[Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

[Reema Jayakar]

Hi Dr. Greve,

Thank you very much for getting back to me so promptly. If memory serves me
right, I am pretty sure that the orientations were incorrect in tkmedit but
will double check soon. Based on what you are saying and based on what I
read in the wiki about mri_convert it seems that I will be able to change
all of my nifti files using mri_convert and then I can use the newly
generated niftis to run reconall? Is this correct?

As I am very new to FS, I don't know what it means to give it an
orientation string? Is there some documentation where I can look this up
further?

In any case, thank you very much and I will keep you posted!

Best,
Reema

-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu


Message: 24
> Date: Tue, 22 Mar 2016 10:56:40 -0400
> From: Douglas Greve 
> Subject: Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1
> qform or sform are valid
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <56f15d28.7040...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="windows-1252"
>
> To check whether the orientation is correct, you can view it in freeview
> or tkmedit. When you click on the axial view it should show up axially,
> etc. Though you cannot tell whether it is left-right reversed this way.
> You cannot feed it a matrix, but you can specify the direction cosines
> on the mri_convert command line (-iid, -ijd, -ikd). You'll have to play
> with it a bit. You can also try giving it an orientation string instead.
> if you run mri_convert without any options, then it will give you lots
> of documentation.
>
> On 3/20/16 8:44 PM, Reema Jayakar wrote:
> > Hello FS list subscribers,
> >
> > Is there a way to manually feed FS with NIfTI-1 qform or sform
> > information? Or correctly add this information to the original .nii
> > files? My sense of the problem is that there is a problem with the
> > header information in my .nii files and FS cannot tell what is
> > anterior, posterior, left, right.
> >
> > That said, I am very new to FS and my interpretation of the error
> > could be wrong. So I am laying out the details below (recon-all.log is
> > also attached to this email):
> >
> >   * When I try to run recon-all there are no output images/files
> > generated and the message I get is that the Talairach transform
> > failed
> >   * When I try to run autorecon1 an autorecon2 with the "-notal check"
> > flag, FS does not give me any error message and proceeds with
> > generating output. However, I can visually see (via brainmask.mgz)
> > that oreintations are messed up (e.g., tried to register coronal
> > orientation on top of sagittal orientation)
> >   * This problem only occurs with .nii files from a particular study
> > that came out of a specific scanner. All my other data are running
> > through FS smoothly, which is why I think there is some problem
> > with the .nii files
> >   * Also, when I view my raw .nii images in FSL view none of the usual
> > orientation markers are visible to me, which again suggest that
> > they may be missing?
> >   * Unfortunately, I do not currently have the original .dcm files
> > available as this is a multi-site archival study
> >
> >
> > Any help you can provide to resolve this issue would be really
> > appreciated!
> >
> > Thank you,
> > Reema
> >
> >
> >
> > --
> > *Reema Jayakar, M.A.*
> > Doctoral Candidate - Clinical Neuropsychology
> > Health Resources and Services Administration (HRSA) Fellow
> > Department of Psychology
> > Georgia State University
> > Email: rjayak...@student.gsu.edu 
> ***
>
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Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

[Elissa Ash]

Thanks! I will take your advice and start to learn it. I appreciate your
help so much!!

Elissa

On Tue, Mar 22, 2016 at 6:28 PM, Bruce Fischl 
wrote:

> something like:
>
>
> set SUBJECTS = (subject1 subject2 ... subject60)
> foreach s ($SUBJECTS)
>foreach hemi (lh rh)
>mris_anatomical_stats -l $hemi.BA45.label $s $hemi
> end
> end
>
>
> definitely worth taking the time to learn! It will save you endless
> amounts of time in the longrun and it's an extremely useful skill We have
> pointers to linux primers if you want to look at one.
>
>
> cheers
> Bruce
>
> On Tue, 22 Mar 2016, Elissa Ash wrote:
>
> Thanks! I am a newbie so I think it would take me longer to learn how to
>> write the
>> script then to just do it one at a time! :)
>>
>> On Tue, Mar 22, 2016 at 6:23 PM, Bruce Fischl 
>> wrote:
>>   oh, no, but write a script to do it! That's what unix is for.
>>
>>   On Tue, 22 Mar
>>   2016, Elissa Ash wrote:
>>
>>   > Thanks Bruce
>>   > I am calculating the thickness for a given ROI (rh.BA45.label) and
>>   comparing it
>>   > across subjects and it is tedious to have to type in the command
>>   separately each time
>>   > (~60 subjects). I was hoping that there was a way to input
>> multiple
>>   subjects at once.
>>   > That's it.
>>   >
>>   > Thanks,
>>   > Elissa
>>   >
>>   > On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl
>>wrote:
>>   >   Hi Elissa
>>   >
>>   >   not really. What would you want it to do? There are tools
>> for
>>   tabulating
>>   >   the output of mris_anatomical_stats across subjects, if
>> that's
>>   what you
>>   >   are trying to do
>>   >
>>   >   cheers
>>   >   Bruce
>>   >   On Tue, 22 Mar 2016, Elissa Ash wrote:
>>   >
>>   >   >
>>   >   > Dear experts,
>>   >   >
>>   >   > Is there any way to run the mris_anatomical_stats command
>> on
>>   more than
>>   >   one subject at
>>   >   > a time?
>>   >   >
>>   >   > Thanks,
>>   >   > Elissa
>>   >   > --
>>   >   > Elissa Ash, MD, PhD
>>   >   > Director, Center for Memory and Attention Disorders
>>   >   > Department of Neurology
>>   >   > Tel Aviv Sourasky Medical Center
>>   >   >
>>   >   > 6 Weizmann St.
>>   >   > Tel Aviv 64239, Israel
>>   >   > 972-3-6973698
>>   >   > fax: 972-3-695-0365
>>   >   >
>>   >   >
>>   > ___
>>   > 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.
>>   >
>>   >
>>   >
>>   >
>>   > --
>>   > Elissa Ash, MD, PhD
>>   > Director, Center for Memory and Attention Disorders
>>   > Department of Neurology
>>   > Tel Aviv Sourasky Medical Center
>>   >
>>   > 6 Weizmann St.
>>   > Tel Aviv 64239, Israel
>>   > 972-3-6973698
>>   > fax: 972-3-695-0365
>>   >
>>   >
>>   ___
>>   Freesurfer mailing list
>>   Freesurfer@nmr.mgh.harvard.edu
>>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>> --
>> Elissa Ash, MD, PhD
>> Director, Center for Memory and Attention Disorders
>> Department of Neurology
>> Tel Aviv Sourasky Medical Center
>>
>> 6 Weizmann St.
>> Tel Aviv 64239, Israel
>> 972-3-6973698
>> fax: 972-3-695-0365
>>
>>
> ___
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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
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
>
>


-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, 

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

[Bruce Fischl]

something like:


set SUBJECTS = (subject1 subject2 ... subject60)
foreach s ($SUBJECTS)
   foreach hemi (lh rh)
   mris_anatomical_stats -l $hemi.BA45.label $s $hemi
end
end


definitely worth taking the time to learn! It will save you endless amounts 
of time in the longrun and it's an extremely useful skill We have pointers 
to linux primers if you want to look at one.


cheers
Bruce

On Tue, 22 Mar 
2016, Elissa 
Ash wrote:



Thanks! I am a newbie so I think it would take me longer to learn how to write 
the
script then to just do it one at a time! :)

On Tue, Mar 22, 2016 at 6:23 PM, Bruce Fischl  
wrote:
  oh, no, but write a script to do it! That's what unix is for.

  On Tue, 22 Mar
  2016, Elissa Ash wrote:

  > Thanks Bruce
  > I am calculating the thickness for a given ROI (rh.BA45.label) and
  comparing it
  > across subjects and it is tedious to have to type in the command
  separately each time
  > (~60 subjects). I was hoping that there was a way to input multiple
  subjects at once.
  > That's it.
  >
  > Thanks,
  > Elissa
  >
  > On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl
   wrote:
  >       Hi Elissa
  >
  >       not really. What would you want it to do? There are tools for
  tabulating
  >       the output of mris_anatomical_stats across subjects, if that's
  what you
  >       are trying to do
  >
  >       cheers
  >       Bruce
  >       On Tue, 22 Mar 2016, Elissa Ash wrote:
  >
  >       >
  >       > Dear experts,
  >       >
  >       > Is there any way to run the mris_anatomical_stats command on
  more than
  >       one subject at
  >       > a time?
  >       >
  >       > Thanks,
  >       > Elissa
  >       > --
  >       > Elissa Ash, MD, PhD
  >       > Director, Center for Memory and Attention Disorders
  >       > Department of Neurology
  >       > Tel Aviv Sourasky Medical Center
  >       >
  >       > 6 Weizmann St.
  >       > Tel Aviv 64239, Israel
  >       > 972-3-6973698
  >       > fax: 972-3-695-0365
  >       >
  >       >
  > ___
  > 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.
  >
  >
  >
  >
  > --
  > Elissa Ash, MD, PhD
  > Director, Center for Memory and Attention Disorders
  > Department of Neurology
  > Tel Aviv Sourasky Medical Center
  >
  > 6 Weizmann St.
  > Tel Aviv 64239, Israel
  > 972-3-6973698
  > fax: 972-3-695-0365
  >
  >
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  Freesurfer@nmr.mgh.harvard.edu
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--
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

