date:20130311

[Freesurfer] qdec question

2013-03-11 Thread Kristina Nalbandian

Hello!

  I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
ipsilateral and contralateral hemispheres. However, ipsilateral patients
need to be grouped together, but qdec only allows me to visualize left or
right hemispheres separately. Is there a way to combine left hemispheres
with right hemispheres in an attempt to study grey matter thickness in
hemispheres ipsilateral to seizure onset? [Because the ipsilateral
hemisphere is the right hemisphere for some patients and left hemisphere
for others]. For example, is it possible to somehow flip the right
hemisphere such that ipsilateral hemispheres align together?

Thank you in advance for your help,
Kristina Nalbandian
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[Freesurfer] qdec question

2013-03-11 Thread Kristina Nalbandian

Hello!

  I am running qdec group analysis on my patient data and have one very
important question. I am studying the differences between two Epilepsy
subtypes. Each one of my patients has a hemisphere of onset, either Left or
Right, that I would like to use in looking for differences between
ipsilateral and contralateral hemispheres. However, ipsilateral patients
need to be grouped together, but qdec only allows me to visualize left or
right hemispheres separately. Is there a way to combine left hemispheres
with right hemispheres in an attempt to study grey matter thickness in
hemispheres ipsilateral to seizure onset? [Because the ipsilateral
hemisphere is the right hemisphere for some patients and left hemisphere
for others]. For example, is it possible to somehow flip the right
hemisphere such that ipsilateral hemispheres align together?

Thank you in advance for your help,
Kristina Nalbandian
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Re: [Freesurfer] Extract pial surface

2013-03-11 Thread Nick Schmansky

VP,

the recon-all stream produces ?h.ribbon.mgz and ribbon.mgz files which
are based on the surfaces, so that is your best option.

Nick

On Mon, 2013-03-11 at 15:28 -0400, Valtina Pouegue wrote:
> Hi Freesurfers, 
> 
> 
> I would like to extract the whole pial surface of a brain volume. I
> already done the segmentation and i have ( rh.pial and
> lh.pial surfaces).  Does it exist a way to get the whole pial surface
> without separation? 
> 
> 
> Thanks. 
> 
> VP
> 
> 
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[Freesurfer] surface area mesurment and qatools

2013-03-11 Thread Knut J Bjuland

Hi

What would be the best way to measure cortical surface either the white 
surface area or pial surface? Is the total surface area calculated by 
mris_anatomical the same pial surface?
When using QA tool which article should I cite?

Knut J
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[Freesurfer] Extract pial surface

2013-03-11 Thread Valtina Pouegue

Hi Freesurfers, 
I would like to extract the whole pial surface of a brain volume. I already 
done the segmentation and i have ( rh.pial and lh.pial surfaces).  Does it 
exist a way to get the whole pial surface without separation? 
Thanks. 

VP
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Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado

I am thinking that that's possible. Same command with same type of
parameters executed successfully before the failure, and now previously
failed command is working. I will try it again...

Thanks for the input.

-Ronny

>
> Probably a network glitch? I'd try restarting it and seeing if the error
> persists.
>
> On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:
>
>> It looks like this is the first *thresh.* label that caused the problem.
>> The following command ran and executed properly just before the error
>> message on the log.
>>
>> mri_label2label --srcsubject fsaverage --srclabel
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label
>> --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh
>> --regmethod surface
>>
>> So looks like lh.BA3a.thresh.label ran just fine, but not
>> lh.BA3b.thresh.label. This ran as part of recon-all and failed in the
>> middle of executing that script so I hadn't even tried to run it any
>> other
>> way (without *.thresh.*)
>>
>> That said, I just ran the problematic piece line of code and it all of a
>> sudden works just fine...
>> mri_label2label --srcsubject fsaverage --srclabel
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>> --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
>> --regmethod surface
>>
>> Any reason why it wouldn't have worked Friday near 7pm and works not?
>>
>> -Ronny
>>
>>>
>>> Hi Ronny - Do you get errors with any other of the *.thresh.* labels?
>>> Or
>>> is BA3b.thresh the only one? If you remove the .thresh do you still get
>>> an
>>> error?
>>>
>>> Thanks,
>>> a.y
>>>
>>> On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:
>>>
 Hello,

 I ran recon-all and left it running Friday afternoon/evening. When I
 next
 checked it this morning, the script had finished with errors. Looks
 like
 there was a problem with the file:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage
 is
 a
 symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage

 Seems like I should be able to read lh.BA3b.thresh.label. Not sure why
 the
 script couldn't open it. Thoughts?

