   67 8.4
   precentral
   5554   4071   8657  2.206 0.527 0.149 0.051  10812.8
   precuneus
975856   2003  2.660 0.591 0.167 0.063   27 2.8
   rostralanteriorcingulate
   8524   6942  13736  2.121 0.581 0.163 0.047  16816.2
   rostralmiddlefrontal
   9820   7927  17866  2.426 0.605 0.150 0.043  14416.4
   superiorfrontal
   8910   6920  12666  1.952 0.561 0.134 0.033  10211.5
   superiorparietal
   5164   4064   9880  2.602 0.579 0.141 0.041  129 8.5
   superiortemporal
   4538   3307   6832  2.129 0.591 0.140 0.035   63 6.4
   supramarginal
395426864  2.488 0.541 0.199 0.0576 0.9
   frontalpole
612699   2018  3.610 0.559 0.213 0.073   17 2.2
   temporalpole
479330680  2.330 0.353 0.110 0.0243 0.5
   transversetemporal
   3442   1950   6183  2.886 0.890 0.376 1.131  154   291.0  insula
[user@localhost label]$ aparcstats2table --hemi rh --subjects
FERNANDORODRIGUES --parc aparcpial --meas area -t
rh_FERNANDORODRIGUES.aparc.surface.pial.txt
Number of subjects : 1
Building the table..
ERROR: cannot find
/home/user/visao/Freesurfer/FERNANDORODRIGUES/stats/

Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hi Doug,

Thank you very much! It did the trick!

However, I've noticed that the surface area obtained from the pial  
surface is bigger than the one obtained from white surface in 3 labels:

Example of a control subject:Bankssts(WM=1161; pial=1026),  
pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).

Example of a patient:Bankssts(WM=1096; pial=1076),  
pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).

This only happens in these 3 labels and in both hemispheres. Is this expected?


Andreia


Quoting Douglas N Greve :

> try this
> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
>
>
> On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
>> Hello all,
>>
>> How do I get aparc stats (area) using the pial surface, please?
>>
>> Thanks,
>> Andreia
>>
>>
>>
>> - Mensagem encaminhada de _andre...@sapo.pt -
>> Data: Thu, 27 Mar 2014 11:31:13 +
>>   De: _andre...@sapo.pt
>> Responder Para: Freesurfer support list 
>>  Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and
>> aparcstats2table
>> Para: freesurfer@nmr.mgh.harvard.edu, vi...@nmr.mgh.harvard.edu
>>
>> Hi Louis,
>>
>> It didn't work either. This is what shows up in the terminal after
>> running mris_anatomical_stats:
>>
>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
>> ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
>> INFO: assuming MGZ format for volumes.
>> computing statistics for each annotation in ./rh.aparc.annot.
>> reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
>> reading input surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
>> reading input pial surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
>> reading input white surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>> Saving annotation colortable ./aparc.ctab
>>
>> table columns are:
>>number of vertices
>>total surface area (mm^2)
>>total gray matter volume (mm^3)
>>average cortical thickness +- standard deviation (mm)
>>integrated rectified mean curvature
>>integrated rectified Gaussian curvature
>>folding index
>>intrinsic curvature index
>>structure name
>>
>> 1272793   2092  2.485 0.342 0.141 0.042   24 2.4
>> bankssts
>> 1184957   2200  2.419 0.757 0.226 0.187  24811.5
>> caudalanteriorcingulate
>> 3222   2408   5307  2.324 0.512 0.136 0.040   58 4.8
>> caudalmiddlefrontal
>> 2468   1735   2917  1.798 0.388 0.150 0.064   54 
>>  5.2  cuneus
>>  504582   1801  3.807 0.663 0.256 0.084   24 2.0
>> entorhinal
>> 4892   3757   9658  2.696 0.715 0.183 0.073  16715.0
>> fusiform
>> 8153   6383  13887  2.315 0.543 0.160 0.049  17916.6
>> inferiorparietal
>> 4885   3695  10298  2.929 0.668 0.171 0.069  18714.8
>> inferiortemporal
>> 1470   1045   2169  2.137 0.673 0.200 0.129  154 8.8
>> isthmuscingulate
>> 6612   4848  10068  2.208 0.530 0.161 0.058  21715.6
>> lateraloccipital
>> 3665   2871   6467  2.380 0.684 0.186 0.067  12311.1
>> lateralorbitofrontal
>> 4593   3224   5598  1.811 0.528 0.170 0.072  165
>> 13.4  lingual
>> 2623   2020   4262  2.290 0.776 0.191 0.072  179 8.1
>> medialorbitofrontal
>> 4570   3991  10068  2.785 0.605 0.169 0.052  15410.0
>> middletemporal
>> 1041802   1923  2.621 0.705 0.161 0.058   20 2.4
>> parahippocampal
>> 2067   1415   2808  2.156 0.580 0.115 0.024   20 2.1
>> paracentral
>> 1534   1130   2779  2.551 0.445 0.149 0.042   29 2.5
>> parsopercularis
>> 1366   1265   2718  2.458 0.607 0.184 0.049   23 2.9
>> parsorbitalis
>> 2166   1826   3699  2.258 0.484 0.166 0.048   34 4.8
>> parstriangularis
>> 2637   1647   2528  1.563 0.436 0.137 0.043   47 4.7
>> pericalcarine
>> 6180   4524   7746  1.879 0.596 0.122 0.030   62 7.3
>> postcentral
>> 1694   1270   2783  2.265 0.721 0.188 0.088   64 7.6
>> posteriorcingulate
>> 7118   5162  11283  2.336 0.590 0.115 0.027   67 8.4
>> precentral
>> 5554   4071   8657  2.206 0.527 0.149 0.051  10812.8
>> precuneus
>>  975856   2003  2.660 0.591  

[Freesurfer] Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hello,

What could be the reason to get bigger surface area from WM surface  
than from the pial surface in the 3 labels?

Thank you!
Andreia



- Mensagem encaminhada de _andre...@sapo.pt -
Data: Fri, 28 Mar 2014 17:43:43 +
  De: _andre...@sapo.pt
Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and  
aparcstats2table
Para: freesurfer@nmr.mgh.harvard.edu

Hi Doug,

Thank you very much! It did the trick!

However, I've noticed that the surface area obtained from the pial  
surface is bigger than the one obtained from white surface in 3 labels:

Example of a control subject:Bankssts(WM=1161; pial=1026),  
pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).

Example of a patient:Bankssts(WM=1096; pial=1076),  
pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).

This only happens in these 3 labels and in both hemispheres. Is this expected?


Andreia


Quoting Douglas N Greve :

> try this
> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
>
>
> On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
>> Hello all,
>>
>> How do I get aparc stats (area) using the pial surface, please?
>>
>> Thanks,
>> Andreia
>>
>>
>>
>> - Mensagem encaminhada de _andre...@sapo.pt -
>>Data: Thu, 27 Mar 2014 11:31:13 +
>>  De: _andre...@sapo.pt
>> Responder Para: Freesurfer support list 
>> Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and
>> aparcstats2table
>>Para: freesurfer@nmr.mgh.harvard.edu, vi...@nmr.mgh.harvard.edu
>>
>> Hi Louis,
>>
>> It didn't work either. This is what shows up in the terminal after
>> running mris_anatomical_stats:
>>
>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
>> ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
>> INFO: assuming MGZ format for volumes.
>> computing statistics for each annotation in ./rh.aparc.annot.
>> reading volume /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
>> reading input surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
>> reading input pial surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
>> reading input white surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>> Saving annotation colortable ./aparc.ctab
>>
>> table columns are:
>>   number of vertices
>>   total surface area (mm^2)
>>   total gray matter volume (mm^3)
>>   average cortical thickness +- standard deviation (mm)
>>   integrated rectified mean curvature
>>   integrated rectified Gaussian curvature
>>   folding index
>>   intrinsic curvature index
>>   structure name
>>
>>1272793   2092  2.485 0.342 0.141 0.042   24 2.4
>>bankssts
>>1184957   2200  2.419 0.757 0.226 0.187  24811.5
>>caudalanteriorcingulate
>>3222   2408   5307  2.324 0.512 0.136 0.040   58 4.8
>>caudalmiddlefrontal
>>2468   1735   2917  1.798 0.388 0.150 0.064   54  
>> 5.2  cuneus
>> 504582   1801  3.807 0.663 0.256 0.084   24 2.0
>>entorhinal
>>4892   3757   9658  2.696 0.715 0.183 0.073  16715.0
>>fusiform
>>8153   6383  13887  2.315 0.543 0.160 0.049  17916.6
>>inferiorparietal
>>4885   3695  10298  2.929 0.668 0.171 0.069  18714.8
>>inferiortemporal
>>1470   1045   2169  2.137 0.673 0.200 0.129  154 8.8
>>isthmuscingulate
>>6612   4848  10068  2.208 0.530 0.161 0.058  21715.6
>>lateraloccipital
>>3665   2871   6467  2.380 0.684 0.186 0.067  12311.1
>>lateralorbitofrontal
>>4593   3224   5598  1.811 0.528 0.170 0.072  165
>> 13.4  lingual
>>2623   2020   4262  2.290 0.776 0.191 0.072  179 8.1
>>medialorbitofrontal
>>4570   3991  10068  2.785 0.605 0.169 0.052  15410.0
>>middletemporal
>>1041802   1923  2.621 0.705 0.161 0.058   20 2.4
>>parahippocampal
>>2067   1415   2808  2.156 0.580 0.115 0.024   20 2.1
>>paracentral
>>1534   1130   2779  2.551 0.445 0.149 0.042   29 2.5
>>parsopercularis
>>1366   1265   2718  2.458 0.607 0.184 0.049   23 2.9
>>parsorbitalis
>>2166   1826   3699  2.258 0.484 0.166 0.048   34 4.8
>>parstriangularis
>>2637   1647   2528  1.563 0.436 0.137 0.043   47 4.7
>>pericalcarine
>>6180   4524   7746  1.879 0.596 0.122 0.030   62 7.3
>>

Re: [Freesurfer] Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hi,

Sorry, I mixed it up in text of the first email. The WM is bigger. The  
values of the example are correct.

Thanks!


Quoting Bruce Fischl :

> Hi Andreia,
>
> which one is bigger? In your first email you said pial (which should be)
> and in your second you said white matter
>
> cheers
> Bruce
>
> On Sun, 30 Mar 2014,
> _andre...@sapo.pt wrote:
>
>> Hello,
>>
>> What could be the reason to get bigger surface area from WM surface
>> than from the pial surface in the 3 labels?
>>
>> Thank you!
>> Andreia
>>
>>
>>
>> - Mensagem encaminhada de _andre...@sapo.pt -
>>Data: Fri, 28 Mar 2014 17:43:43 +
>>  De: _andre...@sapo.pt
>> Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and
>> aparcstats2table
>>Para: freesurfer@nmr.mgh.harvard.edu
>>
>> Hi Doug,
>>
>> Thank you very much! It did the trick!
>>
>> However, I've noticed that the surface area obtained from the pial
>> surface is bigger than the one obtained from white surface in 3 labels:
>>
>> Example of a control subject:Bankssts(WM=1161; pial=1026),
>> pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
>>
>> Example of a patient:Bankssts(WM=1096; pial=1076),
>> pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
>>
>> This only happens in these 3 labels and in both hemispheres. Is  
>> this expected?
>>
>>
>> Andreia
>>
>>
>> Quoting Douglas N Greve :
>>
>>> try this
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
>>> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
>>>
>>>
>>> On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
 Hello all,

 How do I get aparc stats (area) using the pial surface, please?

 Thanks,
 Andreia



 - Mensagem encaminhada de _andre...@sapo.pt -
Data: Thu, 27 Mar 2014 11:31:13 +
  De: _andre...@sapo.pt
 Responder Para: Freesurfer support list 
 Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and
 aparcstats2table
Para: freesurfer@nmr.mgh.harvard.edu, vi...@nmr.mgh.harvard.edu

 Hi Louis,

 It didn't work either. This is what shows up in the terminal after
 running mris_anatomical_stats:

 mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
 ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
 INFO: assuming MGZ format for volumes.
 computing statistics for each annotation in ./rh.aparc.annot.
 reading volume  
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
 reading input surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
 reading input pial surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
 reading input white surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
 Saving annotation colortable ./aparc.ctab

 table columns are:
   number of vertices
   total surface area (mm^2)
   total gray matter volume (mm^3)
   average cortical thickness +- standard deviation (mm)
   integrated rectified mean curvature
   integrated rectified Gaussian curvature
   folding index
   intrinsic curvature index
   structure name

1272793   2092  2.485 0.342 0.141 0.042   24 2.4
bankssts
1184957   2200  2.419 0.757 0.226 0.187  24811.5
caudalanteriorcingulate
3222   2408   5307  2.324 0.512 0.136 0.040   58 4.8
caudalmiddlefrontal
2468   1735   2917  1.798 0.388 0.150 0.064   54
 5.2  cuneus
 504582   1801  3.807 0.663 0.256 0.084   24 2.0
entorhinal
4892   3757   9658  2.696 0.715 0.183 0.073  16715.0
fusiform
8153   6383  13887  2.315 0.543 0.160 0.049  17916.6
inferiorparietal
4885   3695  10298  2.929 0.668 0.171 0.069  18714.8
inferiortemporal
1470   1045   2169  2.137 0.673 0.200 0.129  154 8.8
isthmuscingulate
6612   4848  10068  2.208 0.530 0.161 0.058  21715.6
lateraloccipital
3665   2871   6467  2.380 0.684 0.186 0.067  12311.1
lateralorbitofrontal
4593   3224   5598  1.811 0.528 0.170 0.072  165
 13.4  lingual
2623   2020   4262  2.290 0.776 0.191 0.072  179 8.1
medialorbitofrontal
4570   3991  10068  2.785 0.605 0.169 0.052  15410.0
middletemporal
1041802   1923  2.621 0.70

Re: [Freesurfer] Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

How do I overlay aparc labels in tkmedit? I can load Brodmann area  
labels, but not aparc.