[Elissa Ash]

Thanks! I am a newbie so I think it would take me longer to learn how to
write the script then to just do it one at a time! :)

On Tue, Mar 22, 2016 at 6:23 PM, Bruce Fischl 
wrote:

> oh, no, but write a script to do it! That's what unix is for.
>
> On Tue, 22 Mar
> 2016, Elissa Ash wrote:
>
> > Thanks Bruce
> > I am calculating the thickness for a given ROI (rh.BA45.label) and
> comparing it
> > across subjects and it is tedious to have to type in the command
> separately each time
> > (~60 subjects). I was hoping that there was a way to input multiple
> subjects at once.
> > That's it.
> >
> > Thanks,
> > Elissa
> >
> > On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >   Hi Elissa
> >
> >   not really. What would you want it to do? There are tools for
> tabulating
> >   the output of mris_anatomical_stats across subjects, if that's
> what you
> >   are trying to do
> >
> >   cheers
> >   Bruce
> >   On Tue, 22 Mar 2016, Elissa Ash wrote:
> >
> >   >
> >   > Dear experts,
> >   >
> >   > Is there any way to run the mris_anatomical_stats command on
> more than
> >   one subject at
> >   > a time?
> >   >
> >   > Thanks,
> >   > Elissa
> >   > --
> >   > Elissa Ash, MD, PhD
> >   > Director, Center for Memory and Attention Disorders
> >   > Department of Neurology
> >   > Tel Aviv Sourasky Medical Center
> >   >
> >   > 6 Weizmann St.
> >   > Tel Aviv 64239, Israel
> >   > 972-3-6973698
> >   > fax: 972-3-695-0365
> >   >
> >   >
> > ___
> > 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.
> >
> >
> >
> >
> > --
> > Elissa Ash, MD, PhD
> > Director, Center for Memory and Attention Disorders
> > Department of Neurology
> > Tel Aviv Sourasky Medical Center
> >
> > 6 Weizmann St.
> > Tel Aviv 64239, Israel
> > 972-3-6973698
> > fax: 972-3-695-0365
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>



-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365
___
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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] mris_anatomical_stats on more than one subject at a time?

[Bruce Fischl]

oh, no, but write a script to do it! That's what unix is for.

On Tue, 22 Mar 
2016, Elissa Ash wrote:

> Thanks Bruce
> I am calculating the thickness for a given ROI (rh.BA45.label) and comparing 
> it
> across subjects and it is tedious to have to type in the command separately 
> each time
> (~60 subjects). I was hoping that there was a way to input multiple subjects 
> at once.
> That's it.
> 
> Thanks,
> Elissa
> 
> On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl  
> wrote:
>   Hi Elissa
>
>   not really. What would you want it to do? There are tools for tabulating
>   the output of mris_anatomical_stats across subjects, if that's what you
>   are trying to do
>
>   cheers
>   Bruce
>   On Tue, 22 Mar 2016, Elissa Ash wrote:
>
>   >
>   > Dear experts,
>   >
>   > Is there any way to run the mris_anatomical_stats command on more than
>   one subject at
>   > a time?
>   >
>   > Thanks,
>   > Elissa
>   > --
>   > Elissa Ash, MD, PhD
>   > Director, Center for Memory and Attention Disorders
>   > Department of Neurology
>   > Tel Aviv Sourasky Medical Center
>   >
>   > 6 Weizmann St.
>   > Tel Aviv 64239, Israel
>   > 972-3-6973698
>   > fax: 972-3-695-0365
>   >
>   >
> ___
> 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.
> 
> 
> 
> 
> --
> Elissa Ash, MD, PhD
> Director, Center for Memory and Attention Disorders
> Department of Neurology
> Tel Aviv Sourasky Medical Center
> 
> 6 Weizmann St.
> Tel Aviv 64239, Israel
> 972-3-6973698
> fax: 972-3-695-0365
> 
>
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Re: [Freesurfer] mris_anatomical_stats on more than one subject at a time?