 -Ronny

 Further info below:

 machine: quito
 Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
 /usr/local/freesurfer/dev/bin/freesurfer
 SUBJECTS_DIR:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 Working Directory:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig

 ** the exact command line I ran
 recon-all -autorecon2-cp -autorecon3 -subjid subj004

 ** The command that caused the error (which was as a part of/ within
 the
 recon-all script) is
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 ** ERROR MESSAGE RECEIVED **
 Permission denied
 mri_label2label: could not open label file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 srclabel =
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 srcsubject = fsaverage
 trgsubject = subj004
 trglabel = ./lh.BA3b.thresh.label
 regmethod = surface

 srchemi = lh
 trghemi = lh
 trgsurface = white
 srcsurfreg = sphere.reg
 trgsurfreg = sphere.reg
 usehash = 1
 Use ProjAbs  = 0, 0
 Use ProjFrac = 0, 0
 DoPaint 0

 SUBJECTS_DIR
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 FREESURFER_HOME /usr/local/freesurfer/dev
 Loading source label.
 Invalid argument
 ERROR reading
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC
 2013
 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST
 2013

 For more details, see the log file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>>>
>>>
>>>
>>
>>
>>
>
>
>

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Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread Anastasia Yendiki


Probably a network glitch? I'd try restarting it and seeing if the error 
persists.

On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

> It looks like this is the first *thresh.* label that caused the problem.
> The following command ran and executed properly just before the error
> message on the log.
>
> mri_label2label --srcsubject fsaverage --srclabel
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label
> --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh
> --regmethod surface
>
> So looks like lh.BA3a.thresh.label ran just fine, but not
> lh.BA3b.thresh.label. This ran as part of recon-all and failed in the
> middle of executing that script so I hadn't even tried to run it any other
> way (without *.thresh.*)
>
> That said, I just ran the problematic piece line of code and it all of a
> sudden works just fine...
> mri_label2label --srcsubject fsaverage --srclabel
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
> --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
> --regmethod surface
>
> Any reason why it wouldn't have worked Friday near 7pm and works not?
>
> -Ronny
>
>>
>> Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or
>> is BA3b.thresh the only one? If you remove the .thresh do you still get an
>> error?
>>
>> Thanks,
>> a.y
>>
>> On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:
>>
>>> Hello,
>>>
>>> I ran recon-all and left it running Friday afternoon/evening. When I
>>> next
>>> checked it this morning, the script had finished with errors. Looks like
>>> there was a problem with the file:
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>>
>>> /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is
>>> a
>>> symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage
>>>
>>> Seems like I should be able to read lh.BA3b.thresh.label. Not sure why
>>> the
>>> script couldn't open it. Thoughts?
>>>
>>> -Ronny
>>>
>>> Further info below:
>>>
>>> machine: quito
>>> Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
>>> /usr/local/freesurfer/dev/bin/freesurfer
>>> SUBJECTS_DIR:
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
>>> Working Directory:
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig
>>>
>>> ** the exact command line I ran
>>> recon-all -autorecon2-cp -autorecon3 -subjid subj004
>>>
>>> ** The command that caused the error (which was as a part of/ within the
>>> recon-all script) is
>>> mri_label2label --srcsubject fsaverage --srclabel
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>> --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
>>> --regmethod surface
>>>
>>> ** ERROR MESSAGE RECEIVED **
>>> Permission denied
>>> mri_label2label: could not open label file
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>>
>>> srclabel =
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>> srcsubject = fsaverage
>>> trgsubject = subj004
>>> trglabel = ./lh.BA3b.thresh.label
>>> regmethod = surface
>>>
>>> srchemi = lh
>>> trghemi = lh
>>> trgsurface = white
>>> srcsurfreg = sphere.reg
>>> trgsurfreg = sphere.reg
>>> usehash = 1
>>> Use ProjAbs  = 0, 0
>>> Use ProjFrac = 0, 0
>>> DoPaint 0
>>>
>>> SUBJECTS_DIR
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
>>> FREESURFER_HOME /usr/local/freesurfer/dev
>>> Loading source label.
>>> Invalid argument
>>> ERROR reading
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>> Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC
>>> 2013
>>> x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013
>>>
>>> For more details, see the log file
>>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
>>
>
>
>
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Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado

It looks like this is the first *thresh.* label that caused the problem.
The following command ran and executed properly just before the error
message on the log.

 mri_label2label --srcsubject fsaverage --srclabel
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label
--trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh
--regmethod surface

So looks like lh.BA3a.thresh.label ran just fine, but not
lh.BA3b.thresh.label. This ran as part of recon-all and failed in the
middle of executing that script so I hadn't even tried to run it any other
way (without *.thresh.*)

That said, I just ran the problematic piece line of code and it all of a
sudden works just fine...
mri_label2label --srcsubject fsaverage --srclabel
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
--trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
--regmethod surface

Any reason why it wouldn't have worked Friday near 7pm and works not?

-Ronny

>
> Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or
> is BA3b.thresh the only one? If you remove the .thresh do you still get an
> error?
>
> Thanks,
> a.y
>
> On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:
>
>> Hello,
>>
>> I ran recon-all and left it running Friday afternoon/evening. When I
>> next
>> checked it this morning, the script had finished with errors. Looks like
>> there was a problem with the file:
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>
>> /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is
>> a
>> symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage
>>
>> Seems like I should be able to read lh.BA3b.thresh.label. Not sure why
>> the
>> script couldn't open it. Thoughts?
>>
>> -Ronny
>>
>> Further info below:
>>
>> machine: quito
>> Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
>> /usr/local/freesurfer/dev/bin/freesurfer
>> SUBJECTS_DIR:
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
>> Working Directory:
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig
>>
>> ** the exact command line I ran
>> recon-all -autorecon2-cp -autorecon3 -subjid subj004
>>
>> ** The command that caused the error (which was as a part of/ within the
>> recon-all script) is
>> mri_label2label --srcsubject fsaverage --srclabel
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>> --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
>> --regmethod surface
>>
>> ** ERROR MESSAGE RECEIVED **
>> Permission denied
>> mri_label2label: could not open label file
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>>
>> srclabel =
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>> srcsubject = fsaverage
>> trgsubject = subj004
>> trglabel = ./lh.BA3b.thresh.label
>> regmethod = surface
>>
>> srchemi = lh
>> trghemi = lh
>> trgsurface = white
>> srcsurfreg = sphere.reg
>> trgsurfreg = sphere.reg
>> usehash = 1
>> Use ProjAbs  = 0, 0
>> Use ProjFrac = 0, 0
>> DoPaint 0
>>
>> SUBJECTS_DIR
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
>> FREESURFER_HOME /usr/local/freesurfer/dev
>> Loading source label.
>> Invalid argument
>> ERROR reading
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>> Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC
>> 2013
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013
>>
>> For more details, see the log file
>> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
>

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread Anastasia Yendiki


Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or 
is BA3b.thresh the only one? If you remove the .thresh do you still get an 
error?

Thanks,
a.y

On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

> Hello,
>
> I ran recon-all and left it running Friday afternoon/evening. When I next
> checked it this morning, the script had finished with errors. Looks like
> there was a problem with the file:
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>
> /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a
> symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage
>
> Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the
> script couldn't open it. Thoughts?
>
> -Ronny
>
> Further info below:
>
> machine: quito
> Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
> /usr/local/freesurfer/dev/bin/freesurfer
> SUBJECTS_DIR:
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
> Working Directory:
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig
>
> ** the exact command line I ran
> recon-all -autorecon2-cp -autorecon3 -subjid subj004
>
> ** The command that caused the error (which was as a part of/ within the
> recon-all script) is
> mri_label2label --srcsubject fsaverage --srclabel
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
> --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
> --regmethod surface
>
> ** ERROR MESSAGE RECEIVED **
> Permission denied
> mri_label2label: could not open label file
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
>
> srclabel =
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
> srcsubject = fsaverage
> trgsubject = subj004
> trglabel = ./lh.BA3b.thresh.label
> regmethod = surface
>
> srchemi = lh
> trghemi = lh
> trgsurface = white
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
> FREESURFER_HOME /usr/local/freesurfer/dev
> Loading source label.
> Invalid argument
> ERROR reading
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
> Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013
>
> For more details, see the log file
> /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
>
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[Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado

Hello,

I ran recon-all and left it running Friday afternoon/evening. When I next
checked it this morning, the script had finished with errors. Looks like
there was a problem with the file:
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a
symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage

Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the
script couldn't open it. Thoughts?