Thanks!
Andreia


Quoting Bruce Fischl :

> and what do the surfaces look like in those regions? For the wm surface
> are to be larger it probably needs to be a lot less smooth
>
> On Sun, 30 Mar 2014, _andre...@sapo.pt wrote:
>
>> Hi,
>>
>> Sorry, I mixed it up in text of the first email. The WM is bigger. The
>> values of the example are correct.
>>
>> Thanks!
>>
>>
>> Quoting Bruce Fischl :
>>
>>> Hi Andreia,
>>>
>>> which one is bigger? In your first email you said pial (which should be)
>>> and in your second you said white matter
>>>
>>> cheers
>>> Bruce
>>>
>>> On Sun, 30 Mar 2014,
>>> _andre...@sapo.pt wrote:
>>>
 Hello,

 What could be the reason to get bigger surface area from WM surface
 than from the pial surface in the 3 labels?

 Thank you!
 Andreia



 - Mensagem encaminhada de _andre...@sapo.pt -
Data: Fri, 28 Mar 2014 17:43:43 +
  De: _andre...@sapo.pt
 Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and
 aparcstats2table
Para: freesurfer@nmr.mgh.harvard.edu

 Hi Doug,

 Thank you very much! It did the trick!

 However, I've noticed that the surface area obtained from the pial
 surface is bigger than the one obtained from white surface in 3 labels:

 Example of a control subject:Bankssts(WM=1161; pial=1026),
 pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).

 Example of a patient:Bankssts(WM=1096; pial=1076),
 pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).

 This only happens in these 3 labels and in both hemispheres. Is
 this expected?


 Andreia


 Quoting Douglas N Greve :

> try this
> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
>
>
> On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
>> Hello all,
>>
>> How do I get aparc stats (area) using the pial surface, please?
>>
>> Thanks,
>> Andreia
>>
>>
>>
>> - Mensagem encaminhada de _andre...@sapo.pt -
>>Data: Thu, 27 Mar 2014 11:31:13 +
>>  De: _andre...@sapo.pt
>> Responder Para: Freesurfer support list 
>> Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and
>> aparcstats2table
>>Para: freesurfer@nmr.mgh.harvard.edu,  
>> vi...@nmr.mgh.harvard.edu
>>
>> Hi Louis,
>>
>> It didn't work either. This is what shows up in the terminal after
>> running mris_anatomical_stats:
>>
>> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
>> ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
>> INFO: assuming MGZ format for volumes.
>> computing statistics for each annotation in ./rh.aparc.annot.
>> reading volume
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
>> reading input surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
>> reading input pial surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
>> reading input white surface
>> /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>> Saving annotation colortable ./aparc.ctab
>>
>> table columns are:
>>   number of vertices
>>   total surface area (mm^2)
>>   total gray matter volume (mm^3)
>>   average cortical thickness +- standard deviation (mm)
>>   integrated rectified mean curvature
>>   integrated rectified Gaussian curvature
>>   folding index
>>   intrinsic curvature index
>>   structure name
>>
>>1272793   2092  2.485 0.342 0.141 0.042   24 2.4
>>bankssts
>>1184957   2200  2.419 0.757 0.226 0.187  24811.5
>>caudalanteriorcingulate
>>3222   2408   5307  2.324 0.512 0.136 0.040   58 4.8
>>caudalmiddlefrontal
>>2468   1735   2917  1.798 0.388 0.150 0.064   54
>> 5.2  cuneus
>> 504582   1801  3.807 0.663 0.256 0.084   24 2.0
>>entorhinal
>>4892   3757   9658  2.696 0.715 0.183 0.073  16715.0
>>fusiform
>>8153   6383  13887  2.315 0.543 0.160 0.049  17916.6
>>inferiorparietal
>>4885   3695  10298  2.929 0.668 0.171 0.069  18714.8
>>inferiortemporal
>>1470   1045   2169  2.137 0.673

Re: [Freesurfer] Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

I cannot properly access my desktop PC today, tomorrow I'll give you  
feedback, However, with a corase inspection the surfaces look ok.

Thank you Bruce!

Andreia



Quoting Bruce Fischl :

> the easiest way is to just use the aparc+aseg.mgz
>
> cheers
> Bruce
> On Sun, 30 Mar 2014,
> _andre...@sapo.pt wrote:
>
>> How do I overlay aparc labels in tkmedit? I can load Brodmann area
>> labels, but not aparc.
>>
>> Thanks!
>> Andreia
>>
>>
>> Quoting Bruce Fischl :
>>
>>> and what do the surfaces look like in those regions? For the wm surface
>>> are to be larger it probably needs to be a lot less smooth
>>>
>>> On Sun, 30 Mar 2014, _andre...@sapo.pt wrote:
>>>
 Hi,

 Sorry, I mixed it up in text of the first email. The WM is bigger. The
 values of the example are correct.

 Thanks!


 Quoting Bruce Fischl :

> Hi Andreia,
>
> which one is bigger? In your first email you said pial (which should be)
> and in your second you said white matter
>
> cheers
> Bruce
>
> On Sun, 30 Mar 2014,
> _andre...@sapo.pt wrote:
>
>> Hello,
>>
>> What could be the reason to get bigger surface area from WM surface
>> than from the pial surface in the 3 labels?
>>
>> Thank you!
>> Andreia
>>
>>
>>
>> - Mensagem encaminhada de _andre...@sapo.pt -
>>Data: Fri, 28 Mar 2014 17:43:43 +
>>  De: _andre...@sapo.pt
>> Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and
>> aparcstats2table
>>Para: freesurfer@nmr.mgh.harvard.edu
>>
>> Hi Doug,
>>
>> Thank you very much! It did the trick!
>>
>> However, I've noticed that the surface area obtained from the pial
>> surface is bigger than the one obtained from white surface in 3 labels:
>>
>> Example of a control subject:Bankssts(WM=1161; pial=1026),
>> pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
>>
>> Example of a patient:Bankssts(WM=1096; pial=1076),
>> pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
>>
>> This only happens in these 3 labels and in both hemispheres. Is
>> this expected?
>>
>>
>> Andreia
>>
>>
>> Quoting Douglas N Greve :
>>
>>> try this
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
>>> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
>>>
>>>
>>> On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
 Hello all,

 How do I get aparc stats (area) using the pial surface, please?

 Thanks,
 Andreia



 - Mensagem encaminhada de _andre...@sapo.pt -
Data: Thu, 27 Mar 2014 11:31:13 +
  De: _andre...@sapo.pt
 Responder Para: Freesurfer support list  
 
 Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and
 aparcstats2table
Para: freesurfer@nmr.mgh.harvard.edu,
 vi...@nmr.mgh.harvard.edu

 Hi Louis,

 It didn't work either. This is what shows up in the terminal after
 running mris_anatomical_stats:

 mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
 ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
 INFO: assuming MGZ format for volumes.
 computing statistics for each annotation in ./rh.aparc.annot.
 reading volume
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
 reading input surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
 reading input pial surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
 reading input white surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.white...
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
 Saving annotation colortable ./aparc.ctab

 table columns are:
   number of vertices
   total surface area (mm^2)
   total gray matter volume (mm^3)
   average cortical thickness +- standard deviation (mm)
   integrated rectified mean curvature
   integrated rectified Gaussian curvature
   folding index
   intrinsic curvature index
   structure name

1272793   2092  2.485 0.342 0.141 0.042
 24 2.4
bankssts
1184957   2200  2.419 0.757 0.226 0.187   
 24811.5
caudalanteriorcingulate
3222   2408   5307  2.

[Freesurfer] Fwd: Fwd: Fwd: mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

- Mensagem encaminhada de _andre...@sapo.pt -
Data: Mon, 31 Mar 2014 14:45:00 +0100
Hello!

I'm reposting my email without attachments this time since it is not  
getting to the list if I have attachments.

Could you advice please?

Thank,
Andreia


- Mensagem encaminhada de _andre...@sapo.pt -
Data: Mon, 31 Mar 2014 13:22:14 +0100
  De: _andre...@sapo.pt
Assunto: Re: [Freesurfer] Fwd: Fwd: mris_anatomical_stats aparc pial  
and aparcstats2table
Para: freesurfer@nmr.mgh.harvard.edu

Hi Bruce,

The surfaces look pretty good along the 3 labels. Although it is hard  
to get the whole picture from one slice I've attached some images of 2  
labels (since my previous email was rejected due to excessive size).  
The surfaces look as accurate in the rest of the slices.

Should I do any different procedure?

Could this be due to the intersection of the labels along the grey  
matter that are not picking up exactly the same area in the white and  
pial surfaces??

Moreover, I've obtained the stats using aparcstats2table before  
running qcache with the new mris_preproc (I'm using 5.0), but as far  
as I'm aware the measures obtained from aparcstats2table are not  
affected by the mri_preproc bug, right?


Thanks,
Andreia



Quoting Bruce Fischl :

> the easiest way is to just use the aparc+aseg.mgz
>
> cheers
> Bruce
> On Sun, 30 Mar 2014,
> _andre...@sapo.pt wrote:
>
>> How do I overlay aparc labels in tkmedit? I can load Brodmann area
>> labels, but not aparc.
>>
>> Thanks!
>> Andreia
>>
>>
>> Quoting Bruce Fischl :
>>
>>> and what do the surfaces look like in those regions? For the wm surface
>>> are to be larger it probably needs to be a lot less smooth
>>>
>>> On Sun, 30 Mar 2014, _andre...@sapo.pt wrote:
>>>
 Hi,

 Sorry, I mixed it up in text of the first email. The WM is bigger. The
 values of the example are correct.

 Thanks!


 Quoting Bruce Fischl :

> Hi Andreia,
>
> which one is bigger? In your first email you said pial (which should be)
> and in your second you said white matter
>
> cheers
> Bruce
>
> On Sun, 30 Mar 2014,
> _andre...@sapo.pt wrote:
>
>> Hello,
>>
>> What could be the reason to get bigger surface area from WM surface
>> than from the pial surface in the 3 labels?
>>
>> Thank you!
>> Andreia
>>
>>
>>
>> - Mensagem encaminhada de _andre...@sapo.pt -
>>  Data: Fri, 28 Mar 2014 17:43:43 +
>>De: _andre...@sapo.pt
>> Assunto: Re: [Freesurfer] Fwd: mris_anatomical_stats aparc pial and
>> aparcstats2table
>>  Para: freesurfer@nmr.mgh.harvard.edu
>>
>> Hi Doug,
>>
>> Thank you very much! It did the trick!
>>
>> However, I've noticed that the surface area obtained from the pial
>> surface is bigger than the one obtained from white surface in 3 labels:
>>
>> Example of a control subject:Bankssts(WM=1161; pial=1026),
>> pericalcarine(WM=1614, pial=1412) and insula(WM=1876, pial=1756).
>>
>> Example of a patient:Bankssts(WM=1096; pial=1076),
>> pericalcarine(WM=1293, pial=1255) and insula(WM=2196, pial=2121).
>>
>> This only happens in these 3 labels and in both hemispheres. Is
>> this expected?
>>
>>
>> Andreia
>>
>>
>> Quoting Douglas N Greve :
>>
>>> try this
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c
>>> ../label/aparc.annot.ctab vrfp-oct11-anat lh pial
>>>
>>>
>>> On 03/28/2014 06:31 AM, _andre...@sapo.pt wrote:
 Hello all,

 How do I get aparc stats (area) using the pial surface, please?

 Thanks,
 Andreia



 - Mensagem encaminhada de _andre...@sapo.pt -
  Data: Thu, 27 Mar 2014 11:31:13 +
De: _andre...@sapo.pt
 Responder Para: Freesurfer support list  
 
   Assunto: Re: [Freesurfer] mris_anatomical_stats aparc pial and
 aparcstats2table
  Para: freesurfer@nmr.mgh.harvard.edu,
 vi...@nmr.mgh.harvard.edu

 Hi Louis,

 It didn't work either. This is what shows up in the terminal after
 running mris_anatomical_stats:

 mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
 ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
 INFO: assuming MGZ format for volumes.
 computing statistics for each annotation in ./rh.aparc.annot.
 reading volume
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/mri/wm.mgz...
 reading input surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pial...
 reading input pial surface
 /home/user/visao/Freesurfer//FERNANDORODRIGUES/surf/rh.pi

[Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hello all,

 I generated the lgi.stats file for all my subjects and in one of them I
got this warning:

 mris_anatomical_stats -a aparc.annot -t pial_lgi -f
SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
 computing statistics for each annotation in aparc.annot.
 using thickness file pial_lgi.
 reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz...
 reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
 reading input pial surface
/home/user/visao/Freesurfer//SUBJ/surf/lh.pial...
 reading input white surface
/home/user/visao/Freesurfer//SUBJ/surf/lh.white...
MRISREADANNOTATIONINTOARRAY: VERTEX INDEX OUT OF RANGE: 150843 I=007D324B,
IN_ARRAY_SIZE=150843
 ANNOT FILE: /HOME/USER/VISAO/FREESURFER//SUBJ/SURF/../LABEL/LH.APARC.ANNOT
 MRISreadAnnotationIntoArray: vertex index out of range: 150844 i=007D324B,
in_array_size=150843
     annot file:
/home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
 MRISreadAnnotationIntoArray: vertex index out of range: 150845 i=007D324B,
in_array_size=150843
     annot file:
/home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot

 (...)

 reading colortable from annotation file...
 colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
 structure is "bankssts"
 number of vertices                      = 1139
 total surface area                      = 795 mm^2
 total gray matter volume                = 2868 mm^3
 average cortical thickness              = 3.820 mm +- 0.158 mm
 average integrated rectified mean curvature     = 0.117
 average integrated rectified Gaussian curvature = 0.031
 folding index                           = 10
 intrinsic curvature index               = 1.3
 structure is "caudalanteriorcingulate"
 number of vertices                      = 812

 (...)

 Even thought there was the warning, everything seems to be fine with the
lgi values, should I be concerned about this or I may just ignore it?

 Thank you!