[Elissa Ash]

Thanks Bruce

I am calculating the thickness for a given ROI (rh.BA45.label) and
comparing it across subjects and it is tedious to have to type in the
command separately each time (~60 subjects). I was hoping that there was a
way to input multiple subjects at once. That's it.

Thanks,
Elissa

On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl 
wrote:

> Hi Elissa
>
> not really. What would you want it to do? There are tools for tabulating
> the output of mris_anatomical_stats across subjects, if that's what you
> are trying to do
>
> cheers
> Bruce
> On Tue, 22 Mar 2016, Elissa Ash wrote:
>
> >
> > Dear experts,
> >
> > Is there any way to run the mris_anatomical_stats command on more than
> one subject at
> > a time?
> >
> > Thanks,
> > Elissa
> > --
> > Elissa Ash, MD, PhD
> > Director, Center for Memory and Attention Disorders
> > Department of Neurology
> > Tel Aviv Sourasky Medical Center
> >
> > 6 Weizmann St.
> > Tel Aviv 64239, Israel
> > 972-3-6973698
> > fax: 972-3-695-0365
> >
> >
> ___
> 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.
>
>


-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365
___
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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] mris_anatomical_stats on more than one subject at a time?

[Bruce Fischl]

Hi Elissa

not really. What would you want it to do? There are tools for tabulating 
the output of mris_anatomical_stats across subjects, if that's what you 
are trying to do

cheers
Bruce
On Tue, 22 Mar 2016, Elissa Ash wrote:

> 
> Dear experts,
> 
> Is there any way to run the mris_anatomical_stats command on more than one 
> subject at
> a time?
> 
> Thanks,
> Elissa
> --
> Elissa Ash, MD, PhD
> Director, Center for Memory and Attention Disorders
> Department of Neurology
> Tel Aviv Sourasky Medical Center
> 
> 6 Weizmann St.
> Tel Aviv 64239, Israel
> 972-3-6973698
> fax: 972-3-695-0365
> 
>
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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
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[Freesurfer] mris_anatomical_stats on more than one subject at a time?

[Elissa Ash]

Dear experts,

Is there any way to run the mris_anatomical_stats command on more than one
subject at a time?

Thanks,
Elissa
-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365
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Re: [Freesurfer] mris_flatten error

[Ji Won Bang]

Dear. All.

I tried tksurfer and it works.. It's still very strange why tksurfer-sess
does not work.

The command line that worked successfully is:
tksurfer replay06 lh inflated -curv -gray

Then I overlayed the contrast result sig.nii.gz and the registration file.

Then I cut the plane and then flattenr the cortex.

The command that did not work well is:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower

For some reason, it calls fsaverage map and when I cut the plane, it seems
like the vertex is off the surface that I created... Probably, this cutting
work was done in other surface that I did not intend...

If anyone knows why it's happening, let me know.

Thank you!

Best,
Ji Won

2016-03-22 13:18 GMT-04:00 Ji Won Bang :