-Ronny

Further info below:

machine: quito
Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
/usr/local/freesurfer/dev/bin/freesurfer
SUBJECTS_DIR:
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
Working Directory:
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig

** the exact command line I ran
recon-all -autorecon2-cp -autorecon3 -subjid subj004

** The command that caused the error (which was as a part of/ within the
recon-all script) is
mri_label2label --srcsubject fsaverage --srclabel
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
--trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
--regmethod surface

** ERROR MESSAGE RECEIVED **
Permission denied
mri_label2label: could not open label file
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

srclabel =
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = subj004
trglabel = ./lh.BA3b.thresh.label
regmethod = surface

srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR   
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer/dev
Loading source label.
Invalid argument
ERROR reading
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013

For more details, see the log file
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

2013-03-11 Thread Douglas Greve

Hi Christopher, I'm not sure I understand your question. What do you 
mean by "simple measurements"?
doug

On 3/11/13 10:59 AM, Christopher wrote:
> Thanks Doug. I can know visualize the resected area using freeview.
>
> As the output of mri_vol2surf produces an overlay and not a surface, 
> measurements of area or/and intersection with other outputs from 
> mri_vol2surf are not possible using mris_* functions.
> What is the best strategy to follow to be able to do simple 
> measurments on these mri_vol2surf outputs ? Transform to surface, but 
> how ?
>
> Thanks in advance,
>
> Christopher
>
>
>> The output of mri_vol2surf is not a surface but an overlay on a surface.
>> You will need to run something like:
>>
>> freeview -f
>> $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
>>
>> You'll need to set the threshold to 0.5 in order to see the mask.
>> doug
>
>

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Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

2013-03-11 Thread Alex Hanganu


Hi Jorge,

I see now:

/Y, Beta2, sided_pval/ - have the same number of columns
/fstats.pval/ and /fstats.sgn/ were not generated (or they are not in 
the workspace) !


a.


Le 3/11 11:53, jorge luis a écrit :

Hi Alex

The cmd

/[detvtx,sided_pval,pth//] = 
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//

/

only takes a few seconds to finish. Please check if /Y, Beta2, 
fstats.pval/,/fstats.sgn,/ /sided_pval

/
all have the same number of columns.

Best
-Jorge


*De:* Alex Hanganu 
*Para:* Jorge L. Bernal-Rusiel ; FS
Mailing List 
*Enviado:* Lunes 11 de marzo de 2013 10:53
*Asunto:* [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

Hi Jorge,

I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2];
X = [ones(length(M),1) M M(:,1).*M(:,2)];
[stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
fstats = lme_mass_F1(stats,CM);
fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
nv = length(stats);
Beta2 = zeros(1,nv);
//Beta//4= zeros(1,nv);//
//for //
//.
.//
//end;
//Beta2_Beta//4//_sum = Beta2//+Beta4;//
//mri1 = mri;//
//mri1.vols//z(//4) = 1;//
//fs//_write_Y(Beta2,mri1,'/Beta2.mgh'//);//
//[detvtx,sided_pval,pth//] =
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//
//fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');//
//
//??? Error using //===> reshape//
//To RESHAPE the number of elements must not change.//
//
//Error in ==//> fs_write_Y at 21//
//save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/
-

the cmd: /[detvtx //]/ didn't work, but there was no error
message. I remember in the past this cmd took around 1 day to
analyzebut now it didn't work at all.

/fs_write_Y/ worked fine for Beta, alsothis time I used the
/mri//1 //= mri/ cmd- so the /reshape /error shouldn't be
associated with this.

Please help !

best regards,

Alex.

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Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

2013-03-11 Thread jorge luis

Hi Alex

The cmd 

[detvtx,sided_pval,pth] = lme_mass_FDR2(fstats.pval,fstats.sgn,lhcortex,0.05,0);


only takes a few seconds to finish. Please check if  Y, Beta2, 
fstats.pval,fstats.sgn, sided_pval 

all have the same number of columns.