 Andreia
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Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hi Doug,

I tried to load the annotation and it gave an error. I look in the  
archives and I found someone with the same problem and the advice was  
to run:

recon-all -s  -sd  -make all

I did that and tried to run again mris_anatomical_stats as previously  
and still have this warning


subj/stats/lh.aparc_lgi.stats subj lh
computing statistics for each annotation in aparc.annot.
using thickness file pial_lgi.
reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial...
reading input white surface /home/user/visao/Freesurfer//subj/surf/lh.white...
MRISreadNewCurvature: incompatible vertex number in file  
/home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
No such file or directory
reading colortable from annotation file...
colortable with 36 entries read (originally  
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
structure is "bankssts"
number of vertices  = 1160
total surface area  = 813 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.116
average integrated rectified Gaussian curvature = 0.031
folding index   = 10
intrinsic curvature index   = 1.3
structure is "caudalanteriorcingulate"
number of vertices  = 810
total surface area  = 547 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.129
average integrated rectified Gaussian curvature = 0.034
folding index   =  9
intrinsic curvature index   = 1.2
structure is "caudalmiddlefrontal"
number of vertices  = 4752
total surface area  = 3134 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.123
average integrated rectified Gaussian curvature = 0.033
folding index   = 48
intrinsic curvature index   = 6.1
structure is "cuneus"
number of vertices  = 2701
total surface area  = 1667 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.164
average integrated rectified Gaussian curvature = 0.061
folding index   = 50
intrinsic curvature index   = 7.1

(...)


The LGI values are generated and they seem to be in the normal range  
as all the others... I would like to know if this problem invalidates  
all the other measures that I extracted (cortical thickness and  
surface area from aparc and Brodmann areas, aseg stats)

Andreia


Quoting Douglas N Greve :

> That probably means that the subject is out of synch. Try viewing the
> subject's surface tksurfer or freeview and load the annotation.
> doug
>
> On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
>>
>> Hello all,
>>
>> I generated the lgi.stats file for all my subjects and in one of them
>> I got this warning:
>>
>> mris_anatomical_stats -a aparc.annot -t pial_lgi -f
>> SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
>> computing statistics for each annotation in aparc.annot.
>> using thickness file pial_lgi.
>> reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz...
>> reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>> reading input pial surface
>> /home/user/visao/Freesurfer//SUBJ/surf/lh.pial...
>> reading input white surface
>> /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>> *MRISreadAnnotationIntoArray: vertex index out of range: 150843
>> i=007D324B, in_array_size=150843
>> annot file:
>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot*
>> MRISreadAnnotationIntoArray: vertex index out of range: 150844
>> i=007D324B, in_array_size=150843
>> annot file:
>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
>> MRISreadAnnotationIntoArray: vertex index out of range: 150845
>> i=007D324B, in_array_size=150843
>> annot file:
>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
>>
>> (...)
>>
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>> structure is "bankssts"
>> number of vertices  = 1139
>> total surface area  = 795 mm^2
>> total gray matter volume= 2868 mm^3
>> average cortical thickness  = 3.820 mm +- 0.158 mm
>> average integrated rectified mean curvature = 0.11

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hello,

Only after sending the email below I noticed that now the stats file  
generated give only 0,00 were the LGI values should be, even though  
they appear in the terminal.

How can I solve this issue? And, again, are all the measures (cortical  
thickness, surface area, aseg) invalidated? As well as qcache? In sum,  
should I run this subject all from scratch?

Thank you in advance,
Andreia Pereira


Quoting _andre...@sapo.pt:

> Hi Doug,
>
> I tried to load the annotation and it gave an error. I look in the
> archives and I found someone with the same problem and the advice was
> to run:
>
> recon-all -s  -sd  -make all
>
> I did that and tried to run again mris_anatomical_stats as previously
> and still have this warning
>
>
> subj/stats/lh.aparc_lgi.stats subj lh
> computing statistics for each annotation in aparc.annot.
> using thickness file pial_lgi.
> reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
> reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
> reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial...
> reading input white surface  
> /home/user/visao/Freesurfer//subj/surf/lh.white...
> MRISreadNewCurvature: incompatible vertex number in file
> /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
> No such file or directory
> reading colortable from annotation file...
> colortable with 36 entries read (originally
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> structure is "bankssts"
> number of vertices  = 1160
> total surface area  = 813 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.116
> average integrated rectified Gaussian curvature = 0.031
> folding index   = 10
> intrinsic curvature index   = 1.3
> structure is "caudalanteriorcingulate"
> number of vertices  = 810
> total surface area  = 547 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.129
> average integrated rectified Gaussian curvature = 0.034
> folding index   =  9
> intrinsic curvature index   = 1.2
> structure is "caudalmiddlefrontal"
> number of vertices  = 4752
> total surface area  = 3134 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.123
> average integrated rectified Gaussian curvature = 0.033
> folding index   = 48
> intrinsic curvature index   = 6.1
> structure is "cuneus"
> number of vertices  = 2701
> total surface area  = 1667 mm^2
> total gray matter volume=  0 mm^3
> average cortical thickness  = 0.000 mm +- 0.000 mm
> average integrated rectified mean curvature = 0.164
> average integrated rectified Gaussian curvature = 0.061
> folding index   = 50
> intrinsic curvature index   = 7.1
>
> (...)
>
>
> The LGI values are generated and they seem to be in the normal range
> as all the others... I would like to know if this problem invalidates
> all the other measures that I extracted (cortical thickness and
> surface area from aparc and Brodmann areas, aseg stats)
>
> Andreia
>
>
> Quoting Douglas N Greve :
>
>> That probably means that the subject is out of synch. Try viewing the
>> subject's surface tksurfer or freeview and load the annotation.
>> doug
>>
>> On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
>>>
>>> Hello all,
>>>
>>> I generated the lgi.stats file for all my subjects and in one of them
>>> I got this warning:
>>>
>>> mris_anatomical_stats -a aparc.annot -t pial_lgi -f
>>> SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
>>> computing statistics for each annotation in aparc.annot.
>>> using thickness file pial_lgi.
>>> reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz...
>>> reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>>> reading input pial surface
>>> /home/user/visao/Freesurfer//SUBJ/surf/lh.pial...
>>> reading input white surface
>>> /home/user/visao/Freesurfer//SUBJ/surf/lh.white...
>>> *MRISreadAnnotationIntoArray: vertex index out of range: 150843
>>> i=007D324B, in_array_size=150843
>>> annot file:
>>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot*
>>> MRISreadAnnotationIntoArray: vertex index out of range: 150844
>>> i=007D324B, in_array_size=150843
>>> annot file:
>>> /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot
>>> MRISreadAnnotationIntoArray: vertex index out of range: 150845
>>> i=007D324B, in_array_size=150843

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hello again,

Sorry for not waiting for your reply, but I realized that I get the  
same warning with another different subject when trying to get  
destrieux lgi and this happens only for the left hemisphere:

[user@localhost Freesurfer]# mris_anatomical_stats -a  
aparc.a2009s.annot -t pial_lgi -f subj/stats/lh.aparc.a2009s_lgi.stats  
subjs lh


computing statistics for each annotation in aparc.a2009s.annot.
using thickness file pial_lgi.
reading volume /home/user/visao/Freesurfer//subj/mri/wm.mgz...
reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
reading input pial surface /home/user/visao/Freesurfer//subj/surf/lh.pial...
reading input white surface /home/user/visao/Freesurfer//subj/surf/lh.white...
MRISreadAnnotationIntoArray: vertex index out of range: 120388  
i=0014C8B5, in_array_size=120388
 annot file:  
/home/user/visao/Freesurfer//subj/surf/../label/lh.aparc.a2009s.annot
MRISreadAnnotationIntoArray: vertex index out of range: 120389  
i=0014C8B5, in_array_size=120388
 annot file:  
/home/user/visao/Freesurfer//subj/surf/../label/lh.aparc.a2009s.annot
MRISreadAnnotationIntoArray: vertex index out of range: 120390  
i=0014C8B5, in_array_size=120388
 annot file:  
/home/user/visao/Freesurfer//subj/surf/../label/lh.aparc.a2009s.annot

(...)

With the first subject this happens only for Brodman areas, in both  
hemispheres.

The thing is that the lgi values look alright when I look at them  
among all the other subjects...

Any thoughts?

Thank you very much!




Quoting Marie Schaer :

> Hi Andreia,
>
> You probably have lGI values that correspond to earlier versions of  
> your surfaces (I.e. maybe you ran lGI first, then did corrections on  
> the surfaces and reprocessed them, but forgot to recalculate lGI for  
> this new surfaces).
>
> If you simply reprocess lGI now, that should solve the problem.
>
> If not let me know,
>
> Marie
>
>
> On May 16, 2014, at 1:08 PM, "_andre...@sapo.pt" <_andre...@sapo.pt> wrote:
>
>> Hello,
>>
>> Only after sending the email below I noticed that now the stats file
>> generated give only 0,00 were the LGI values should be, even though
>> they appear in the terminal.
>>
>> How can I solve this issue? And, again, are all the measures (cortical
>> thickness, surface area, aseg) invalidated? As well as qcache? In sum,
>> should I run this subject all from scratch?
>>
>> Thank you in advance,
>> Andreia Pereira
>>
>>
>> Quoting _andre...@sapo.pt:
>>
>>> Hi Doug,
>>>
>>> I tried to load the annotation and it gave an error. I look in the
>>> archives and I found someone with the same problem and the advice was
>>> to run:
>>>
>>> recon-all -s  -sd  -make all
>>>
>>> I did that and tried to run again mris_anatomical_stats as previously
>>> and still have this warning
>>>
>>>
>>> subj/stats/lh.aparc_lgi.stats subj lh
>>> computing statistics for each annotation in aparc.annot.
>>> using thickness file pial_lgi.
>>> reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
>>> reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
>>> reading input pial surface  
>>> /home/user/visao/Freesurfer//subj/surf/lh.pial...
>>> reading input white surface
>>> /home/user/visao/Freesurfer//subj/surf/lh.white...
>>> MRISreadNewCurvature: incompatible vertex number in file
>>> /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
>>> No such file or directory
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally
>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>>> structure is "bankssts"
>>> number of vertices  = 1160
>>> total surface area  = 813 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.116
>>> average integrated rectified Gaussian curvature = 0.031
>>> folding index   = 10
>>> intrinsic curvature index   = 1.3
>>> structure is "caudalanteriorcingulate"
>>> number of vertices  = 810
>>> total surface area  = 547 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.129
>>> average integrated rectified Gaussian curvature = 0.034
>>> folding index   =  9
>>> intrinsic curvature index   = 1.2
>>> structure is "caudalmiddlefrontal"
>>> number of vertices  = 4752
>>> total surface area  = 3134 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.123
>>> average integrated rectified Gaussian curvature = 0.033
>>> folding index   = 48
>>> intrinsi

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hi Doug,

I just ran that command on the first subject I referred and the output is:

> [user@localhost Freesurfer]$ vno_match_check subj lh
Checking subj/surf/lh.orig...
Checking subj/surf/lh.white...
Checking subj/surf/lh.pial...
Checking subj/surf/lh.inflated...
Checking subj/surf/lh.smoothwm...
Checking subj/surf/lh.sphere...
Checking subj/surf/lh.curv...
Checking subj/surf/lh.sulc...
Checking subj/surf/lh.area...
Checking subj/surf/lh.thickness...
Checking subj/label/lh.aparc.annot...
Checking subj/label/lh.aparc.a2009s.annot...
Pass: all surfaces and surface data for subject subj have the same  
number of vertices.

Thank you!

Andreia


Quoting Douglas N Greve :

> I think it is still out of synch. Try running
>
> vno_match_check subject lh
>
> doug

>
>
> On 05/16/2014 01:06 PM, _andre...@sapo.pt wrote:
>> Hello,
>>
>> Only after sending the email below I noticed that now the stats  
>> file generated give only 0,00 were the LGI values should be, even  
>> though they appear in the terminal.
>>
>> How can I solve this issue? And, again, are all the measures  
>> (cortical thickness, surface area, aseg) invalidated? As well as  
>> qcache? In sum, should I run this subject all from scratch?
>>
>> Thank you in advance,
>> Andreia Pereira
>>
>>
>> Quoting _andre...@sapo.pt:
>>
>>> Hi Doug,
>>>
>>> I tried to load the annotation and it gave an error. I look in the
>>> archives and I found someone with the same problem and the advice was
>>> to run:
>>>
>>> recon-all -s  -sd  -make all
>>>
>>> I did that and tried to run again mris_anatomical_stats as previously
>>> and still have this warning
>>>
>>>
>>> subj/stats/lh.aparc_lgi.stats subj lh
>>> computing statistics for each annotation in aparc.annot.
>>> using thickness file pial_lgi.
>>> reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
>>> reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
>>> reading input pial surface  
>>> /home/user/visao/Freesurfer//subj/surf/lh.pial...
>>> reading input white surface  
>>> /home/user/visao/Freesurfer//subj/surf/lh.white...
>>> MRISreadNewCurvature: incompatible vertex number in file
>>> /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
>>> No such file or directory
>>> reading colortable from annotation file...
>>> colortable with 36 entries read (originally
>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>>>  structure is  
>>> "bankssts"
>>> number of vertices  = 1160
>>> total surface area  = 813 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.116
>>> average integrated rectified Gaussian curvature = 0.031
>>> folding index   = 10
>>> intrinsic curvature index   = 1.3
>>> structure is "caudalanteriorcingulate"
>>> number of vertices  = 810
>>> total surface area  = 547 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.129
>>> average integrated rectified Gaussian curvature = 0.034
>>> folding index   =  9
>>> intrinsic curvature index   = 1.2
>>> structure is "caudalmiddlefrontal"
>>> number of vertices  = 4752
>>> total surface area  = 3134 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.123
>>> average integrated rectified Gaussian curvature = 0.033
>>> folding index   = 48
>>> intrinsic curvature index   = 6.1
>>> structure is "cuneus"
>>> number of vertices  = 2701
>>> total surface area  = 1667 mm^2
>>> total gray matter volume=  0 mm^3
>>> average cortical thickness  = 0.000 mm +- 0.000 mm
>>> average integrated rectified mean curvature = 0.164
>>> average integrated rectified Gaussian curvature = 0.061
>>> folding index   = 50
>>> intrinsic curvature index   = 7.1
>>>
>>> (...)
>>>
>>>
>>> The LGI values are generated and they seem to be in the normal range
>>> as all the others... I would like to know if this problem invalidates
>>> all the other measures that I extracted (cortical thickness and
>>> surface area from aparc and Brodmann areas, aseg stats)
>>>
>>> Andreia
>>>
>>>
>>> Quoting Douglas N Greve :
>>>
 That probably means that the subject is out of synch. Try viewing the
 subject's surface tksurfer or freeview and load the annotation.
 doug

 On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
>
> Hello all,
>
> I generated the lgi.stats file for all my su

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Sorry for all the emails..