> Oh, I see.
>
> I showed the contrast results on a surface using the command:
> tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> -contrast UpperLower
>
> Then I select 3 points along a boundary between upper and lower visual
> fields (near calcarine sulcus) and press "Cut line". Then, select 4 points
> to define the cutting plane: 1 on lower side of the line, 2 on upper side
> of the line, 3 on the opposite surface (use rotation tool), and 4 to
> specify which portion of surface is kept, and press "Cur plane".
> File->Patch->Save Patch As {lh, rh}.oc.patch.3d
>
> This is the usual way that I've been doing...
>
> 1 thing that's weird is when I run:
> tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> -contrast UpperLower
> It calls fsaverage..such as:
> Reading source surface reg
> /home/jbang/Projects/replay/mri//replay06/surf/lh.sphere.reg
> Loading source data
> Reading target surface reg
> /home/jbang/Projects/replay/mri//fsaverage/surf/lh.sphere.reg
> Done
>
> Previously when everything went smooth, I think it did not call fsaverage.
>
> Is it normal?
>
> Thank you.
>
> Best,
> Ji Won
>
>
>
> 2016-03-22 13:06 GMT-04:00 Bruce Fischl :
>
>> then you must not have cut the patch from those surfaces. The error is
>> about a vertex # in the patch (147220), which is larger than the total
>> number of vertices in those surfaces (144977), so it's out of bounds. How
>> did you do the cutting?
>>
>>
>> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>>
>> Oh, I see.
>>>
>>> When I run all of these surfaces, it gave me the exactly same numbers...
>>>
>>> [jbang@cpu156 surf]$ mris_euler_number lh.inflated
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>>   F =2V-4:  289950 = 289954-4 (0)
>>>   2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.white
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>>   F =2V-4:  289950 = 289954-4 (0)
>>>   2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.pial
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>>   F =2V-4:  289950 = 289954-4 (0)
>>>   2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.orig
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>>   F =2V-4:  289950 = 289954-4 (0)
>>>   2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>>   F =2V-4:  289950 = 289954-4 (0)
>>>   2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>>   F =2V-4:  289950 = 289954-4 (0)
>>>   2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>>
>>> Thanks,
>>> Ji Won
>>>
>>> 2016-03-22 12:59 GMT-04:00 Bruce Fischl :
>>>   no, for all surfaces for the same hemi (lh and rh). lh.inflated.K
>>> is not
>>>   a surface - it's a scalar field over the surface. The ones that
>>> should be
>>>   the same are:
>>>
>>>   lh.inflated
>>>   lh.white
>>>   lh.pial
>>>   lh.orig
>>>   lh.sphere
>>>   lh.sphere.reg
>>>
>>>
>>>
>>>   and same for the rh (but different from the lh ones)
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Tue, 22 Mar 2016, Ji Won Bang wrote:
>>>
>>> Dear. Bruce.
>>>
>>> Thanks for your help.
>>>
>>> When I tried:
>>> mris_euler_number rh.inflated.K
>>>
>>> It gave me:
>>> nquads=15728644,  nvertices=574
>>> ERROR: MRISread: file 'rh.inflated.K' has many more faces
>>> than vertices!
>>> Probably trying to use a scalar data file as a surface!
>>>
>>> When I tried:
>>> mris_euler_number lh.inflated
>>>
>>> It gave me:
>>> eul

Re: [Freesurfer] PET voxelwise

[Douglas N Greve]

That looks ok, but if you want to do a group analysis, you can add 
--trgsubject fsaverage and the output surface will be in fsaverage 
space. You can then concatenate the data together (mri_concat) into one 
stack and then run mri_glmfit etc for your group analysis. You may or 
may not want to smooth on the surface (mri_surf2surf) as the PET will 
already be smooth (unless you did PVC).

On 03/22/2016 01:04 PM, Elijah Mak wrote:
> Hi Freesurfer Community,
>
> I am trying to run a vertex-wise analyses of PET data.
>
> I have already performed bbregister. Next, I did mri_vol2surf for each 
> subject, left and right hemispheres.
>
> for i in `cat subjects`; do mri_vol2surf --src 
> FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out 
> FS6_${i}_MPRAGE_Neuro.nii/surf/lh.PETSurface.mgh --hemi lh --regheader 
> FS6_${i}_MPRAGE_Neuro.nii --projfrac 0.5 --interp nearest; done
>
> Is this command correct? Visual inspection on freeview looks OK.
>
> How may I derive the group average from these individual surfaces and 
> perform the mri_glmfit?
>
> Any help will be greatly appreciated.
>
> Best Wishes,
> Eli
>
>
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Re: [Freesurfer] cannot allocate memory

[Douglas N Greve]

The problem is not the command, it is the size of the data it generates. 
You can try reducing the size of the anatomical to a bounding box around 
the brain. This is a bit tricky as you also have to compute a new 
registration. I can help step you through the process if you want to go 
in that direction.