Best
-Jorge




>
> De: Alex Hanganu 
>Para: Jorge L. Bernal-Rusiel ; FS Mailing List 
> 
>Enviado: Lunes 11 de marzo de 2013 10:53
>Asunto: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work
> 
>
>Hi Jorge,
>
>I got an error in the correction, and I can't find a way out.
>this is the cmd I use:
>-
>[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
>Qdec = fReadQdec('.../LME.dat');
>Qdec = rmQdecCol(Qdec,1);
>sID = Qdec(2:end,1);
>Qdec = rmQdecCol(Qdec,1);
>M = Qdec2num(Qdec);
>ni = [2 2... 2];
>X = [ones(length(M),1) M M(:,1).*M(:,2)];
>[stats,st] =
lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
>CM.C = [0 0 0 1];
>fstats = lme_mass_F1(stats,CM);
>fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
>nv = length(stats);
>Beta2 = zeros(1,nv);
>Beta4= zeros(1,nv);
>for 
>.
>.
>end;
>Beta2_Beta4_sum = Beta2+Beta4;
>mri1 = mri;
>mri1.volsz(4) = 1;
>fs_write_Y(Beta2,mri1,'/Beta2.mgh');
>[detvtx,sided_pval,pth] = 
>lme_mass_FDR2(fstats.pval,fstats.sgn,lhcortex,0.05,0);
>fs_write_Y(sided_pval,mri1,'.../spval.mgh');
>
>??? Error using ===> reshape
>To RESHAPE the number of elements must not change.
>
>Error in ==> fs_write_Y at 21
>save_mgh(reshape(Y',mri.volsz),fname,mri.M,mri.mr_parms);
>-
>
>the cmd: [detvtx ] didn't work, but there was no error message. I remember 
>in the past this cmd took around 1 day to analyzebut now it didn't work at all.
>
>fs_write_Y worked fine for Beta, alsothis time I used the mri1 = mri cmd- so 
>the reshape error shouldn't be associated with this.
>
>Please help !
>
>best regards,
>
>Alex.
> 
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>at
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Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

2013-03-11 Thread Michael Harms


Hi Laura,
If you're looking for another reference that has used this approach, you
could see our 2010 paper:
http://www.ncbi.nlm.nih.gov/pubmed/20118463

cheers,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From:  "Laura M. Tully" 
Date:  Saturday, March 9, 2013 5:58 PM
To:  "Anderson M. Winkler" 
Cc:  free 
Subject:  Re: [Freesurfer] mean thickness covariate, mean area covariate, &
mri_anatomical_stats for multiple subjects

Hi Anderson, 

Thanks, that reference is particularly helpful.

Re: the usage of the white versus pial area question - I believe that the
default area calculation in freesurfer is the white surface area, so unless
one specifies the pial in calculations, the standard surface area output for
surface area by parcellation will be white. This suggests the use of the
global measurement of white surface area as a covariate would be an
appropriate, whereas if one was specifically using pial surface area in the
aparc calculations, it may make more sense to use the global measure of pial
surface area as a covariate, correct? As for which one to use in analysis,
I'm not sure - conceptually it might be that the pial surface area is more
sensitive to atrophy but I don't know if that is born out in the data...

Laura. 


On Sat, Mar 9, 2013 at 11:49 AM, Anderson M. Winkler
 wrote:
> Hi Laura,
> 
> 
>> 1. Is there a paper that I could cite that recommends using mean cortical
>> thickness rather than ICV?
>  
> If it helps, we used cortical thickness and area as covariate for the
> respective analysis of regional thickness and area. Brain volume, which is
> more closely related to ICV, correlates well with area, but not with
> thickness. We computed a global thickness average by weighting the thickness
> of each region by their respective areas. The paper is this:
> http://surfer.nmr.mgh.harvard.edu/ftp/articles/Winkler2010_Neuroimage.pdf
>  
>> 1. Would the same logic be applied to surface area analyses? i.e. would it
>> make more sense to use mean surface area as a covariate in surface area
>> analyses? If so, which mean surface area calculation should be used?
>> mri_anatomical_stats can produce both pial and white matter mean surface area
>> stats. 
> 
> Yes, I think so. It seems more logical to have a global measurement of area in
> the model than a measurement of brain volume. On the other hand, area and
> thickness are not correlated one to another (as shown in the paper above and
> also in Panizzon et al, 2009, in Cereb Cortex). I don't think there is a clear
> answer on which, pial or white, should be used. I'd probably go with the
> white, as I think it may be more robust to image quality, but I admit this is
> a rather weak justification and if the images are good, perhaps the pial could
> be just as good, despite the fact that it somewhat depends on the white for
> its construction.
> 
>  
>> 1. Is there a way to run mri_anatomical_stats on multiple subjects at once
>> and write to a tablefile (similar to asegstats2table output)?
> 
> I think you can use aparcstats2table, then add up all regions in a spreadsheet
> (or even with awk/gawk). Alternatively, you can use "grep" to pick the
> WhiteSurfArea for each hemisphere from the ?h.aparc.stats file for each
> subject.
> 
> Hope this helps!
> 
> All the best,
> 
> Anderson
> 