Now I ran that same command on the second subject in which I only  
detected a problem for the left hemisphere when trying to get  
Destrieux lgi, and got this error but for both hemispheres:

ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere  
has 121312 vertices

Is there a way to check this in all subjects at once?

Does this invalidate all the measures I extracted and qcache?

Andreia


Quoting _andre...@sapo.pt:

> Hi Doug,
>
> I just ran that command on the first subject I referred and the output is:
>
>> [user@localhost Freesurfer]$ vno_match_check subj lh
> Checking subj/surf/lh.orig...
> Checking subj/surf/lh.white...
> Checking subj/surf/lh.pial...
> Checking subj/surf/lh.inflated...
> Checking subj/surf/lh.smoothwm...
> Checking subj/surf/lh.sphere...
> Checking subj/surf/lh.curv...
> Checking subj/surf/lh.sulc...
> Checking subj/surf/lh.area...
> Checking subj/surf/lh.thickness...
> Checking subj/label/lh.aparc.annot...
> Checking subj/label/lh.aparc.a2009s.annot...
> Pass: all surfaces and surface data for subject subj have the same
> number of vertices.
>
> Thank you!
>
> Andreia
>
>
> Quoting Douglas N Greve :
>
>> I think it is still out of synch. Try running
>>
>> vno_match_check subject lh
>>
>> doug
>
>>
>>
>> On 05/16/2014 01:06 PM, _andre...@sapo.pt wrote:
>>> Hello,
>>>
>>> Only after sending the email below I noticed that now the stats
>>> file generated give only 0,00 were the LGI values should be, even
>>> though they appear in the terminal.
>>>
>>> How can I solve this issue? And, again, are all the measures
>>> (cortical thickness, surface area, aseg) invalidated? As well as
>>> qcache? In sum, should I run this subject all from scratch?
>>>
>>> Thank you in advance,
>>> Andreia Pereira
>>>
>>>
>>> Quoting _andre...@sapo.pt:
>>>
 Hi Doug,

 I tried to load the annotation and it gave an error. I look in the
 archives and I found someone with the same problem and the advice was
 to run:

 recon-all -s  -sd  -make all

 I did that and tried to run again mris_anatomical_stats as previously
 and still have this warning


 subj/stats/lh.aparc_lgi.stats subj lh
 computing statistics for each annotation in aparc.annot.
 using thickness file pial_lgi.
 reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
 reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
 reading input pial surface
 /home/user/visao/Freesurfer//subj/surf/lh.pial...
 reading input white surface
 /home/user/visao/Freesurfer//subj/surf/lh.white...
 MRISreadNewCurvature: incompatible vertex number in file
 /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
 No such file or directory
 reading colortable from annotation file...
 colortable with 36 entries read (originally
 /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
  structure  
 is
 "bankssts"
 number of vertices  = 1160
 total surface area  = 813 mm^2
 total gray matter volume=  0 mm^3
 average cortical thickness  = 0.000 mm +- 0.000 mm
 average integrated rectified mean curvature = 0.116
 average integrated rectified Gaussian curvature = 0.031
 folding index   = 10
 intrinsic curvature index   = 1.3
 structure is "caudalanteriorcingulate"
 number of vertices  = 810
 total surface area  = 547 mm^2
 total gray matter volume=  0 mm^3
 average cortical thickness  = 0.000 mm +- 0.000 mm
 average integrated rectified mean curvature = 0.129
 average integrated rectified Gaussian curvature = 0.034
 folding index   =  9
 intrinsic curvature index   = 1.2
 structure is "caudalmiddlefrontal"
 number of vertices  = 4752
 total surface area  = 3134 mm^2
 total gray matter volume=  0 mm^3
 average cortical thickness  = 0.000 mm +- 0.000 mm
 average integrated rectified mean curvature = 0.123
 average integrated rectified Gaussian curvature = 0.033
 folding index   = 48
 intrinsic curvature index   = 6.1
 structure is "cuneus"
 number of vertices  = 2701
 total surface area  = 1667 mm^2
 total gray matter volume=  0 mm^3
 average cortical thickness  = 0.000 mm +- 0.000 mm
 average integrated rectified mean curvature = 0.164
 average integrated rectified Gaussian curvature = 0.061
 folding index   = 50
 intrinsic curvature index   = 7.1

 (...)


 The LGI values are gen

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hi Doug,

That's really bad news. So I'll check all my subjects to track the  
ones who give the error. Then I'll have to run each one from scratch?

I don't quite understand what went wrong with only a few subjects  
since I did (as far as I'm aware) everything in the same way for all  
of them. And what worries me the most now is that I only realized this  
because I wanted to extract the lgi values for the BA.thresh and the  
Destrieux atlas. If I stopped at just getting the thickness, the  
surface area and running qcahe as I have been doing for a while I  
wouldn't have noticed any problem.

So, the hard question again: will I need to run the ones that give  
this error from scratch or is there any other solution?

Thank you,
Andreia


Quoting Douglas N Greve :

> On 05/19/2014 02:32 PM, _andre...@sapo.pt wrote:
>> Sorry for all the emails..
>>
>> Now I ran that same command on the second subject in which I only
>> detected a problem for the left hemisphere when trying to get
>> Destrieux lgi, and got this error but for both hemispheres:
>>
>> ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere
>> has 121312 vertices
>>
>> Is there a way to check this in all subjects at once?
> No, but you could write a little shell script to do it.
>>
>> Does this invalidate all the measures I extracted and qcache?
> Yes, I think so
>
>>
>> Andreia
>>
>>
>> Quoting _andre...@sapo.pt:
>>
>>> Hi Doug,
>>>
>>> I just ran that command on the first subject I referred and the output is:
>>>
 [user@localhost Freesurfer]$ vno_match_check subj lh
>>> Checking subj/surf/lh.orig...
>>> Checking subj/surf/lh.white...
>>> Checking subj/surf/lh.pial...
>>> Checking subj/surf/lh.inflated...
>>> Checking subj/surf/lh.smoothwm...
>>> Checking subj/surf/lh.sphere...
>>> Checking subj/surf/lh.curv...
>>> Checking subj/surf/lh.sulc...
>>> Checking subj/surf/lh.area...
>>> Checking subj/surf/lh.thickness...
>>> Checking subj/label/lh.aparc.annot...
>>> Checking subj/label/lh.aparc.a2009s.annot...
>>> Pass: all surfaces and surface data for subject subj have the same
>>> number of vertices.
>>>
>>> Thank you!
>>>
>>> Andreia
>>>
>>>
>>> Quoting Douglas N Greve :
>>>
 I think it is still out of synch. Try running

 vno_match_check subject lh

 doug

 On 05/16/2014 01:06 PM, _andre...@sapo.pt wrote:
> Hello,
>
> Only after sending the email below I noticed that now the stats
> file generated give only 0,00 were the LGI values should be, even
> though they appear in the terminal.
>
> How can I solve this issue? And, again, are all the measures
> (cortical thickness, surface area, aseg) invalidated? As well as
> qcache? In sum, should I run this subject all from scratch?
>
> Thank you in advance,
> Andreia Pereira
>
>
> Quoting _andre...@sapo.pt:
>
>> Hi Doug,
>>
>> I tried to load the annotation and it gave an error. I look in the
>> archives and I found someone with the same problem and the advice was
>> to run:
>>
>> recon-all -s  -sd  -make all
>>
>> I did that and tried to run again mris_anatomical_stats as previously
>> and still have this warning
>>
>>
>> subj/stats/lh.aparc_lgi.stats subj lh
>> computing statistics for each annotation in aparc.annot.
>> using thickness file pial_lgi.
>> reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
>> reading input surface /home/user/visao/Freesurfer//subj/surf/lh.white...
>> reading input pial surface
>> /home/user/visao/Freesurfer//subj/surf/lh.pial...
>> reading input white surface
>> /home/user/visao/Freesurfer//subj/surf/lh.white...
>> MRISreadNewCurvature: incompatible vertex number in file
>> /home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
>> No such file or directory
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally
>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
>>   
>> structure
>> is
>> "bankssts"
>> number of vertices  = 1160
>> total surface area  = 813 mm^2
>> total gray matter volume=  0 mm^3
>> average cortical thickness  = 0.000 mm +- 0.000 mm
>> average integrated rectified mean curvature = 0.116
>> average integrated rectified Gaussian curvature = 0.031
>> folding index   = 10
>> intrinsic curvature index   = 1.3
>> structure is "caudalanteriorcingulate"
>> number of vertices  = 810
>> total surface area  = 547 mm^2
>> total gray matter volume=  0 mm^3
>> average cortical thickness  = 0.000 mm +- 0.000 mm
>> average integrated rectified mean curvature = 0.129
>> average integrated rectified Gaussian curvature 

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

I just ran vno_match_check for all my subjects and the scenario is:

S_UBJ1_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
subj1/stats/lh.BA_lgi.stats subj1 lh

 the warning appears: MRISREADANNOTATIONINTOARRAY: vertex index out of
range: 120389 i=0014C8B5, in_array_size=120388

ONLY FOR BRODMAN areas, not for Desikan-killiany nor Destrieux

 vno_match_check: NO PROBLEM DETECTED!

_SUBJ2_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
subj1/stats/lh.BA_lgi.stats subj1 lh

 the warning appears for all parcellation (BA, aparc, aparc.a2009s), but
ONLY FOR THE LEFH HEMISPHERE, everything's fine with the right.

 vno_match_check: ERRO FOR BOTH HEMISPHERES

 

These are conflicting information.

Any thoughts?

I cannot be sure of what to do...

Andreia

Quoting _andre...@sapo.pt:


Hi Doug,

That's really bad news. So I'll check all my subjects to track the
ones who give the error. Then I'll have to run each one from scratch?

I don't quite understand what went wrong with only a few subjects
since I did (as far as I'm aware) everything in the same way for all
of them. And what worries me the most now is that I only realized
this because I wanted to extract the lgi values for the BA.thresh and
the Destrieux atlas. If I stopped at just getting the thickness, the
surface area and running qcahe as I have been doing for a while I
wouldn't have noticed any problem.

So, the hard question again: will I need to run the ones that give
this error from scratch or is there any other solution?

Thank you,
Andreia


Quoting Douglas N Greve :


On 05/19/2014 02:32 PM, _andreia_@sapo.ptwrote:

Sorry for all the emails..

Now I ran that same command on the second subject in which I only
detected a problem for the left hemisphere when trying to get
Destrieux lgi, and got this error but for both hemispheres:

ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere
has 121312 vertices

Is there a way to check this in all subjects at once?

No, but you could write a little shell script to do it.


Does this invalidate all the measures I extracted and qcache?

Yes, I think so



Andreia


Quoting _andre...@sapo.pt:


Hi Doug,

I just ran that command on the first subject I referred and the output

is:



[user@localhostFreesurfer]$ vno_match_check subj lh

Checking subj/surf/lh.orig...
Checking subj/surf/lh.white...
Checking subj/surf/lh.pial...
Checking subj/surf/lh.inflated...
Checking subj/surf/lh.smoothwm...
Checking subj/surf/lh.sphere...
Checking subj/surf/lh.curv...
Checking subj/surf/lh.sulc...
Checking subj/surf/lh.area...
Checking subj/surf/lh.thickness...
Checking subj/label/lh.aparc.annot...
Checking subj/label/lh.aparc.a2009s.annot...
Pass: all surfaces and surface data for subject subj have the same
number of vertices.

Thank you!

Andreia


Quoting Douglas N Greve :


I think it is still out of synch. Try running

vno_match_check subject lh

doug

On 05/16/2014 01:06 PM, _andreia_@sapo.ptwrote:

Hello,

Only after sending the email below I noticed that now the stats
file generated give only 0,00 were the LGI values should be, even
though they appear in the terminal.

How can I solve this issue? And, again, are all the measures
(cortical thickness, surface area, aseg) invalidated? As well as
qcache? In sum, should I run this subject all from scratch?

Thank you in advance,
Andreia Pereira


Quoting _andre...@sapo.pt:


Hi Doug,

I tried to load the annotation and it gave an error. I look in the
archives and I found someone with the same problem and the advice

was

to run:

recon-all -s  -sd  -make all

I did that and tried to run again mris_anatomical_stats as

previously

and still have this warning


subj/stats/lh.aparc_lgi.stats subj lh
computing statistics for each annotation in aparc.annot.
using thickness file pial_lgi.
reading volume /home/user/visao/Freesurfer//sub/mri/wm.mgz...
reading input surface
/home/user/visao/Freesurfer//subj/surf/lh.white...
reading input pial surface
/home/user/visao/Freesurfer//subj/surf/lh.pial...
reading input white surface
/home/user/visao/Freesurfer//subj/surf/lh.white...
MRISreadNewCurvature: incompatible vertex number in file
/home/user/visao/Freesurfer//subj/surf/lh.pial_lgi
No such file or directory
reading colortable from annotation file...
colortable with 36 entries read (originally


/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

structure
is
"bankssts"
number of vertices                      = 1160
total surface area                      = 813 mm^2
total gray matter volume                =  0 mm^3
average cortical thickness              = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature     = 0.116
average integrated rectified Gaussian curvature = 0.031
folding index                           = 10
intrinsic curvature index               = 1.3
structure is "caudalanteriorcingulate"
number of vertices                      = 810
total 

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

BA.annot I think that was created before any problem because I had no  
error (at least I didn't see any)  untill I extracted aparcstats2table  
of those values. But I just checked my notes and these two subjects  
were the only ones that gave aberrantly high LGI values when running  
-localGI. I then went to the mailing list and I saw posts with this  
error and it was suggested to run recon-all -autorecon2-wm -randomness  
which at that time solved the error and lgi computation went untill  
the end without any error.