On 03/22/2016 11:50 AM, Ehsan Tadayon wrote:
> Hi Doug,
>
> Thanks for your response. What I'm trying to do is to get each voxel's 
> times course in structural space and I was under the impression that 
> mri_vol2vol --mov func.nii would be the right way to go. Would you 
> please let me know what the best way would be to do this?
>
> best,
> Ehsan,.
>
>
> On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> that's going to create a pretty big volume as it will map your
> functional time course to a 256^3 float volume. If you have 100
> time points, then that will be about 7G.
>
> On 3/16/16 3:27 PM, Ehsan Tadayon wrote:
>> Hi Bruce,
>>
>> Thanks for your response. I'm using :
>>
>> freesurfer version:
>> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite
>> 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using:
>>
>> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
>> func.anat.nii.gz
>>
>> Thanks in advance for your help.
>>
>> best regards,
>> Ehsan.
>>
>>
>>
>>
>> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>>
>> wrote:
>>
>> Hi Ehsan
>>
>> We need the full command line and screen output and also what
>> your hardware and software environments are to help you.
>> Certainly sounds like you ran out of memory though
>>
>> Cheers
>> Bruce
>>
>> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon
>> > > wrote:
>> >
>> > Ehsan
>>
>> ___
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>>
>> The information in this e-mail is intended only for the
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>
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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] Surface based analysis using FA maps

[Douglas N Greve]

I don't know of a reference where someone has done this (though I would 
be surprised if it is not out there), so just be aware of this if you 
try to publish. The commands look correct, however, you may or may not 
want to sample in the middle of the cortical ribbon (--projfrac 0.5). 
Since this is a DTI analysis, wouldn't you want to sample in the WM? 
Doing that is a little tricky, but you can use something like --projabs 
-1 to sample 1mm *away* from the ribbon into the WM.

On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:
>
> Dear FS experts,
>
> I would like to run surface based analysis using FA maps. I am not 
> exactly sure that what I am doing is totally right specially step 2 . 
> I used the following commands:
>
> 1.I registered the FA maps to T1 using the command:  bbregister --s 
> bert --mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat
>
> 2.I concatenated the subject’s FA maps using the command : 
>  mris_preproc –target fsaverage –hemi lh –iv .bert1/dtifit_FA.nii 
> reg.dat –iv bert2/dtifit_FA.nii reg.dat …. --projfrac 0.5 --out lh.FA.mgz
>
> 3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 
> --cortex --sval  lh.FA.mgz --tval lh.FA_5mm.mgz
>
> 4.Then GLM analysis using mri_glmfit
>
> 5.Correction for multiple comparison mri_glmfit-sim
>
> Kindly, are these steps correct? I used the previous steps to do 
> surface based analysis using PET images and it worked very well. While 
> for the FA maps it seems that there is something wrong and I can’t 
> figure out what it is!
>
> I highly appreciate any input on this!
>
> Best,
>
> Mohamad
>
>
>
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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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Re: [Freesurfer] mri_glmfit-sim ( cluster wise analysis)

[Douglas N Greve]

answers below

On 03/22/2016 11:03 AM, Alshikho, Mohamad J. wrote:
>
> Dear FS experts,
>
> I ran cortical thickness analysis as previously explained in Wiki :
>
> Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>
> My data is previously cached so I ran the command : mris_preproc 
> --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage  --target 
> fsaverage --hemi lh  --out lh.gender_age.thickness.10.mgh
>
> GLM analysis: mri_glmfit  --y lh.gender_age.thickness.10.mgh  --fsgd 
> gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx  --surf 
> fsaverage lh --cortex  --glmdir lh.gender_age.glmdir
>
> Correction for multiple comparison  mri_glmfit-sim  --glmdir 
> lh.gender_age.glmdir  --cache 4 neg  --cwp  0.05  --2spaces
>
> In order to do cluster-wise correction for multiple comparisons, I ran 
> the command “mri_glmfit-sim” (step3). This command is calling, 
> internally, the command “mri_surfcluster” as follow:
>
> mdline mri_surfcluster --in lh//2G0C/sig.mgh --csd 
> /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd
>  
> --mask lh//mask.mgh --cwsig lh//2G0C/cache.th13.pos.sig.cluster.mgh 
> --vwsig lh//2G0C/cache.th13.pos.sig.voxel.mgh --sum 
> lh//2G0C/cache.th13.pos.sig.cluster.summary --ocn 
> lh//2G0C/cache.th13.pos.sig.ocn.mgh --oannot 
> lh//2G0C/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf 
> lh//2G0C/cache.th13.pos.pdf.dat --cwpvalthresh 0.05 --o 
> lh//2G0C/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 
> --surf white
>
> Kindly, I have the following questions:
>
> 1.How the command mri_surfcluster choose the fwhm=?? for the flag 
> “csd” . In the previous command it shows fwhm=15. Is this depends on 
> how much I am smoothing in the previous steps?
>
mri_glmfit measures the actual FWHM from the residuals of the data. This 
maybe (probably will be) larger than the amount that you applied because 
there is some inherent smoothness to the data as well as spatially 
coherent errors in the glm fit that show up as spatial correlations in 
the residual.
>
> 2.What is purpose of using the flag Bonferroni in the previous command
>
It corrects for the two spaces (lh and rh)
>
> 3.If we are doing cluster wise correction, what is theexact usage of 
> the flag “--vwsig” ?
>
mri_surfcluster actually does clusterwise and voxel-wise (--vwsig) 
correction. the voxel-wise tends to be pretty harsh, so most people use 
cluster-wise
>
> Thanks for your patience !
>
> Looking forward to learn from you
>
> Mohamad
>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Using digital tablet pen

