[Freesurfer] qdec GLMDesign Problem

[Bruehl, Hannah]

Hi there,

I am having a problem with qdec when trying to rerun analyses (meaning this 
worked before), I get the following error message:

Data table loading completed successfully.
SUBJECTS_DIR is '/Users/bruehh01/Borderline_2'
ERROR: QdecGlmDesign::Create: could not create directory 
/Users/bruehh01/Borderline_2/qdec/Untitled


Since I haven't changed anything since I last ran analyses, I don't understand 
what the problem is. Any suggestions?

Thanks and regards,

Hannah



..
Dr. Hannah Brühl
Freie Universität Berlin
Institut für Psychologie
Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft
Habelschwerdter Allee 45 — Raum JK 25/222h 
14195 Berlin
Tel.: +49 (0)30 838 564 72
..



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Re: [Freesurfer] converting analyse roi to fs

[Bruce Fischl]

Hi Prapti,

FreeSurfer can read analyze directly, but you have to be careful about 
left/right reversals and the orientation being incorrect in general, as 
analyze doesn't contain the direction cosines

cheers
Bruce


On Thu, 5 Aug 2010, 
Prapti Gautam wrote:

> Dear FreeSurfers,
>
>
>
> I am trying to convert an Analyze object map (saved as a set of .img
> /.hdr files) where I've traced ROIs so that I can load them as labels or
> overlays in FreeSurfer. Has anybody done this before? What would be the
> best way to proceed?
>
>
>
> Thanks,
>
>
>
> Prapti
>
>
>
>
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Re: [Freesurfer] keyboard problem in freesurfer

[Bruce Fischl]

thanks Don,

Katie: what OS are you running?

Bruce
On Wed, 4 Aug 2010, Don Hagler wrote:

>
> We had exactly that problem on machines running RedHat 5, but it was solved 
> by reinstalling with the latest CentOS.
>
>
> From: kc...@bu.edu
> Date: Wed, 4 Aug 2010 15:44:52 -0400
> To: fis...@nmr.mgh.harvard.edu
> CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] keyboard problem in freesurfer
>
> Nope, no errors when tksurfer starts, and I've tried running it with both my 
> own data/folder and with the tutorial data/folders, and have the same 
> problem.  I don't currently have freesurfer installed on a laptop, and the 
> only laptop I have access to is a mac (whereas I am using linux for most of 
> my analysis).  I can see what happens if I try installing it on the mac and 
> see if it has the same problem, but I assume it's somehow specific to my 
> linux machine if others aren't having the same problem.
>
>
> Katie
>
> On Wed, Aug 4, 2010 at 3:19 PM, Bruce Fischl  
> wrote:
>
>
> Hi Katie,
>
> can you replicate this problem on a laptop? If so, maybe you want to swing by 
> MGH with it and we can take a look? There are no errors when tksurfer starts?
>
> Bruce
>
> On Wed, 4 Aug 2010, Katie Bettencourt wrote:
>
>
>
>
> Ok, I tried to unset the FSLTCLSH variable (which is the only one that came
>
> up when I grep TCL) to see if that allowed me to use keyboard input with
>
> tksurfer, but it didn't work.
>
>
>
> I really need to be able to use the keyboard with tksurfer so that I can
>
> save label files and rgbs, etc.  Is there any way I can get this fixed?
>
> Please?
>
>
>
> Katie
>
>
>
>
>
>
>
>
> 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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>
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> contains patient information, please contact the Partners Compliance HelpLine 
> at
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> properly
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Re: [Freesurfer] aparc.anot of average contains 35 ROIs

[Douglas N Greve]

make_average_surface is not using the latest atlas when creating
the .annot files.  below is a link to a fixed version of make_average_surface
which you should copy to your $FREESURFER_HOME/bin directory.

doug




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


wanlin wrote:
> HI,
> I am using freesurfer4.5.0. After processed using recon-all, 
> the ?aparc.annot of each subject contains 36 ROIs (including insula), 
> However the ?aparc.annot of average subject ( make_average_subject) 
> only has 35 ROIs(without insula). Did i do anything wrong or it is a 
> bug? Thanks.
>
>
>
> 
>
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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

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Re: [Freesurfer] keyboard problem in freesurfer

[Katie Bettencourt]

Centos 5.5, which seems to be the newest one.  I guess I could try
reinstalling it.