-- 
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
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but d

[Freesurfer] LME - lme_mass_FDR2 correction doesn't work

2013-03-11 Thread Alex Hanganu


Hi Jorge,

I got an error in the correction, and I can't find a way out.
this is the cmd I use:
-
/[Y,mri] = fs_read_Y('.../thickness-sm10.mgh');
Qdec = fReadQdec('.../LME.dat');
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
ni = [2 2... 2];
X = [ones(length(M),1) M M(:,1).*M(:,2)];
[stats,st] = lme_mass_fit_vw1(X,[1],Y,ni,lhcortex);
CM.C = [0 0 0 1];
fstats = lme_mass_F1(stats,CM);
fs_write_fstats(fstats,mri,'.../lh.sig.mgh','sig');
nv = length(stats);
Beta2 = zeros(1,nv);
//Beta//4= zeros(1,nv);//
//for //
//.
.//
//end;
//Beta2_Beta//4//_sum = Beta2//+Beta4;//
//mri1 = mri;//
//mri1.vols//z(//4) = 1;//
//fs//_write_Y(Beta2,mri1,'/Beta2.mgh'//);//
//[detvtx,sided_pval,pth//] = 
lme//_mass_F//DR2(fstats.pval,fstats.sgn,lhcor//tex,0.05,0);//

//fs_write_Y(sided_pva//l,mri1,//'.../spval.mgh');//
//
//??? Error using //===> reshape//
//To RESHAPE the number of elements must not change.//
//
//Error in ==//> fs_write_Y at 21//
//save_mgh(reshape(Y',mri.volsz),//fname,mri.M,mri.mr//_parms);/
-

the cmd: /[detvtx //]/ didn't work, but there was no error message. 
I remember in the past this cmd took around 1 day to analyzebut now it 
didn't work at all.


/fs_write_Y/ worked fine for Beta, alsothis time I used the /mri//1 //= 
mri/ cmd- so the /reshape /error shouldn't be associated with this.


Please help !

best regards,

Alex.
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Re: [Freesurfer] nu_correct: Command not found error

2013-03-11 Thread Nick Schmansky

Sinead,

In your freesurfer directory, is there an 'mni' directory?  under that
directory is a 'bin' directory where nu_correct should be.

Nick

> Hi Nick,
>
> I had a look in the bin directory and there is a command called
> 'mri_nu_correct.mni'. Is this the command the script is trying to call?
> This is the only nu_correct command I could find. I specify v5.2 in the
> script as there are other versions installed on the clusters.
>
> Thanks again for your help!
>
> Sinead
>
> On 9 March 2013 23:23, Nick Schmansky  wrote:
>
>> Sinead,
>>
>> Is 'nu_correct' in your freesurfer/mni/bin directory?  Are you being
>> careful to run the setup script for just freeview 5.2 and not other
>> packages or versions which might mess-up the perl paths?
>>
>> Nick
>>
>>
>> On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote:
>> > Dear all,
>> >
>> >
>> > I am currently running cortical thickness analysis using Freesurfer
>> > v5.2 on a high performance computing cluster however, when I run the
>> > 'recon_all' command I get the following error
>> >
>> >
>> > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
>> > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
>> > INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140
>> > Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0
>> > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
>> > EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>> > nu_correct: Command not found.
>> > #
>> > #@# MotionCor Thu Mar  7 11:44:10 GMT 2013
>> > Found 1 runs
>> > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
>> > Checking for (invalid) multi-frame inputs...
>> > WARNING: only one run found. This is OK, but motion
>> > correction cannot be performed on one run, so I'll
>> > copy the run to rawavg and continue.
>> >
>> >
>> >  cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
>> /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
>> >
>> >
>> > /home/users/kellys37/CT_TEST/CON3140/001
>> >
>> >
>> >  mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
>> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
>> >
>> >
>> > mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
>> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> > reading
>> > from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz...
>> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> > i_ras = (-0.9997, 0.0244327, -0.00148148)
>> > j_ras = (0.0239203, 0.987991, 0.152651)
>> > k_ras = (-0.00519336, -0.15257, 0.988279)
>> > Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256,
>> > 180) voxels.
>> > Data is conformed to 1 mm size and 256 voxels for all directions
>> > changing data type from float to uchar (noscale = 0)...
>> > MRIchangeType: Building histogram
>> > Reslicing using trilinear interpolation
>> > writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
>> >
>> >
>> >  mri_add_xform_to_header
>> > -c
>> /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm
>> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
>> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
>> >
>> >
>> > INFO: extension is mgz
>> > #
>> > #@# Talairach Thu Mar  7 11:44:32 GMT 2013
>> > /home/users/kellys37/CT_TEST/CON3140/001/mri
>> >
>> >
>> >  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>> > --no-rescale --i orig.mgz --o orig_nu.mgz
>> >
>> >
>> > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
>> > EST 2012 x86_64 x86_64 x86_64 GNU/Linux
>> >
>> >
>> > recon-all -s 001 exited with ERRORS at Thu Mar  7 11:44:38 GMT 2013
>> >
>> >
>> > For more details, see the log
>> > file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log
>> > To report a problem, see
>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> >
>> >
>> >
>> >
>> > I had did not encounter this error when using an older version of
>> > Freesurfer on our clusters. Do you know if there is any way to resolve
>> > this problem? Any advice would be appreciated.
>> >
>> >
>> > Kind regards,
>> >
>> >
>> > Sinead
>> >
>> >
>> > --
>> > Sinead Kelly
>> > Neuropsychiatric Genetics Group
>> > Trinity Centre
>> > St. James's Hospital
>> > Dublin 8
>> > ___
>> > 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