I have no error notes for qcache that was ran previously.

Could I solve this issue running recon-all -autorecon2-cp/wm  
-autorecon3 (depending on the manual edits) and running again only the  
commands lgi and the ones to get pial surface area from Destrieux  
(since this was the only one I ran after the lgi error)? Or would it  
be safer to just run all commands to get BA thresholded, pial surface  
from Desikan-Killiany and Destrieux and all the necessary ones to get  
the stats?

Thank you very much for your help!

Andreia


Quoting Douglas N Greve :

> On 05/19/2014 04:10 PM, _andre...@sapo.pt wrote:
>>
>> I just ran vno_match_check for all my subjects and the scenario is:
>>
>> *S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f  
>> subj1/stats/lh.BA_lgi.stats subj1 lh
>>
>> the warning appears: *MRISreadAnnotationIntoArray*: vertex index  
>> out of range: 120389 i=0014C8B5, in_array_size=120388
>>
>> *Only for Brodman* areas, not for Desikan-killiany nor Destrieux
>>
>> vno_match_check: *no problem detected*!
>>
> vno_match_check was not checking the BA annot. I've fixed this and  
> put a new version here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/vno_match_check
>>
>>
>>
>>
>> _*Subj2*_: mris_anatomical_stats -a BA.annot -t pial_lgi -f  
>> subj1/stats/lh.BA_lgi.stats subj1 lh
>>
>> the warning appears for all parcellation (BA, aparc, aparc.a2009s),  
>> but *only for the lefh hemisphere*, everything's fine with the right.
>>
>> vno_match_check: *erro for BOTH hemispheres*
>>
> Is it the the case that pial_lgi and BA.annot were created before  
> the subject became out of synch?
> doug
>>
>>
>> These are conflicting information.
>>
>> Any thoughts?
>>
>> I cannot be sure of what to do...
>>
>> Andreia
>>
>>
>>
>>
>> Quoting _andre...@sapo.pt :
>>
>>> Hi Doug,
>>>
>>> That's really bad news. So I'll check all my subjects to track the
>>> ones who give the error. Then I'll have to run each one from scratch?
>>>
>>> I don't quite understand what went wrong with only a few subjects
>>> since I did (as far as I'm aware) everything in the same way for all
>>> of them. And what worries me the most now is that I only realized
>>> this because I wanted to extract the lgi values for the BA.thresh and
>>> the Destrieux atlas. If I stopped at just getting the thickness, the
>>> surface area and running qcahe as I have been doing for a while I
>>> wouldn't have noticed any problem.
>>>
>>> So, the hard question again: will I need to run the ones that give
>>> this error from scratch or is there any other solution?
>>>
>>> Thank you,
>>> Andreia
>>>
>>>
>>> Quoting Douglas N Greve >> >:
>>>
 On 05/19/2014 02:32 PM, _andre...@sapo.pt  
  wrote:
> Sorry for all the emails..
>
> Now I ran that same command on the second subject in which I only
> detected a problem for the left hemisphere when trying to get
> Destrieux lgi, and got this error but for both hemispheres:
>
> ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere
> has 121312 vertices
>
> Is there a way to check this in all subjects at once?
 No, but you could write a little shell script to do it.
>
> Does this invalidate all the measures I extracted and qcache?
 Yes, I think so

>
> Andreia
>
>
> Quoting _andre...@sapo.pt :
>
>> Hi Doug,
>>
>> I just ran that command on the first subject I referred and the  
>> output is:
>>
>>> [user@localhost  Freesurfer]$  
>>> vno_match_check subj lh
>> Checking subj/surf/lh.orig...
>> Checking subj/surf/lh.white...
>> Checking subj/surf/lh.pial...
>> Checking subj/surf/lh.inflated...
>> Checking subj/surf/lh.smoothwm...
>> Checking subj/surf/lh.sphere...
>> Checking subj/surf/lh.curv...
>> Checking subj/surf/lh.sulc...
>> Checking subj/surf/lh.area...
>> Checking subj/surf/lh.thickness...
>> Checking subj/label/lh.aparc.annot...
>> Checking subj/label/lh.aparc.a2009s.annot...
>> Pass: all surfaces and surface data for subject subj have the same
>> number of vertices.
>>
>> Thank you!
>>
>> Andreia
>>
>>
>> Quoting Douglas N Greve > >:
>>
>>> I think it is still out of synch

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hi Marie,

Thanks for the input! Actually, from the recon-all log I can see that  
autorecon3 was caled in the terminal, and comparing it to a subject  
without any error they look the same to me. Also, qcache gave no error.

Anyway, I'll rerun -autorecon3 for these 2 subjects and all the  
commands to get the specific stats (BA.thresholed, pial area from the  
3 parcellations, aparc, aparc.a2009s and BA) as well as qcache.

Andreia


Quoting Marie Schaer :

> Hi Andreia,
>
> Then I would guess that your error comes from the fact that you  
> didn't rerun the autorecon3 at that stage for these 2 subjects. As  
> the randomness flag changes the number of vertices when recreating  
> the surfaces, that explains the error. So for your subjects, just  
> rerun autorecon3 (and qcache and mris_anatomical_stats), and you  
> should be fine.  But if I were you I would then carefully check for  
> all my subjects that registration (i.e. autorecon3) was processed  
> after autorecon2, and then qcache / mris_anatomical_stats after  
> autorecon3 (my understanding is that without the randomness flag  
> that kind of errors can be more difficult to trace back as the  
> number of vertices remain the same).
>
> Best,
>
> Marie
>
> On May 19, 2014, at 3:55 PM, <_andre...@sapo.pt>
>  wrote:
>
>> BA.annot I think that was created before any problem because I had no
>> error (at least I didn't see any)  untill I extracted aparcstats2table
>> of those values. But I just checked my notes and these two subjects
>> were the only ones that gave aberrantly high LGI values when running
>> -localGI. I then went to the mailing list and I saw posts with this
>> error and it was suggested to run recon-all -autorecon2-wm -randomness
>> which at that time solved the error and lgi computation went untill
>> the end without any error.
>>
>> I have no error notes for qcache that was ran previously.
>>
>> Could I solve this issue running recon-all -autorecon2-cp/wm
>> -autorecon3 (depending on the manual edits) and running again only the
>> commands lgi and the ones to get pial surface area from Destrieux
>> (since this was the only one I ran after the lgi error)? Or would it
>> be safer to just run all commands to get BA thresholded, pial surface
>> from Desikan-Killiany and Destrieux and all the necessary ones to get
>> the stats?
>>
>> Thank you very much for your help!
>>
>> Andreia
>>
>>
>> Quoting Douglas N Greve :
>>
>>> On 05/19/2014 04:10 PM, _andre...@sapo.pt wrote:

 I just ran vno_match_check for all my subjects and the scenario is:

 *S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f
 subj1/stats/lh.BA_lgi.stats subj1 lh

 the warning appears: *MRISreadAnnotationIntoArray*: vertex index
 out of range: 120389 i=0014C8B5, in_array_size=120388

 *Only for Brodman* areas, not for Desikan-killiany nor Destrieux

 vno_match_check: *no problem detected*!

>>> vno_match_check was not checking the BA annot. I've fixed this and
>>> put a new version here:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/vno_match_check




 _*Subj2*_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
 subj1/stats/lh.BA_lgi.stats subj1 lh

 the warning appears for all parcellation (BA, aparc, aparc.a2009s),
 but *only for the lefh hemisphere*, everything's fine with the right.

 vno_match_check: *erro for BOTH hemispheres*

>>> Is it the the case that pial_lgi and BA.annot were created before
>>> the subject became out of synch?
>>> doug


 These are conflicting information.

 Any thoughts?

 I cannot be sure of what to do...

 Andreia




 Quoting _andre...@sapo.pt :

> Hi Doug,
>
> That's really bad news. So I'll check all my subjects to track the
> ones who give the error. Then I'll have to run each one from scratch?
>
> I don't quite understand what went wrong with only a few subjects
> since I did (as far as I'm aware) everything in the same way for all
> of them. And what worries me the most now is that I only realized
> this because I wanted to extract the lgi values for the BA.thresh and
> the Destrieux atlas. If I stopped at just getting the thickness, the
> surface area and running qcahe as I have been doing for a while I
> wouldn't have noticed any problem.
>
> So, the hard question again: will I need to run the ones that give
> this error from scratch or is there any other solution?
>
> Thank you,
> Andreia
>
>
> Quoting Douglas N Greve  >:
>
>> On 05/19/2014 02:32 PM, _andre...@sapo.pt
>>  wrote:
>>> Sorry for all the emails..
>>>
>>> Now I ran that same command on the second subject in which I only
>>> detected a problem for the left hemisphere when trying to ge

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hi,

Do I need to run laleb2label and label2annot to get once again the BA.thresh?

Or is it enough to just extract the stats?

I already extracted the aseg stats and one of the subjects came out  
with slightly different values this time, while the other presented  
the same values. Was this supposed to happen?

Another question: when I run recon-all -s subj -localGI I get a  
warning from matlab:

Warning: Unable to open display 'iconic'.  You will not be able to  
display graphics on the screen.

 < M A T L A B (R) >
   Copyright 1984-2013 The MathWorks, Inc.
 R2013a (8.1.0.604) 64-bit (glnxa64)
  February 15, 2013


To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

Is this problematic?

Thanks for the patient!
Andreia


Quoting Marie Schaer :

> Hi Andreia,
>
> Then I would guess that your error comes from the fact that you  
> didn't rerun the autorecon3 at that stage for these 2 subjects. As  
> the randomness flag changes the number of vertices when recreating  
> the surfaces, that explains the error. So for your subjects, just  
> rerun autorecon3 (and qcache and mris_anatomical_stats), and you  
> should be fine.  But if I were you I would then carefully check for  
> all my subjects that registration (i.e. autorecon3) was processed  
> after autorecon2, and then qcache / mris_anatomical_stats after  
> autorecon3 (my understanding is that without the randomness flag  
> that kind of errors can be more difficult to trace back as the  
> number of vertices remain the same).
>
> Best,
>
> Marie
>
> On May 19, 2014, at 3:55 PM, <_andre...@sapo.pt>
>  wrote:
>
>> BA.annot I think that was created before any problem because I had no
>> error (at least I didn't see any)  untill I extracted aparcstats2table
>> of those values. But I just checked my notes and these two subjects
>> were the only ones that gave aberrantly high LGI values when running
>> -localGI. I then went to the mailing list and I saw posts with this
>> error and it was suggested to run recon-all -autorecon2-wm -randomness
>> which at that time solved the error and lgi computation went untill
>> the end without any error.
>>
>> I have no error notes for qcache that was ran previously.
>>
>> Could I solve this issue running recon-all -autorecon2-cp/wm
>> -autorecon3 (depending on the manual edits) and running again only the
>> commands lgi and the ones to get pial surface area from Destrieux
>> (since this was the only one I ran after the lgi error)? Or would it
>> be safer to just run all commands to get BA thresholded, pial surface
>> from Desikan-Killiany and Destrieux and all the necessary ones to get
>> the stats?
>>
>> Thank you very much for your help!
>>
>> Andreia
>>
>>
>> Quoting Douglas N Greve :
>>
>>> On 05/19/2014 04:10 PM, _andre...@sapo.pt wrote:

 I just ran vno_match_check for all my subjects and the scenario is:

 *S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f
 subj1/stats/lh.BA_lgi.stats subj1 lh

 the warning appears: *MRISreadAnnotationIntoArray*: vertex index
 out of range: 120389 i=0014C8B5, in_array_size=120388

 *Only for Brodman* areas, not for Desikan-killiany nor Destrieux

 vno_match_check: *no problem detected*!

>>> vno_match_check was not checking the BA annot. I've fixed this and
>>> put a new version here:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/vno_match_check




 _*Subj2*_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
 subj1/stats/lh.BA_lgi.stats subj1 lh

 the warning appears for all parcellation (BA, aparc, aparc.a2009s),
 but *only for the lefh hemisphere*, everything's fine with the right.

 vno_match_check: *erro for BOTH hemispheres*

>>> Is it the the case that pial_lgi and BA.annot were created before
>>> the subject became out of synch?
>>> doug


 These are conflicting information.

 Any thoughts?

 I cannot be sure of what to do...

 Andreia




 Quoting _andre...@sapo.pt :

> Hi Doug,
>
> That's really bad news. So I'll check all my subjects to track the
> ones who give the error. Then I'll have to run each one from scratch?
>
> I don't quite understand what went wrong with only a few subjects
> since I did (as far as I'm aware) everything in the same way for all
> of them. And what worries me the most now is that I only realized
> this because I wanted to extract the lgi values for the BA.thresh and
> the Destrieux atlas. If I stopped at just getting the thickness, the
> surface area and running qcahe as I have been doing for a while I
> wouldn't have noticed any problem.
>
> So, the hard question again: will I need to run the ones that give
> this er

Re: [Freesurfer] mris_anatomical_stats lgi error

[_andreia_]

Hi Bruce,

Thank you!