Katie

On Thu, Aug 5, 2010 at 9:40 AM, Bruce Fischl wrote:

> thanks Don,
>
> Katie: what OS are you running?
>
> Bruce
>
> On Wed, 4 Aug 2010, Don Hagler wrote:
>
>
>> We had exactly that problem on machines running RedHat 5, but it was
>> solved by reinstalling with the latest CentOS.
>>
>>
>> From: kc...@bu.edu
>> Date: Wed, 4 Aug 2010 15:44:52 -0400
>> To: fis...@nmr.mgh.harvard.edu
>> CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] keyboard problem in freesurfer
>>
>> Nope, no errors when tksurfer starts, and I've tried running it with both
>> my own data/folder and with the tutorial data/folders, and have the same
>> problem.  I don't currently have freesurfer installed on a laptop, and the
>> only laptop I have access to is a mac (whereas I am using linux for most of
>> my analysis).  I can see what happens if I try installing it on the mac and
>> see if it has the same problem, but I assume it's somehow specific to my
>> linux machine if others aren't having the same problem.
>>
>>
>> Katie
>>
>> On Wed, Aug 4, 2010 at 3:19 PM, Bruce Fischl 
>> wrote:
>>
>>
>> Hi Katie,
>>
>> can you replicate this problem on a laptop? If so, maybe you want to swing
>> by MGH with it and we can take a look? There are no errors when tksurfer
>> starts?
>>
>> Bruce
>>
>> On Wed, 4 Aug 2010, Katie Bettencourt wrote:
>>
>>
>>
>>
>> Ok, I tried to unset the FSLTCLSH variable (which is the only one that
>> came
>>
>> up when I grep TCL) to see if that allowed me to use keyboard input with
>>
>> tksurfer, but it didn't work.
>>
>>
>>
>> I really need to be able to use the keyboard with tksurfer so that I can
>>
>> save label files and rgbs, etc.  Is there any way I can get this fixed?
>>
>> Please?
>>
>>
>>
>> Katie
>>
>>
>>
>>
>>
>>
>>
>>
>> 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.
>>
>>
>>
>>
>>
>>
>> ___
>> 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.
>>
>
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[Freesurfer] Command line to map volume data to surface data

[Xinian Zuo]

Dear surfers,

Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
surface in the way:

tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg

, then save surface overlay as a mgh file. My question is, how can I
get the identical mgh data by using a command line without launching
the tksurfer gui? I found there is a command mri_vol2surf, but not
sure about these default settings in tksurfer gui. Really appreciate
it if some know and like to give your suggestions.

-- 
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: (212) 263 2485
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Re: [Freesurfer] Command line to map volume data to surface data

[Douglas N Greve]

mri_vol2surf is the right command. Have you looked at the help for it? 
You can get it by running

mri_vol2surf --help

I think tksurfer uses a projfrac of 0 and nearest neighbor 
interpolation. You can load the result directly into tksurfer to see if 
it looks the same.

doug


Xinian Zuo wrote:
> Dear surfers,
>
> Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
> surface in the way:
>
> tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg
>
> , then save surface overlay as a mgh file. My question is, how can I
> get the identical mgh data by using a command line without launching
> the tksurfer gui? I found there is a command mri_vol2surf, but not
> sure about these default settings in tksurfer gui. Really appreciate
> it if some know and like to give your suggestions.
>
>   

-- 
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

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Re: [Freesurfer] qdec GLMDesign Problem

[Nick Schmansky]

qdec by defaults puts its results in the directory
$SUBJECTS_DIR/qdec/Untitled, which can create problems when qdec is run
multiple times.  try either deleting that Untitled dir (it might have
permissions set to another user), or try changing the name of the design
in the Design tab (look for the text box with 'Untitled') which will
create a new directory with your design name and save stuff there.  in
general it is best to give different analysis (say, left and right hemi,
or different factor selections) their own name so results are saved in
separate directories (also this is an easy way to recover results later,
or to view them in tksurfer or with other tools).

n.
 