[Freesurfer] Definition of anatomical regions

2013-03-11 Thread akshay pai

Hi,

I have been working on a DBM based method to obtain longitudinal atrophy on
some brain data. To quantify ROI, i use aseg.mgz. Several papers talk about
Whole Brain, ventricular atrophy but do not actually define what
substructures they use? It will be great if somebody can help me get the
actual definition of whole brain and ventricles. For ex: WM Hypointensities
are part of whole brain?, Since they increase in volume.

Thank you ,

Akshay
University of Copehagen
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Re: [Freesurfer] nu_correct: Command not found error

2013-03-11 Thread Sinead Kelly

Hi Nick,

I had a look in the bin directory and there is a command called
'mri_nu_correct.mni'. Is this the command the script is trying to call?
This is the only nu_correct command I could find. I specify v5.2 in the
script as there are other versions installed on the clusters.

Thanks again for your help!

Sinead

On 9 March 2013 23:23, Nick Schmansky  wrote:

> Sinead,
>
> Is 'nu_correct' in your freesurfer/mni/bin directory?  Are you being
> careful to run the setup script for just freeview 5.2 and not other
> packages or versions which might mess-up the perl paths?
>
> Nick
>
>
> On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote:
> > Dear all,
> >
> >
> > I am currently running cortical thickness analysis using Freesurfer
> > v5.2 on a high performance computing cluster however, when I run the
> > 'recon_all' command I get the following error
> >
> >
> > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
> > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
> > INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140
> > Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0
> > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
> > EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> > nu_correct: Command not found.
> > #
> > #@# MotionCor Thu Mar  7 11:44:10 GMT 2013
> > Found 1 runs
> > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
> > Checking for (invalid) multi-frame inputs...
> > WARNING: only one run found. This is OK, but motion
> > correction cannot be performed on one run, so I'll
> > copy the run to rawavg and continue.
> >
> >
> >  cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
> /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
> >
> >
> > /home/users/kellys37/CT_TEST/CON3140/001
> >
> >
> >  mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
> >
> >
> > mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading
> > from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz...
> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-0.9997, 0.0244327, -0.00148148)
> > j_ras = (0.0239203, 0.987991, 0.152651)
> > k_ras = (-0.00519336, -0.15257, 0.988279)
> > Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256,
> > 180) voxels.
> > Data is conformed to 1 mm size and 256 voxels for all directions
> > changing data type from float to uchar (noscale = 0)...
> > MRIchangeType: Building histogram
> > Reslicing using trilinear interpolation
> > writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
> >
> >
> >  mri_add_xform_to_header
> > -c /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm
> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
> >
> >
> > INFO: extension is mgz
> > #
> > #@# Talairach Thu Mar  7 11:44:32 GMT 2013
> > /home/users/kellys37/CT_TEST/CON3140/001/mri
> >
> >
> >  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
> > --no-rescale --i orig.mgz --o orig_nu.mgz
> >
> >
> > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
> > EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> >
> >
> > recon-all -s 001 exited with ERRORS at Thu Mar  7 11:44:38 GMT 2013
> >
> >
> > For more details, see the log
> > file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log
> > To report a problem, see
> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> >
> >
> > I had did not encounter this error when using an older version of
> > Freesurfer on our clusters. Do you know if there is any way to resolve
> > this problem? Any advice would be appreciated.
> >
> >
> > Kind regards,
> >
> >
> > Sinead
> >
> >
> > --
> > Sinead Kelly
> > Neuropsychiatric Genetics Group
> > Trinity Centre
> > St. James's Hospital
> > Dublin 8
> > ___
> > 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.
>