Andreia


Quoting Bruce Fischl :

> Hi Andreia
>
> I haven't been following this whole thread, but the matlab warning is not
> a problem
>
> cheers
> Bruce
> On Tue, 20 May 2014, _andre...@sapo.pt wrote:
>
>> Hi,
>>
>> Do I need to run laleb2label and label2annot to get once again the  
>> BA.thresh?
>>
>> Or is it enough to just extract the stats?
>>
>> I already extracted the aseg stats and one of the subjects came out
>> with slightly different values this time, while the other presented
>> the same values. Was this supposed to happen?
>>
>> Another question: when I run recon-all -s subj -localGI I get a
>> warning from matlab:
>>
>> Warning: Unable to open display 'iconic'.  You will not be able to
>> display graphics on the screen.
>>
>> < M A T L A B (R) >
>>   Copyright 1984-2013 The MathWorks, Inc.
>> R2013a (8.1.0.604) 64-bit (glnxa64)
>>  February 15, 2013
>>
>>
>> To get started, type one of these: helpwin, helpdesk, or demo.
>> For product information, visit www.mathworks.com.
>>
>> Is this problematic?
>>
>> Thanks for the patient!
>> Andreia
>>
>>
>> Quoting Marie Schaer :
>>
>>> Hi Andreia,
>>>
>>> Then I would guess that your error comes from the fact that you
>>> didn't rerun the autorecon3 at that stage for these 2 subjects. As
>>> the randomness flag changes the number of vertices when recreating
>>> the surfaces, that explains the error. So for your subjects, just
>>> rerun autorecon3 (and qcache and mris_anatomical_stats), and you
>>> should be fine.  But if I were you I would then carefully check for
>>> all my subjects that registration (i.e. autorecon3) was processed
>>> after autorecon2, and then qcache / mris_anatomical_stats after
>>> autorecon3 (my understanding is that without the randomness flag
>>> that kind of errors can be more difficult to trace back as the
>>> number of vertices remain the same).
>>>
>>> Best,
>>>
>>> Marie
>>>
>>> On May 19, 2014, at 3:55 PM, <_andre...@sapo.pt>
>>>  wrote:
>>>
 BA.annot I think that was created before any problem because I had no
 error (at least I didn't see any)  untill I extracted aparcstats2table
 of those values. But I just checked my notes and these two subjects
 were the only ones that gave aberrantly high LGI values when running
 -localGI. I then went to the mailing list and I saw posts with this
 error and it was suggested to run recon-all -autorecon2-wm -randomness
 which at that time solved the error and lgi computation went untill
 the end without any error.

 I have no error notes for qcache that was ran previously.

 Could I solve this issue running recon-all -autorecon2-cp/wm
 -autorecon3 (depending on the manual edits) and running again only the
 commands lgi and the ones to get pial surface area from Destrieux
 (since this was the only one I ran after the lgi error)? Or would it
 be safer to just run all commands to get BA thresholded, pial surface
 from Desikan-Killiany and Destrieux and all the necessary ones to get
 the stats?

 Thank you very much for your help!

 Andreia


 Quoting Douglas N Greve :

> On 05/19/2014 04:10 PM, _andre...@sapo.pt wrote:
>>
>> I just ran vno_match_check for all my subjects and the scenario is:
>>
>> *S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f
>> subj1/stats/lh.BA_lgi.stats subj1 lh
>>
>> the warning appears: *MRISreadAnnotationIntoArray*: vertex index
>> out of range: 120389 i=0014C8B5, in_array_size=120388
>>
>> *Only for Brodman* areas, not for Desikan-killiany nor Destrieux
>>
>> vno_match_check: *no problem detected*!
>>
> vno_match_check was not checking the BA annot. I've fixed this and
> put a new version here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/vno_match_check
>>
>>
>>
>>
>> _*Subj2*_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
>> subj1/stats/lh.BA_lgi.stats subj1 lh
>>
>> the warning appears for all parcellation (BA, aparc, aparc.a2009s),
>> but *only for the lefh hemisphere*, everything's fine with the right.
>>
>> vno_match_check: *erro for BOTH hemispheres*
>>
> Is it the the case that pial_lgi and BA.annot were created before
> the subject became out of synch?
> doug
>>
>>
>> These are conflicting information.
>>
>> Any thoughts?
>>
>> I cannot be sure of what to do...
>>
>> Andreia
>>
>>
>>
>>
>> Quoting _andre...@sapo.pt :
>>
>>> Hi Doug,
>>>
>>> That's really bad news. So I'll check all my subjects to track the
>>> ones who give the error. Then I'll have to run each one from scratch?
>>>
>>> I don't quite understand what went wrong with only a few subjects
>>> since I

Re: [Freesurfer] Cortical gray matter surface area

[_andreia_]

Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab SUBJ lh pial

 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f
../stats/rh.APARC.PIAL.stats -b -a ../label/rh.aparc.annot -c
../label/aparc.annot.ctab SUBJ rh pial
 

Then run aparcstats2table using APARC.PIAL instead of aparc (only because I
called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:

 mris_anatomical_stats -l ../label/lh.cortex.label -f lh.TOTAL_PIAL.stats
-b SUBJ lh pial

 mris_anatomical_stats -l ../label/rh.cortex.label -f rh.TOTAL_PIAL.stats
-b SUBJ rh pial

 Then run aparcstats2table using TOTAL_PIAL instead of aparc (again, only
because I called this new parcellation total_pial. You may call it whatever
you'd like)

Just remeber to leave the specified dirs when creating the tables. If you
dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best,
Andreia

 Citando will brown :


Hi all,   
   I messed up this question recently so just want to clarify and try
again. We want to know the cortical gray matter surface area of our
subjects but are unclear about how to get this info.
    
   ?.aparc.stats reports:
    
   Measure Cortex, WhiteSurfArea, White Surface Total Area, , mm^2
    
   How about the gray matter?
    
   Thanks,
   Will
    
    


  
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Re: [Freesurfer] Cortical gray matter surface area

[_andreia_]

Hi Will,

Just to clarify, what version of FS are you using? I think it might not be
5.0 and I don't know if everything aplies if we are using different
versions.

1) Yes, it is only based on the pial surface (and these command lines are
for the aparc, DK altas). The second set provides the surface area for each
hemisphere without including, for example, the pial surface that you see in
the hippocampus which is not accurate and one should not care about. In the
end, the second set gives you the sum of the areas in aparc, thus, you can
just make a sum of that parcellation if you want. I just realized that.

2) No. In the new stats file, the value that you want is at the bottom:

# ColHeaders StructName NumVert SURFAREA GrayVol ThickAvg ThickStd MeanCurv
GausCurv FoldInd CurvInd

And when running aparcstats2table that's the value you should get in the
table. I think that # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL
AREA may be including more stuff since it is bigger.

If what you want is only the total hemisphere surface area you only need to
run the second set of commands. If you want the area of each DK altas
parcellation then run the first set and then simply add them to get total
hemisphere surface area.

Someone from Freesurfer staff will correct me if I'm wrong. (Please) I'm
Ccing Doug since he was replying to your previous emails.

Let's wait for their feedback.

Andreia

 Citando will brown :


Thanks Andreia, this does appear to have worked. Please forgive my
ignorance but I do just want to double check two things;
 
1) The first commands you have given provide the stats for the two
hemispheres of the cerebral cortex only based on the pial surface,
whereas the second set of commands provide the pial boundary stats for
the whole brain rather than just cortex?
 
2) The surface area value that I am looking for (grey matter surface
area at the grey/pial boundary) is listed in the new stats table next
to: # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA, ?
 
   Thanks again,
Will


   On Tue, Sep 9, 2014 at 5:36 PM, will brown 
wrote:


Thanks very much Andreia, yes this does look like what I want. I
haven't had a chance to test it yet but it does indeed appear to answer
my question. Thanks to those that have offered answers, to clarify, I
did indeed mean the surface area of the pial surface rather than the
white/grey boundary. 
  Will



On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt> wrote:


_Hi Will,

I use the following commands to get surface area from the pial surface:

In the subject label dir:_
 

   _mris_anatomical_stats -mgz -cortex
../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a
../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial_

   _mris_anatomical_stats -mgz -cortex
../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a
../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial
 _


_Then run aparcstats2table using APARC.PIAL instead of aparc (only
because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:_
 

   _mris_anatomical_stats -l ../label/lh.cortex.label -f
lh.TOTAL_PIAL.stats -b SUBJ lh pial_

   _mris_anatomical_stats -l ../label/rh.cortex.label -f
rh.TOTAL_PIAL.stats -b SUBJ rh pial_

   _Then run aparcstats2table using TOTAL_PIAL instead of
aparc (again, only because I called this new parcellation total_pial.
You may call it whatever you'd like)_



_Just remeber to leave the specified dirs when creating the tables. If
you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best,
Andreia_

 

   _Citando will brown :_


_Hi all, _ _ _
   _I messed up this question recently so just want to
clarify and try again. We want to know the cortical gray matter
surface area of our subjects but are unclear about how to get this
info._
   _ _
   _?.aparc.stats reports:_
   _ _
   _Measure Cortex, WhiteSurfArea, White Surface Total
Area, , mm^2_
   _ _
   _How about the gray matter?_
   _ _
   _Thanks,_
   _Will_
   _ _
   _ _



 
 _ _


  
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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.

Re: [Freesurfer] Cortical gray matter surface area

[_andreia_]

Ok. Then, I'm not sure if everything is correct with the command lines
since I use 5.0.

Any thought on this Freesurfer team?

Thanks,
Andreia

 Citando will brown :


Thanks again, for the record, I'm using freesurfer version 5.3.0 on
Centos 6.
  On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:


_Hi Will,

Just to clarify, what version of FS are you using? I think it might not
be 5.0 and I don't know if everything aplies if we are using different
versions.

1) Yes, it is only based on the pial surface (and these command lines
are for the aparc, DK altas). The second set provides the surface area
for each hemisphere without including, for example, the pial surface
that you see in the hippocampus which is not accurate and one should
not care about. In the end, the second set gives you the sum of the
areas in aparc, thus, you can just make a sum of that parcellation if
you want. I just realized that.

2) No. In the new stats file, the value that you want is at the bottom:

# ColHeaders StructName NumVert SURFAREA GrayVol ThickAvg ThickStd
MeanCurv GausCurv FoldInd CurvInd

And when running aparcstats2table that's the value you should get in
the table. I think that # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE
TOTAL AREA may be including more stuff since it is bigger.

If what you want is only the total hemisphere surface area you only
need to run the second set of commands. If you want the area of each DK
altas parcellation then run the first set and then simply add them to
get total hemisphere surface area.

Someone from Freesurfer staff will correct me if I'm wrong. (Please)
I'm Ccing Doug since he was replying to your previous emails.

Let's wait for their feedback.

Andreia_

 

 _Citando will brown :_


_Thanks Andreia, this does appear to have worked. Please forgive my
ignorance but I do just want to double check two things;
 _
_1) The first commands you have given provide the stats for the two
hemispheres of the cerebral cortex only based on the pial surface,
whereas the second set of commands provide the pial boundary stats for
the whole brain rather than just cortex?
 _
_2) The surface area value that I am looking for (grey matter surface
area at the grey/pial boundary) is listed in the new stats table next
to: # MEASURE CORTEX, WHITESURFAREA, WHITE SURFACE TOTAL AREA, ?
 _
   _Thanks again,
Will_


   _On Tue, Sep 9, 2014 at 5:36 PM, will brown
 wrote:_


_Thanks very much Andreia, yes this does look like what I want. I
haven't had a chance to test it yet but it does indeed appear to
answer my question. Thanks to those that have offered answers, to
clarify, I did indeed mean the surface area of the pial surface
rather than the white/grey boundary. _   _ _
  _Will_



_On Wed, Sep 3, 2014 at 1:12 AM, <_andre...@sapo.pt>
wrote:_


__Hi Will,

I use the following commands to get surface area from the pial
surface:

In the subject label dir:_
 _

   __mris_anatomical_stats -mgz -cortex
../label/lh.cortex.label -f ../stats/lh.APARC.PIAL.stats -b -a
../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial__

   __mris_anatomical_stats -mgz -cortex
../label/rh.cortex.label -f ../stats/rh.APARC.PIAL.stats -b -a
../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial
 __


__Then run aparcstats2table using APARC.PIAL instead of aparc (only
because I called this new parcellation aparc.pial)

To get the total surface area of each hemisphere I use:

In the subject stats dir:_
 _

   __mris_anatomical_stats -l ../label/lh.cortex.label
-f lh.TOTAL_PIAL.stats -b SUBJ lh pial__

   __mris_anatomical_stats -l ../label/rh.cortex.label
-f rh.TOTAL_PIAL.stats -b SUBJ rh pial__

   __Then run aparcstats2table using TOTAL_PIAL instead
of aparc (again, only because I called this new parcellation
total_pial. You may call it whatever you'd like)__



__Just remeber to leave the specified dirs when creating the tables.
If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?

Best,
Andreia_

 _

   __Citando will brown :__


__Hi all,_ _ __ __
   __I messed up this question recently so just
want to clarify and try again. We want to know the cortical gray
matter surface area of our subjects but are unclear about how to
get this info.__
   __ __
   __?.aparc.stats reports:__
   __ __
   __Measure Cortex, WhiteSurfArea, White Surface
Total Area, , mm^2__
   __ __
   __How about the gray matter?__
   __ __
   __Thanks,__
   __Will__
   __ __
   __ __



_ _
 __ __




 
 _ _


  
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[Freesurfer] Defining an mrs voxel in the anatomical dataset for partial volume correction

[_andreia_]

Dear list,

I am performing single-voxel and multivoxel spectroscopy analysis and I need to 
do partial volume correction. I found a thread on the list of someone asking if 
it possible to achieve this using Freesurfer (see below), but there is no 
answer saying how it is done. My question is how can I define the voxel (for 
single-voxel) and the chosen voxels (for multivoxel) in the anatomical data set 
to use the segmentation of only that defined voxel? I'm using a Siemens TrioTim 
3T. All acquisitions are in the same session. The anatomical dataset is an 
average of 2 MPRAGEs which I've already processed using FS, and the spectra 
files are .rda. The header of the MRS data has info on vectors, but I don't 
know how to use them.