On Thu, 2010-08-05 at 11:52 +0200, Bruehl, Hannah wrote:
> Hi there,
> 
> I am having a problem with qdec when trying to rerun analyses (meaning this 
> worked before), I get the following error message:
> 
> Data table loading completed successfully.
> SUBJECTS_DIR is '/Users/bruehh01/Borderline_2'
> ERROR: QdecGlmDesign::Create: could not create directory 
> /Users/bruehh01/Borderline_2/qdec/Untitled
> 
> 
> Since I haven't changed anything since I last ran analyses, I don't 
> understand what the problem is. Any suggestions?
> 
> Thanks and regards,
> 
> Hannah
> 
> 
> 
> ..
> Dr. Hannah Brühl
> Freie Universität Berlin
> Institut für Psychologie
> Arbeitsbereich Emotionspsychologie und affektive Neurowissenschaft
> Habelschwerdter Allee 45 — Raum JK 25/222h 
> 14195 Berlin
> Tel.: +49 (0)30 838 564 72
> ..
> 
> 
> 
> ___
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> 
> 

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[Freesurfer] creation of special image...

[Gonzalo Rojas Costa]

Hi:

  How can I create an image such as the "Be happy" one that appeared in the
last slide of "Surface-based Analysis: Intersubject Registration and
Smoothing" PPT?...

  Sincerely,



Gonzalo Rojas Costa


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Re: [Freesurfer] creation of special image...

[Douglas N Greve]

There's no standard way to make that. That took a long time ...

Gonzalo Rojas Costa wrote:
> Hi:
>
>   How can I create an image such as the "Be happy" one that appeared in the
> last slide of "Surface-based Analysis: Intersubject Registration and
> Smoothing" PPT?...
>
>   Sincerely,
>
>
>
> Gonzalo Rojas Costa
>
>
> ___
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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

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Re: [Freesurfer] creation of special image...

[Pedro Paulo de Magalhães Oliveira Junior]

You can edit the .thickness files to use this hack.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Thu, Aug 5, 2010 at 12:40, Gonzalo Rojas Costa  wrote:

> Hi:
>
>  How can I create an image such as the "Be happy" one that appeared in the
> last slide of "Surface-based Analysis: Intersubject Registration and
> Smoothing" PPT?...
>
>  Sincerely,
>
>
>
> Gonzalo Rojas Costa
>
>
> ___
> 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] creation of special image...

[Bruce Fischl]

the easiest would be to draw a label on the inflated surface in tksurfer 
I would think. Or contract it out to Doug at some exhorbitant rate :)
On 
Thu, 5 Aug 2010, Douglas N Greve wrote:

> There's no standard way to make that. That took a long time ...
>
> Gonzalo Rojas Costa wrote:
>> Hi:
>>
>>   How can I create an image such as the "Be happy" one that appeared in the
>> last slide of "Surface-based Analysis: Intersubject Registration and
>> Smoothing" PPT?...
>>
>>   Sincerely,
>>
>>
>>
>> Gonzalo Rojas Costa
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
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Re: [Freesurfer] creation of special image...

[Pedro Paulo de Magalhães Oliveira Junior]

An easier way other than paying some exhorbitant rate to Doug is to use this
tutorial I've made and apply an UV texture.

http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel

Further consulting at an exhorbitant rate too :)
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Thu, Aug 5, 2010 at 12:51, Bruce Fischl wrote:

> the easiest would be to draw a label on the inflated surface in tksurfer
> I would think. Or contract it out to Doug at some exhorbitant rate :)
> On
> Thu, 5 Aug 2010, Douglas N Greve wrote:
>
> > There's no standard way to make that. That took a long time ...
> >
> > Gonzalo Rojas Costa wrote:
> >> Hi:
> >>
> >>   How can I create an image such as the "Be happy" one that appeared in
> the
> >> last slide of "Surface-based Analysis: Intersubject Registration and
> >> Smoothing" PPT?...
> >>
> >>   Sincerely,
> >>
> >>
> >>
> >> Gonzalo Rojas Costa
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >>
> >
> >
> ___
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>
>
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> is
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> e-mail
> contains patient information, please contact the Partners Compliance
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] creation of special image...

[Christian Lambert]

You can achieve it *very* easily using brain-visa package (see attached)

Bruce Fischl wrote:
the easiest would be to draw a label on the inflated surface in tksurfer 
I would think. Or contract it out to Doug at some exhorbitant rate :)
On 
Thu, 5 Aug 2010, Douglas N Greve wrote:


  

There's no standard way to make that. That took a long time ...