-- 
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

2013-03-11 Thread Christopher

Thanks Doug. I can know visualize the resected area using freeview.

As the output of mri_vol2surf produces an overlay and not a surface, 
measurements of area or/and intersection with other outputs from 
mri_vol2surf are not possible using mris_* functions.
What is the best strategy to follow to be able to do simple measurments 
on these mri_vol2surf outputs ? Transform to surface, but how ?

Thanks in advance,

Christopher


> The output of mri_vol2surf is not a surface but an overlay on a surface.
> You will need to run something like:
>
> freeview -f
> $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
>
> You'll need to set the threshold to 0.5 in order to see the mask.
> doug

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Re: [Freesurfer] bbregister error

2013-03-11 Thread Douglas Greve

Hi Charles, can you verify that brainmask.mgz exists for that subject? 
What do you get if you run

stem2fname $SUBJECTS_DIR/$subject/mri/brainmask

doug

On 3/11/13 4:07 AM, Charles Malpas wrote:

Hi Doug,

I think I am having the same problem, but only when running on our Red 
Hut cluster (CentOS 6 was fine). I have attached the terminal output 
with --debug

Many thanks,

- Charles

On 9 March 2013 03:47, Douglas N Greve > wrote:

Salil, can you run fslregister with --debug as the first option,
capture
the terminal output, and send it to me?
thanks
doug

On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
>
> Hi Salil - I'm cc-ing Doug who may be able to help. The error
happens
> when bbregister invokes fslregister, in this particular line of
> fslregister:
>   set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
>
> When run on brainmask.mgz, it returns "ERROR: could not
determine file".
>
> a.y
>
> On Wed, 6 Mar 2013, Salil Soman wrote:
>
>>
>> Thank you for your email. Changing the mask option got me past the
>> error I
>> was having initially, but now I get these new errors:
>>
>> mri_convert ERROR: could not determine file for
>>

/mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
>>
>> ter.30396/fslregister/refvol.fslregister.nii
>> mri_convert ERROR: could not determine file for
>>

/mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
>>
>> ter.30396/fslregister/refvol.fslregister.nii
>>
>> Thank you for your consideration.
>>
>> Best wishes,
>>
>> -S
>>
>> On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki
>> mailto:ayend...@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi Salil - The problem is that you've set dob0 = 1 but you
haven't set
>> b0mlist and b0plist, so it doesn't know where to find your
field maps
>> to do
>> the B0 unwarping.
>>
>> a.y
>>
>>
>>
>
>

--
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

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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http://www.partners.org/complianceline . If the e-mail was sent to
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--
*Charles Malpas *
Master of Psychology (Clinical Neuropsychology) / PhD Candidate
Melbourne School of Psychological Sciences & Department of Medicine (RMH)
The University of Melbourne 3010

*Melbourne Brain Centre @ RMH*
Neuropsychiatry Research Group**
Level 4, Main Building, Royal Melbourne Hospital
Phone: 0451 116 434
Email: c.mal...@student.unimelb.edu.au 

Skype: charles.malpas

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[Freesurfer] qdec question

[Freesurfer] qdec question

Re: [Freesurfer] Extract pial surface

[Freesurfer] surface area mesurment and qatools

[Freesurfer] Extract pial surface

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

[Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

Re: [Freesurfer] LME - lme_mass_FDR2 correction doesn't work

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

[Freesurfer] LME - lme_mass_FDR2 correction doesn't work

Re: [Freesurfer] nu_correct: Command not found error

[Freesurfer] Definition of anatomical regions

Re: [Freesurfer] nu_correct: Command not found error

Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

Re: [Freesurfer] bbregister error

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