"Re: [Freesurfer] need info for beginner

Bruce Fischl
Thu, 26 Apr 2007 11:17:01 -0700

Hi Pom,

yes, people here are using it for spectroscopy and for partial volume 
correction (also for voxel placement).

cheers,
Bruce

On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote:

Hi,

I am about to install FREE SURFER for my Spectroscopy work.
I want to use the software to perform GM/WM segmentation on my
single voxel data sets.

I am wondering if any one on this mailing list is currently
doing this task. I would like to get comments.

My study is on a GE 3T scanner.

thank you,

Pom"

Any advice, please?

Thank you!

Andreia

-- 

Andreia Pereira, MSc student
Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-354 Coimbra Portugal
Phone +(351) 239480220
Fax  +(351) 239480280___
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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 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] Defining an mrs voxel in the anatomical dataset for partial volume correction

[_andreia_]

Hi Doug,

Ok. Thank you! :)

Andreia

Citando Douglas N Greve :

> Yes, that should work. You will need a registration matrix to give to
> mri_compute_volume_fractions. You can get this from tkregister2:
>
> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat
>
> when you run this, hit the compare button to make sure that the mrs box
> falls on the part of the anatomical you think it should be. Then hit
> "Save" to save the registration.
>
> doug
>
> _andre...@sapo.pt wrote:
>> Hi Doug,
>>
>> This already sheds some light on the issue!  I didn't know
>> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have
>> the anatomical and the MRS data acquired in the same session, so I
>> won't need the EPI. If I manage to create the MRS volume using the
>> header info and mri_volsynth I only need to coregister my anatomical
>> with the synthetised volume and then run mri_compute_volume_fractions
>> through the synthesed volume and the identity matrix (?) (since my
>> data are from the same session) to get the % of the different tissue
>> types only inside the voxel. Of course I'll need more advice on this
>> later, but one thing at a time.
>>
>> Thanks!
>> Andreia
>>
>>
>>
>> Citando Douglas N Greve :
>>
>>> Sorry, I don't know anyone who can help with that. As you note, people
>>> do it, so there must be people around who can extract the relevant
>>> information out of the header. The information you need are the
>>> direction cosines and RAS of the corner of the voxel. You can feed this
>>> into mri_volsynth.
>>>
>>> To register to FS, you'll need to have a whole-brain volume collected
>>> during the same session. If you collected the anatomical analyzed in FS
>>> at the same time, then you don't need another. If you did not, you can
>>> literally use any whole brain acquisition, eg, a single TR of an EPI
>>> (less than 10 sec to acquire). You can then register the EPI to the
>>> anatomical with bbregister. This gives you a "register.dat".  You can
>>> then concatenate that with the EPI-MRS registration (I can show you
>>> how). After that, you can run mri_compute_volume_fractions passing it
>>> the synthesized volume and the register.dat (or identity matrix if same
>>> session).
>>>
>>> Another alternative is to collect an actual MRI volume that spans your
>>> MRS volume. You can then substitute that for the synthetic volume. Note
>>> that the actual pixel content of this volume is irrelevant -- it's just
>>> used to get geometry information out of it. This will be the easiest if
>>> you can do it.
>>>
>>> doug
>>>
>>> _andre...@sapo.pt wrote:
 Hi Doug,

 Do you know who can help me with this? That's exactly what I think
 that I need to do... The thing is that, unfortunately, I can't find
 anyone who can describe how the creation of an MRI "volume" from the
 MRS voxel is done, although this approach is present in many many
 papers.

 About the second part, how do I register the synthetized MRI "volume"
 to the FS anatomical? And how can I get the volumes of only that
 "volume"?

 (Hopefully I'll find a way to do the first part...)

 Thanks,
 Andreia




 Citando Douglas N Greve :

> Hi Andreia,  I've done this before using information in the
> spectroscopy
> header, then synthesizing an MRI "volume" with one voxel that
> covers the
> size of your spectroscopy voxel, then registering that to the FS
> anatomical, then computing the partial volume fractions from the
> anatomical. The hard part is the first step, which I can't really
> advise
> you on.
>
> doug
>
> _andre...@sapo.pt wrote:
>> Dear list,
>>
>> I am performing single-voxel and multivoxel spectroscopy analysis and
>> I need to do partial volume correction. I found a thread on the list
>> of someone asking if it possible to achieve this using Freesurfer
>> (see
>> below), but there is no answer saying how it is done. My question is
>> how can I define the voxel (for single-voxel) and the chosen voxels
>> (for multivoxel) in the anatomical data set to use the
>> segmentation of
>> only that defined voxel? I'm using a Siemens TrioTim 3T. All
>> acquisitions are in the same session. The anatomical dataset is an
>> average of 2 MPRAGEs which I've already processed using FS, and the
>> spectra files are .rda. The header of the MRS data has info on
>> vectors, but I don't know how to use them.
>>
>>
>>
>> "Re: [Freesurfer] need info for beginner
>>
>> Bruce Fischl
>> Thu, 26 Apr 2007 11:17:01 -0700
>>
>> Hi Pom,
>>
>> yes, people here are using it for spectroscopy and for partial volume
>> correction (also for voxel placement).
>>
>> cheers,
>> Bruce
>>
>> On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote:
>>
>> Hi,
>>
>> I am about to install FREE S

Re: [Freesurfer] Defining an mrs voxel in the anatomical dataset for partial volume correction

[_andreia_]

Hello!

About synthesising a volume using mri_volsynth with direction cosines  
and RAS from mrs header:

In the mrs header I have:
- VOI position in the 3 views (sag, cor and tra) which are from the  
left upper corner of the voxel (these are the RAS coordinates that I  
need to feed into mri_volsynth, correct?)
- position vectors [0] [1] [2]
- row and columns vectors (but I think that these are not the ones  
used to get the direction cosines, is that right?)
- VOIRotationInPlane
- and I know that my voxel is 3x3x3 cm

How do I introduce these infos in mri_volsynth to have a 3x3x3 cube to  
coregister with the anatomical? Typing mri_volsynth --help I got lots  
of asked information and I don't know how to feed it into. Also, for  
defining the geometry the "center" voxel and the first voxel are  
needed. Shouldn't it be only the RAS of the corner of the voxel?


Also, all these infos are in the scanner space, and the anatomical  
image processed in FS is spacially transformed. What should I use to  
coregister the synthesized volume to the processed anatomical to get  
the same transformation in the 3x3x3 volume?

Can you give me an example of how this process is done?

Thank you very much!

Andreia



> Hi Doug,
>
> Ok. Thank you! :)
>
> Andreia
>
> Citando Douglas N Greve :
>
>> Yes, that should work. You will need a registration matrix to give to
>> mri_compute_volume_fractions. You can get this from tkregister2:
>>
>> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat
>>
>> when you run this, hit the compare button to make sure that the mrs box
>> falls on the part of the anatomical you think it should be. Then hit
>> "Save" to save the registration.
>>
>> doug
>>
>> _andre...@sapo.pt wrote:
>>> Hi Doug,
>>>
>>> This already sheds some light on the issue!  I didn't know
>>> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have
>>> the anatomical and the MRS data acquired in the same session, so I
>>> won't need the EPI. If I manage to create the MRS volume using the
>>> header info and mri_volsynth I only need to coregister my anatomical
>>> with the synthetised volume and then run mri_compute_volume_fractions
>>> through the synthesed volume and the identity matrix (?) (since my
>>> data are from the same session) to get the % of the different tissue
>>> types only inside the voxel. Of course I'll need more advice on this
>>> later, but one thing at a time.
>>>
>>> Thanks!
>>> Andreia
>>>
>>>
>>>
>>> Citando Douglas N Greve :
>>>
 Sorry, I don't know anyone who can help with that. As you note, people
 do it, so there must be people around who can extract the relevant
 information out of the header. The information you need are the
 direction cosines and RAS of the corner of the voxel. You can feed this
 into mri_volsynth.

 To register to FS, you'll need to have a whole-brain volume collected
 during the same session. If you collected the anatomical analyzed in FS
 at the same time, then you don't need another. If you did not, you can
 literally use any whole brain acquisition, eg, a single TR of an EPI
 (less than 10 sec to acquire). You can then register the EPI to the
 anatomical with bbregister. This gives you a "register.dat".  You can
 then concatenate that with the EPI-MRS registration (I can show you
 how). After that, you can run mri_compute_volume_fractions passing it
 the synthesized volume and the register.dat (or identity matrix if same
 session).

 Another alternative is to collect an actual MRI volume that spans your
 MRS volume. You can then substitute that for the synthetic volume. Note
 that the actual pixel content of this volume is irrelevant -- it's just
 used to get geometry information out of it. This will be the easiest if
 you can do it.

 doug

 _andre...@sapo.pt wrote:
> Hi Doug,
>
> Do you know who can help me with this? That's exactly what I think
> that I need to do... The thing is that, unfortunately, I can't find
> anyone who can describe how the creation of an MRI "volume" from the
> MRS voxel is done, although this approach is present in many many
> papers.
>
> About the second part, how do I register the synthetized MRI "volume"
> to the FS anatomical? And how can I get the volumes of only that
> "volume"?
>
> (Hopefully I'll find a way to do the first part...)
>
> Thanks,
> Andreia
>
>
>
>
> Citando Douglas N Greve :
>
>> Hi Andreia,  I've done this before using information in the
>> spectroscopy
>> header, then synthesizing an MRI "volume" with one voxel that
>> covers the
>> size of your spectroscopy voxel, then registering that to the FS
>> anatomical, then computing the partial volume fractions from the
>> anatomical. The hard part is the first step, which I can't really
>> advise
>> you on.
>>

Re: [Freesurfer] gray matter not incuded in pial surface

[_andreia_]

Hi,

I'm not being able to solve the segmentation problem on in this  
subject. What files do I need to upload and were, please?

Thank you,
Andreia


Citando Bruce Fischl :

> Hi Andreia
>
> it's tough to tell from one slice. There appear to be some bright stuff
> in the superficial gray matter, which may be messing stuff up, not sure
> what it is, or it could be something happening through-plane that we
> can't see. If you want to upload the dataset I'll take a look
>
> cheers
> Bruce
> On Mon, 1 Aug
> 2011, _andre...@sapo.pt wrote:
>
>> Dear FS experts,
>>
>> I'm correcting the pial surface when it includes more than it is  
>> supposed, but now I got to a subject where the pial is not incluing  
>> what is supposed.
>> How do I correct this? You can see the problem in the attachd image.
>>
>> Thank you!
>> Andreia
>>
>>
> ___
> Freesurfer mailing list
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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.
>
>



-- 

Andreia Pereira, MSc student
Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-354 Coimbra Portugal
Phone +(351) 239480220
Fax  +(351) 239480280

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[Freesurfer] Brodmann areas stats table

[_andreia_]

FreeSurfers,

Is there a way to get BA cortical thickness in a table to export from  
FS? As there is for aseg and aparc stats.

Thanks!
Andreia


-- 

Andreia Pereira, MSc student
Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-354 Coimbra Portugal
Phone +(351) 239480220
Fax  +(351) 239480280
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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 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.

[Freesurfer] Fwd: Re: Defining an mrs voxel in the anatomical dataset for partial volume correction

[_andreia_]

Hello all!

I got no answer on this email, thus I'm posting these questions again,  
hoe someone can help:


Hello!

About synthesising a volume using mri_volsynth with direction cosines  
and RAS from mrs header:

In the mrs header I have:
- VOI position in the 3 views (sag, cor and tra) which are from the  
left upper corner of the voxel (these are the RAS coordinates that I  
need to feed into mri_volsynth, correct?)
- position vectors [0] [1] [2]
- row and columns vectors (but I think that these are not the ones  
used to get the direction cosines, is that right?)
- VOIRotationInPlane
- and I know that my voxel is 3x3x3 cm

How do I introduce these infos in mri_volsynth to have a 3x3x3 cube to  
coregister with the anatomical? Typing mri_volsynth --help I got lots  
of asked information and I don't know how to feed into it. Also, for  
defining the geometry the "center" voxel and the first voxel are  
needed. Shouldn't it be only the RAS of the corner of the voxel?


Also, all these infos are in the scanner space, and the anatomical  
image processed in FS is spacially transformed. What should I use to  
coregister the synthesized volume to the processed anatomical to get  
the same transformation in the 3x3x3 volume?

Can you give me an example of how this process is done?

Thank you very much!

Andreia



> Hi Doug,
>
> Ok. Thank you! :)
>
> Andreia
>
> Citando Douglas N Greve :
>
>> Yes, that should work. You will need a registration matrix to give to
>> mri_compute_volume_fractions. You can get this from tkregister2:
>>
>> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat
>>
>> when you run this, hit the compare button to make sure that the mrs box
>> falls on the part of the anatomical you think it should be. Then hit
>> "Save" to save the registration.
>>
>> doug
>>
>> _andre...@sapo.pt wrote:
>>> Hi Doug,
>>>
>>> This already sheds some light on the issue!  I didn't know
>>> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have
>>> the anatomical and the MRS data acquired in the same session, so I
>>> won't need the EPI. If I manage to create the MRS volume using the
>>> header info and mri_volsynth I only need to coregister my anatomical
>>> with the synthetised volume and then run mri_compute_volume_fractions
>>> through the synthesed volume and the identity matrix (?) (since my
>>> data are from the same session) to get the % of the different tissue
>>> types only inside the voxel. Of course I'll need more advice on this
>>> later, but one thing at a time.
>>>
>>> Thanks!
>>> Andreia
>>>
>>>
>>>
>>> Citando Douglas N Greve :
>>>
 Sorry, I don't know anyone who can help with that. As you note, people
 do it, so there must be people around who can extract the relevant
 information out of the header. The information you need are the
 direction cosines and RAS of the corner of the voxel. You can feed this
 into mri_volsynth.