Gonzalo Rojas Costa wrote:


Hi:

  How can I create an image such as the "Be happy" one that appeared in the
last slide of "Surface-based Analysis: Intersubject Registration and
Smoothing" PPT?...

  Sincerely,



Gonzalo Rojas Costa


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Re: [Freesurfer] creation of special image...

[Pedro Paulo de Magalhães Oliveira Junior]

It's not the same. As you can see in Doug's image the smile is hidden by the
sulci and it shows up when you inflate the surface.
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile




On Thu, Aug 5, 2010 at 13:01, Christian Lambert  wrote:

> You can achieve it *very* easily using brain-visa package (see attached)
>
>
> Bruce Fischl wrote:
>
>> the easiest would be to draw a label on the inflated surface in tksurfer I
>> would think. Or contract it out to Doug at some exhorbitant rate :)
>> On Thu, 5 Aug 2010, Douglas N Greve wrote:
>>
>>
>>
>>> There's no standard way to make that. That took a long time ...
>>>
>>> Gonzalo Rojas Costa wrote:
>>>
>>>
 Hi:

  How can I create an image such as the "Be happy" one that appeared in
 the
 last slide of "Surface-based Analysis: Intersubject Registration and
 Smoothing" PPT?...

  Sincerely,



 Gonzalo Rojas Costa


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>>>
>>>
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Re: [Freesurfer] Command line to map volume data to surface data

[Xinian Zuo]

Hey Doug,

Following your suggestions, I ran the command below:

mri_vol2surf --mov data.nii.gz --reg
${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o
./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre
--projfrac 0 --interp nearest

but, seems the values in rh.test.vol2surf.mgh is different (little
higher) from what I got from tksurfer gui by saving overlay surface.
any thoughts?

Thanks!

On Thu, Aug 5, 2010 at 11:04 AM, Douglas N Greve
 wrote:
> mri_vol2surf is the right command. Have you looked at the help for it? You
> can get it by running
>
> mri_vol2surf --help
>
> I think tksurfer uses a projfrac of 0 and nearest neighbor interpolation.
> You can load the result directly into tksurfer to see if it looks the same.
>
> doug
>
>
> Xinian Zuo wrote:
>>
>> Dear surfers,
>>
>> Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
>> surface in the way:
>>
>> tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg
>>
>> , then save surface overlay as a mgh file. My question is, how can I
>> get the identical mgh data by using a command line without launching
>> the tksurfer gui? I found there is a command mri_vol2surf, but not
>> sure about these default settings in tksurfer gui. Really appreciate
>> it if some know and like to give your suggestions.
>>
>>
>
> --
> 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
>
>



-- 
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: (212) 263 2485
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[Freesurfer] averaging subject error

[rsachdev]

I am trying to average subjects and I don't know why I am getting this error.

Is it because limitations on user account or is it something else.

output subject: average
mri_add_xform_to_header -c auto
/space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz
/space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz
sh: /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz:
Permission denied
ERROR: make_average_surface



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Re: [Freesurfer] Command line to map volume data to surface data

[Douglas N Greve]

I'm not entirely sure how tksurfer is sampling from the volume to the 
surface. mri_vol2surf is the gold standard, so use that.

doug

Xinian Zuo wrote:
> Hey Doug,
>
> Following your suggestions, I ran the command below:
>
> mri_vol2surf --mov data.nii.gz --reg
> ${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o
> ./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre
> --projfrac 0 --interp nearest
>
> but, seems the values in rh.test.vol2surf.mgh is different (little
> higher) from what I got from tksurfer gui by saving overlay surface.
> any thoughts?
>
> Thanks!
>
> On Thu, Aug 5, 2010 at 11:04 AM, Douglas N Greve
>  wrote:
>   
>> mri_vol2surf is the right command. Have you looked at the help for it? You
>> can get it by running
>>
>> mri_vol2surf --help
>>
>> I think tksurfer uses a projfrac of 0 and nearest neighbor interpolation.
>> You can load the result directly into tksurfer to see if it looks the same.
>>
>> doug
>>
>>
>> Xinian Zuo wrote:
>> 
>>> Dear surfers,
>>>
>>> Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
>>> surface in the way:
>>>
>>> tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg
>>>
>>> , then save surface overlay as a mgh file. My question is, how can I
>>> get the identical mgh data by using a command line without launching
>>> the tksurfer gui? I found there is a command mri_vol2surf, but not
>>> sure about these default settings in tksurfer gui. Really appreciate
>>> it if some know and like to give your suggestions.
>>>
>>>
>>>   
>> --
>> 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
>>
>>
>> 
>
>
>
>   

-- 
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

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[Freesurfer] label 28 error

[Ilana Hairston]

Hi there,
We've been getting this label 28 error more often recently, and found that
by adding '-no-ca-align' to the end of recon-all command, the error went
away and visually the brain looks OK (at least first pass).
Does this make sense?
thanks
ilana


-- 
***
Ilana Hairston ,PhD
Research Assistant Professor
4250 Plymouth Rd. (rm 2439)
Psychiatry Department, Addiction Research Center
University of Michigan, Ann Arbor MI 48109-2700
Tel: 734-232-0232; Mobile: 650-906-8449
 
Sentimental Insomnia and Nostalgia Disorders Sciences


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Re: [Freesurfer] label 28 error

[Bruce Fischl]

Hi Ilana,

I think Martin has fixed this error. I wouldn't use -no-ca-align as it 
may degrade the accuracy depending on what sequence you are using for 
acquisition.

cheers
Bruce
On Thu, 5 Aug 2010, Ilana Hairston wrote:

> Hi there,
> We've been getting this label 28 error more often recently, and found that
> by adding '-no-ca-align' to the end of recon-all command, the error went
> away and visually the brain looks OK (at least first pass).
> Does this make sense?
> thanks
> ilana
>
>
>
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Re: [Freesurfer] creation of special image...

[Christophe Destrieux]

Hi

At the begining of the surface atlas, I used such a code to "paint" rgb 
files on the surface before the painting/filling tools were developped 
in fs interface. I don't remember the name of the code ; Maybe Bruce 
does  (I  don't remember if he wrote it or if Anders did) ?. It worked 
by 1/creating the flat representation of the surface, 2/by exporting it 
as a rgb picture , 3/ editing this picture with photoshop, 4 importing 
it back in fs;



cheers
> It's not the same. As you can see in Doug's image the smile is hidden 
> by the sulci and it shows up when you inflate the surface.
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br 
> -- For mobile: http://www.netfilter.com.br/mobile
>
>
>
>
> On Thu, Aug 5, 2010 at 13:01, Christian Lambert 
> mailto:c.lamb...@fil.ion.ucl.ac.uk>> wrote:
>
> You can achieve it *very* easily using brain-visa package (see
> attached)
>
>
> Bruce Fischl wrote:
>
> the easiest would be to draw a label on the inflated surface
> in tksurfer I would think. Or contract it out to Doug at some
> exhorbitant rate :)
> On Thu, 5 Aug 2010, Douglas N Greve wrote:
>
>  
>
> There's no standard way to make that. That took a long
> time ...
>
> Gonzalo Rojas Costa wrote:
>
>
> Hi:
>
>  How can I create an image such as the "Be happy" one
> that appeared in the
> last slide of "Surface-based Analysis: Intersubject
> Registration and
> Smoothing" PPT?...
>
>  Sincerely,
>
>
>
> Gonzalo Rojas Costa
>
>
> ___
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>
>
>  
>
>
>
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>  
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-- 
Christophe Destrieux,

Directeur du Département Communication et Multimedia
http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612

Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
37032 Tours - France
tel (33) 2 47 36 61 36  - fax (33) 2 47 36 62 07



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Re: [Freesurfer] averaging subject error

[Douglas N Greve]

It means that you do not have write permission to that directory. You 
need to find out who does and ask them to change the permissions.

doug

rsach...@nmr.mgh.harvard.edu wrote:
> I am trying to average subjects and I don't know why I am getting this error.
>
> Is it because limitations on user account or is it something else.
>
> output subject: average
> mri_add_xform_to_header -c auto
> /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz
> /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz
> sh: /space/huygens/1/users/dgow/subjects//average/mri/mni305.cor.mgz:
> Permission denied
> ERROR: make_average_surface
>
>
>
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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

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[Freesurfer] change overlay color

[Michael Scheel]

Hi FS experts, 

I want to change the visualization of some overlay data in tkmedit. Instead of 
the Heat (Red-Yellow) Color-Scale I'd like to use a Green-Red or Rainbow Color 
Scale.
Is there a way to achieve this? Do I need to create a respective LUT and where 
do I have to put it. 