 To register to FS, you'll need to have a whole-brain volume collected
 during the same session. If you collected the anatomical analyzed in FS
 at the same time, then you don't need another. If you did not, you can
 literally use any whole brain acquisition, eg, a single TR of an EPI
 (less than 10 sec to acquire). You can then register the EPI to the
 anatomical with bbregister. This gives you a "register.dat".  You can
 then concatenate that with the EPI-MRS registration (I can show you
 how). After that, you can run mri_compute_volume_fractions passing it
 the synthesized volume and the register.dat (or identity matrix if same
 session).

 Another alternative is to collect an actual MRI volume that spans your
 MRS volume. You can then substitute that for the synthetic volume. Note
 that the actual pixel content of this volume is irrelevant -- it's just
 used to get geometry information out of it. This will be the easiest if
 you can do it.

 doug

 _andre...@sapo.pt wrote:
> Hi Doug,
>
> Do you know who can help me with this? That's exactly what I think
> that I need to do... The thing is that, unfortunately, I can't find
> anyone who can describe how the creation of an MRI "volume" from the
> MRS voxel is done, although this approach is present in many many
> papers.
>
> About the second part, how do I register the synthetized MRI "volume"
> to the FS anatomical? And how can I get the volumes of only that
> "volume"?
>
> (Hopefully I'll find a way to do the first part...)
>
> Thanks,
> Andreia
>
>
>
>
> Citando Douglas N Greve :
>
>> Hi Andreia,  I've done this before using information in the
>> spectroscopy
>> header, then synthesizing an MRI "volume" with one voxel that
>> covers the
>> size of your spectroscopy voxel, then registering that to the FS
>> anatomical, then computing the partial volume fractions from the

[Freesurfer] GM, WM and CSF segmentation for partial volume correction

[_andreia_]

Hello list,

Following this email that I found in the archives:


"(...)
For the segmentation, FS still works voxelwise, but it's objective is  
to identify each structure as a whole, whereas SPM and FSL/FAST  
attempt to classify each voxel as being GM, WM or CSF. A short  
description of the method in FS is here:  
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream
 You may want also to have a look at this paper:  
http://dx.doi.org/10.1016/S0896-6273(02)00569-X

Hope this helps!

All the best,

Anderson"

I need to obtain the different % of tissue (GM, WM and CSF) inside one  
defined voxel. Does FS has a file that can be exported to Matlab to  
then get these values? Or only FSL/FAST and SPM have this type of info?

Thanks!
Andreia
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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 Partners Compliance HelpLine at
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Re: [Freesurfer] GM, WM and CSF segmentation for partial volume correction

[_andreia_]

Thanks Bruce and Douglas!

Andreia



Citando Douglas N Greve :

> mri_compute_volume_fractions will compute the fractions for each of  
> the tissue types, no need to alter the segmentations.
> doug
>
>
>
> Bruce Fischl wrote:
>> Hi Andreia
>>
>> you could certainly change our segmentation labels to just these 3  
>> classes easily enough in matlab. Then we have tools for computing  
>> partial volume fractions (I think mri_compute_volume_fractions)
>>
>> cheers
>> Bruce
>>
>>
>> On Wed, 28 Sep 2011, _andre...@sapo.pt wrote:
>>
>>
>>> Hello list,
>>>
>>> Following this email that I found in the archives:
>>>
>>>
>>> "(...)
>>> For the segmentation, FS still works voxelwise, but it's objective is
>>> to identify each structure as a whole, whereas SPM and FSL/FAST
>>> attempt to classify each voxel as being GM, WM or CSF. A short
>>> description of the method in FS is here:
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream
>>>  You may want also to have a look at this  
>>> paper:
>>> http://dx.doi.org/10.1016/S0896-6273(02)00569-X
>>>
>>> Hope this helps!
>>>
>>> All the best,
>>>
>>> Anderson"
>>>
>>> I need to obtain the different % of tissue (GM, WM and CSF) inside one
>>> defined voxel. Does FS has a file that can be exported to Matlab to
>>> then get these values? Or only FSL/FAST and SPM have this type of info?
>>>
>>> Thanks!
>>> Andreia
>>> ___
>>> 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
>>
>>
>>
>
> -- 
> 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
>
>
>
> 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] Fwd: Talairach transformation

[_andreia_]

Hi all,

I have the same problem. I'm also working with 3T, and I need to  
stretch the movable template with tkregister2 in almost every subject.  
It would be nice if this wasn't necessary, is there a workaround?

Thanks,
Andreia

Citando Maria Felber :

> Dear Ms. Kakunoori,
>
> sorry to bother you again, but as I did not get a reply to my last  
> message to everyone so far troubled with my question, I am trying  
> here for a second time.
> It is indeed the case, that all my data were scanned with a 3T. And  
> if that is indeed the problem Dr. Snyder figured out, then what can  
> I do about it? Or is anyone already working on this problem? I can  
> hardly imagine I am the only one recording with a 3T instead of a  
> 1.5T.
> Yours sincerely,
> Maria Felber
>
> - Forwarded Message -
> From: "Maria Felber" 
> To: "Avi Snyder" 
> Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\"  
> ,  
> freesurfer@nmr.mgh.harvard.edu
> Sent: Thursday, September 15, 2011 10:46:55 AM
> Subject: Re: [Freesurfer]  Talairach transformation
>
> Dear all,
>
> indeed all my T1-scans were recorded with a 3T scanner. So what can  
> I do about it or do you have something in progress which would fix  
> this problem anytime soon?
> Thanks,
> Maria
>
> - Original Message -
> From: "Avi Snyder" 
> To: "Sita Kakunoori" , fel...@cbs.mpg.de,  
> "Avi Snyder" 
> Cc: "Bruce Fischl" 
> Sent: Tuesday, September 13, 2011 11:03:28 PM
> Subject: Re: [Freesurfer]  Talairach transformation
>
> Hi Sita,
>
> Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are
> expected if the contrast properties of the sample image are far from those
> of the target. This condition can easily occur if the target is based on
> 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images
> tend to be relatively bright in the center of the head.) Gd++ contrasted
> MP-RAGE scans routinely do not produce decent atlas transforms unless
> special measures are taken. A FreeSurfer fix for this problem is
> theoretically feasible.
>
> Avi
> ---
> On 9/13/11 2:26 PM, "Sita Kakunoori"  wrote:
>>
>> I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this
>> e-mail.
>> Hi Dr.Snyder, Not sure if you remember but we saw something similar in a
>> dataset here at the center where the talairach was much smaller than the
>> orig.mgz volume and you created a new talairach template to be used with
>> that dataset. I just wondered if this issue is similar to that.
>>
>> Thanks much,
>> Sita.
>> -- Forwarded message --
>> Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST)
>> From: Maria Felber 
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [Freesurfer]  Talairach transformation
>>
>> Hi Bruce,
>>
>> so we are back at the beginning. After I ran recon-all -all, I did
>> exactly that and checked the xform using tkregister2. And here I always
>> see that my talairach volume (the transform) is always smaller, which can
>> be very well seen as the orig surfaces of the subjects are always a
>> little outside the brain and reach well into the skull areas. Of course I
>> can make the adjustments as descriped in the short instructions. But this
>> also means I ran the recon-all precess anew for another 30 h per subject.
>> And that is the reason, why I asked if this is normal that the tailarach
>> transform is a) always smaller than the original brain, and b) if I can
>> make any adjustments to prevent that from happening and thus saving
>> another 30h per subject.
>> In short: How acurate hat the talairach.xfm has to be and is it possible
>> to change some parameters to make this transformation a little more
>> accurate while running the recon-all process only once?
>> Best,
>> Maria
>>
>>
>> - Original Message -
>> From: "Bruce Fischl" 
>> To: "Maria Felber" 
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Sent: Tuesday, September 13, 2011 4:07:55 PM
>> Subject: Re: [Freesurfer] Talairach transformation
>>
>> Hi Maria
>>
>> you can use tkregister2 to check the accuracy of the talairach.xfm
>> transform ("xform" for short), and correct it if you want.
>>
>> cheers
>> Bruce
>> On Tue, 13 Sep 2011, Maria Felber wrote:
>>
>>> Hi Bruce,
>>>
>>> thanks for the first response. I tried to find some information on the
>>> webpage about xform, but failed. So what is xform standing for and
>>> where/how can I check it?
>>> As in the later processing stages I want to do localization and
>> DCM-Modeling with my data, I guess the correct talairach coords are kind
>> of
>> important for later comparisons.
>>> Thanks again,
>>> Maria
>>>
>>> - Original Message -
>>> From: "Bruce Fischl" 
>>> To: "Maria Felber" 
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Sent: Friday, September 9, 2011 2:13:05 PM
>>> Subject: Re: [Freesurfer] Talairach transformation
>>>
>>> Hi Maria
>>>
>>> as long as the tal xform is reasonable I wouldn't worry about it, unless
>>> for some reason you car

Re: [Freesurfer] Fwd: Talairach transformation

[_andreia_]

Thanks! I'll try that!

Andreia




Citando Nick Schmansky :

> you can try:
>
> -talairach -use-mritotal
>
> which will use an alternate talarairch alignment scheme (from the MNI).
> it sometimes works better.
>
> you should also probably add:
>
> -nuintensitycor-3T
>
> to the end of your recon-all command, which will run the nu_correct
> stage optimized for 3T.  it wont help you with your talairach issue, but
> people have found that it produces better results for 3T data (versus
> the default nu_correct parameters, which are optimized for 1.5T).
>
> n.
>
>
> On Mon, 2011-10-03 at 15:53 +0100, _andre...@sapo.pt wrote:
>> Hi all,
>>
>> I have the same problem. I'm also working with 3T, and I need to
>> stretch the movable template with tkregister2 in almost every subject.
>> It would be nice if this wasn't necessary, is there a workaround?
>>
>> Thanks,
>> Andreia
>>
>> Citando Maria Felber :
>>
>> > Dear Ms. Kakunoori,
>> >
>> > sorry to bother you again, but as I did not get a reply to my last
>> > message to everyone so far troubled with my question, I am trying
>> > here for a second time.
>> > It is indeed the case, that all my data were scanned with a 3T. And
>> > if that is indeed the problem Dr. Snyder figured out, then what can
>> > I do about it? Or is anyone already working on this problem? I can
>> > hardly imagine I am the only one recording with a 3T instead of a
>> > 1.5T.
>> > Yours sincerely,
>> > Maria Felber
>> >
>> > - Forwarded Message -
>> > From: "Maria Felber" 
>> > To: "Avi Snyder" 
>> > Cc: "Sita Kakunoori\", fel...@cbs.mpg.de, \"Avi Snyder\"
>> > ,
>> > freesurfer@nmr.mgh.harvard.edu
>> > Sent: Thursday, September 15, 2011 10:46:55 AM
>> > Subject: Re: [Freesurfer]  Talairach transformation
>> >
>> > Dear all,
>> >
>> > indeed all my T1-scans were recorded with a 3T scanner. So what can
>> > I do about it or do you have something in progress which would fix
>> > this problem anytime soon?
>> > Thanks,
>> > Maria
>> >
>> > - Original Message -
>> > From: "Avi Snyder" 
>> > To: "Sita Kakunoori" , fel...@cbs.mpg.de,
>> > "Avi Snyder" 
>> > Cc: "Bruce Fischl" 
>> > Sent: Tuesday, September 13, 2011 11:03:28 PM
>> > Subject: Re: [Freesurfer]  Talairach transformation
>> >
>> > Hi Sita,
>> >
>> > Wrong-stretch (e.g., too fat or too thin) MP-RAGE atlas transforms are
>> > expected if the contrast properties of the sample image are far from those
>> > of the target. This condition can easily occur if the target is based on
>> > 1.5T data and the sample is acquired at 3T. (3T but not 1.5T T1W images
>> > tend to be relatively bright in the center of the head.) Gd++ contrasted
>> > MP-RAGE scans routinely do not produce decent atlas transforms unless
>> > special measures are taken. A FreeSurfer fix for this problem is
>> > theoretically feasible.
>> >
>> > Avi
>> > ---
>> > On 9/13/11 2:26 PM, "Sita Kakunoori"  wrote:
>> >>
>> >> I might have seen this in a dataset. I am cc'ing Dr.Avi Anyder on this
>> >> e-mail.
>> >> Hi Dr.Snyder, Not sure if you remember but we saw something similar in a
>> >> dataset here at the center where the talairach was much smaller than the
>> >> orig.mgz volume and you created a new talairach template to be used with
>> >> that dataset. I just wondered if this issue is similar to that.
>> >>
>> >> Thanks much,
>> >> Sita.
>> >> -- Forwarded message --
>> >> Date: Tue, 13 Sep 2011 16:27:17 +0200 (CEST)
>> >> From: Maria Felber 
>> >> To: freesurfer@nmr.mgh.harvard.edu
>> >> Subject: [Freesurfer]  Talairach transformation
>> >>
>> >> Hi Bruce,
>> >>
>> >> so we are back at the beginning. After I ran recon-all -all, I did
>> >> exactly that and checked the xform using tkregister2. And here I always
>> >> see that my talairach volume (the transform) is always smaller, which can
>> >> be very well seen as the orig surfaces of the subjects are always a
>> >> little outside the brain and reach well into the skull areas. Of course I
>> >> can make the adjustments as descriped in the short instructions. But this
>> >> also means I ran the recon-all precess anew for another 30 h per subject.
>> >> And that is the reason, why I asked if this is normal that the tailarach
>> >> transform is a) always smaller than the original brain, and b) if I can
>> >> make any adjustments to prevent that from happening and thus saving
>> >> another 30h per subject.
>> >> In short: How acurate hat the talairach.xfm has to be and is it possible
>> >> to change some parameters to make this transformation a little more
>> >> accurate while running the recon-all process only once?
>> >> Best,
>> >> Maria
>> >>
>> >>
>> >> - Original Message -
>> >> From: "Bruce Fischl" 
>> >> To: "Maria Felber" 
>> >> Cc: freesurfer@nmr.mgh.harvard.edu
>> >> Sent: Tuesday, September 13, 2011 4:07:55 PM
>> >> Subject: Re: [Freesurfer] Talairach transformation
>> >>
>> >> Hi Maria
>> >>
>> >> you can use tkregister2 to check t