thanks, michael
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Re: [Freesurfer] change overlay color

[Douglas N Greve]

sorry, there is no way to do this.

doug

Michael Scheel wrote:
> Hi FS experts, 
>
> I want to change the visualization of some overlay data in tkmedit. Instead 
> of the Heat (Red-Yellow) Color-Scale I'd like to use a Green-Red or Rainbow 
> Color Scale.
> Is there a way to achieve this? Do I need to create a respective LUT and 
> where do I have to put it. 
>
> thanks, michael
> ___
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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

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[Freesurfer] [freesurfer] installation failure

[Glen Lee]

 Dear freesurfer experts,
 I'm running into installation failure and can't quite figure this out (I'm
a novice Linux user too).
 It complains there is no such file or directory when I simply followed the
instruction by typing the command below in the /usr/local directory.

tar xzvf freesurfer-Linux-centos4-stable-pub-v4.5.0-full.tar.gz

Would anybody help me how to resolve this issue?
 Below is the error message and platform info. Many thanks!

 -GL
---
g...@ubuntu:/usr/local$ uname -a
Linux ubuntu 2.6.32-24-generic-pae #39-Ubuntu SMP Wed Jul 28 07:39:26 UTC
2010 i686 GNU/Linux.


tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh: Cannot
open: No such file or directory
freesurfer/average/surf/
tar: freesurfer/average/surf: Cannot mkdir: No such file or directory
freesurfer/average/surf/lh.sphere.reg
tar: freesurfer/average/surf/lh.sphere.reg: Cannot open: No such file or
directory
freesurfer/average/surf/rh.sphere.reg
tar: freesurfer/average/surf/rh.sphere.reg: Cannot open: No such file or
directory
freesurfer/average/lh.atlas2002_simple.gcs
tar: freesurfer/average/lh.atlas2002_simple.gcs: Cannot open: No such file
or directory
freesurfer/average/rigidly_aligned_brain_template.tif
tar: freesurfer/average/rigidly_aligned_brain_template.tif: Cannot open: No
such file or directory
freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst
tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst: Cannot open: No
such file or directory
freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr
tar: freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr: Cannot open: No
such file or directory
freesurfer/average/mni305.cor.subfov1.reg
tar: freesurfer/average/mni305.cor.subfov1.reg: Cannot open: No such file or
directory
freesurfer/average/rh.average.CURVATURE.tif
tar: freesurfer/average/rh.average.CURVATURE.tif: Cannot open: No such file
or directory
freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
tar:
freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs:
Cannot open: No such file or directory
freesurfer/average/mni_average_305.4dfp.img.rec
tar: freesurfer/average/mni_average_305.4dfp.img.rec: Cannot open: No such
file or directory
freesurfer/average/rh.average.curvature.filled.buckner40.tif
tar: freesurfer/average/rh.average.curvature.filled.buckner40.tif: Cannot
open: No such file or directory
freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr
tar: freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.hdr: Cannot
open: No such file or directory
freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec
tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.img.rec: Cannot open:
No such file or directory
freesurfer/average/711-2C_as_mni_average_305.4dfp.mat
tar: freesurfer/average/711-2C_as_mni_average_305.4dfp.mat: Cannot open: No
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freesurfer/average/mni_average_305.4dfp.ifh
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freesurfer/average/mni305.cor.subfov2.reg
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freesurfer/average/mni_average_305.4dfp.img
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freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh
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freesurfer/average/face.gca
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freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs
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freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec
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freesurfer/average/rh.average.tif
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freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
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freesurfer/average/mni152.register.dat
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freesurfer/average/lh.at

[Freesurfer] installation on mac

[Babb, Casey]

I am trying to install freesurfer on Mac OS X 10.6. I get an error message that 
there is no license file. Does anyone know how to get this license? I have 
joined the mail group and registered (I thought). Please help!

Casey
--
Casey Babb
Data Analyst
Department of Psychiatry
Washington University School of Medicine
314-747-3962

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Re: [Freesurfer] Command line to map volume data to surface data

[Xinian Zuo]

Nice to know the gold standard, now going with the mri_vol2surf :)
One more question: As for the overlay surface smoothing option, in
tksurfer gui, I can set it by following ' tools -> surface -> smooth
overlay -> number of steps', or give an value to option ' --surf-fwhm
' in the command. What is the relationship between the two?

xinian

On Thu, Aug 5, 2010 at 2:13 PM, Douglas N Greve
 wrote:
> I'm not entirely sure how tksurfer is sampling from the volume to the
> surface. mri_vol2surf is the gold standard, so use that.
>
> doug
>
> Xinian Zuo wrote:
>>
>> Hey Doug,
>>
>> Following your suggestions, I ran the command below:
>>
>> mri_vol2surf --mov data.nii.gz --reg
>> ${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o
>> ./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre
>> --projfrac 0 --interp nearest
>>
>> but, seems the values in rh.test.vol2surf.mgh is different (little
>> higher) from what I got from tksurfer gui by saving overlay surface.
>> any thoughts?
>>
>> Thanks!
>>
>> On Thu, Aug 5, 2010 at 11:04 AM, Douglas N Greve
>>  wrote:
>>
>>>
>>> mri_vol2surf is the right command. Have you looked at the help for it?
>>> You
>>> can get it by running
>>>
>>> mri_vol2surf --help
>>>
>>> I think tksurfer uses a projfrac of 0 and nearest neighbor interpolation.
>>> You can load the result directly into tksurfer to see if it looks the
>>> same.
>>>
>>> doug
>>>
>>>
>>> Xinian Zuo wrote:
>>>

 Dear surfers,

 Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
 surface in the way:

 tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg

 , then save surface overlay as a mgh file. My question is, how can I
 get the identical mgh data by using a command line without launching
 the tksurfer gui? I found there is a command mri_vol2surf, but not
 sure about these default settings in tksurfer gui. Really appreciate
 it if some know and like to give your suggestions.



>>>
>>> --
>>> 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
>>>
>>>
>>>
>>
>>
>>
>>
>
> --
> 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
>
>



-- 
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: (212) 263 2485
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[Freesurfer] skull strip on raw data

[Zhang, Yuning]

  hi,experts,

is there a way to use -skullstrip of freesurfer on my raw data (.mgz format)  
without any  correction,i.e , intensity correction , normalization ?

thanks a lot

yuning
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[Freesurfer] Sulci

[Oya, Hiroyuki]

Dear All,

Looking at pial surface, sulci looks wider than those of the actual
brain.
Is there any parameter to be tuned?

Does watershed threshold have any effect on the pial surface
estimation ?


Hiroyuki


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Re: [Freesurfer] aparc.anot of average contains 35 ROIs

[wanlin]

Thank you very much. But i still run into problems. There are errors
indicate that i don't have
"curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs" and file. Where
could i download it?

On Fri, Aug 6, 2010 at 12:38 AM, Douglas N Greve
wrote:

> make_average_surface is not using the latest atlas when creating
> the .annot files.  below is a link to a fixed version of
> make_average_surface
> which you should copy to your $FREESURFER_HOME/bin directory.
>
> doug
>
>
>
>
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
>
>
> wanlin wrote:
>
>> HI,
>>I am using freesurfer4.5.0. After processed using recon-all, the
>> ?aparc.annot of each subject contains 36 ROIs (including insula), However
>> the ?aparc.annot of average subject ( make_average_subject) only has 35
>> ROIs(without insula). Did i do anything wrong or it is a bug? Thanks.
>>
>>
>>
>> 
>>
>> ___
>> 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
>
>
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Re: [Freesurfer] skull strip on raw data

[Bruce Fischl]

sure, you can try it, but it won't work as well. Just run mri_watershed 
directly

cheers
Bruce
On Thu, 5 Aug 2010, Zhang, Yuning wrote:

>  hi,experts,
>
> is there a way to use -skullstrip of freesurfer on my raw data (.mgz format)  
> without any  correction,i.e , intensity correction , normalization ?
>
> thanks a lot
>
> yuning
>
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Re: [Freesurfer] Sulci

[Bruce Fischl]

How does the ?h.pial surface look overlaid on say the norm.mgz volume?

Bruce
On 
Thu, 5 Aug 2010, Oya, Hiroyuki wrote:

> Dear All,
>
> Looking at pial surface, sulci looks wider than those of the actual
> brain.
> Is there any parameter to be tuned?
>
> Does watershed threshold have any effect on the pial surface
> estimation ?
>
>
> Hiroyuki
>
>
>
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