[Mahmoud]

Thank you so much Lilla !

On Tue, Mar 22, 2016 at 12:29 PM, Lilla Zollei 
wrote:

>
> Hi Mahmoud,
>
> At the below link you will find some suggestions / settings that we use
> with our Cintiq tablet:
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations
> "Segmenting using a Cintiq tablet or display"
>
> Best, Lilla
>
>
> On Tue, 22 Mar 2016, Mahmoud wrote:
>
> Dear Experts,
>>
>> I was wondering if someone could share with me and others the experience
>> using digital tablet pen and those sort of things instead of mouse to edit
>> and touch the images especially the masks.
>> I appreciate your help.
>>
>> Thank you!
>> Mahmoud
>>
>>
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Re: [Freesurfer] mris_flatten error

[Ji Won Bang]

Oh, I see.

I showed the contrast results on a surface using the command:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower

Then I select 3 points along a boundary between upper and lower visual
fields (near calcarine sulcus) and press "Cut line". Then, select 4 points
to define the cutting plane: 1 on lower side of the line, 2 on upper side
of the line, 3 on the opposite surface (use rotation tool), and 4 to
specify which portion of surface is kept, and press "Cur plane".
File->Patch->Save Patch As {lh, rh}.oc.patch.3d

This is the usual way that I've been doing...

1 thing that's weird is when I run:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower
It calls fsaverage..such as:
Reading source surface reg
/home/jbang/Projects/replay/mri//replay06/surf/lh.sphere.reg
Loading source data
Reading target surface reg
/home/jbang/Projects/replay/mri//fsaverage/surf/lh.sphere.reg
Done

Previously when everything went smooth, I think it did not call fsaverage.

Is it normal?

Thank you.

Best,
Ji Won



2016-03-22 13:06 GMT-04:00 Bruce Fischl :

> then you must not have cut the patch from those surfaces. The error is
> about a vertex # in the patch (147220), which is larger than the total
> number of vertices in those surfaces (144977), so it's out of bounds. How
> did you do the cutting?
>
>
> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>
> Oh, I see.
>>
>> When I run all of these surfaces, it gave me the exactly same numbers...
>>
>> [jbang@cpu156 surf]$ mris_euler_number lh.inflated
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.white
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.pial
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.orig
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>>
>> Thanks,
>> Ji Won
>>
>> 2016-03-22 12:59 GMT-04:00 Bruce Fischl :
>>   no, for all surfaces for the same hemi (lh and rh). lh.inflated.K
>> is not
>>   a surface - it's a scalar field over the surface. The ones that
>> should be
>>   the same are:
>>
>>   lh.inflated
>>   lh.white
>>   lh.pial
>>   lh.orig
>>   lh.sphere
>>   lh.sphere.reg
>>
>>
>>
>>   and same for the rh (but different from the lh ones)
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Tue, 22 Mar 2016, Ji Won Bang wrote:
>>
>> Dear. Bruce.
>>
>> Thanks for your help.
>>
>> When I tried:
>> mris_euler_number rh.inflated.K
>>
>> It gave me:
>> nquads=15728644,  nvertices=574
>> ERROR: MRISread: file 'rh.inflated.K' has many more faces
>> than vertices!
>> Probably trying to use a scalar data file as a surface!
>>
>> When I tried:
>> mris_euler_number lh.inflated
>>
>> It gave me:
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0
>> holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> When I tried:
>> mris_euler_number rh.inflated
>>
>> It gave me:
>> euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0
>> holes
>>   F =2V-4:  294364 = 294368-4 (0)
>>   2E=3F:883092 = 883092 (0)
>>
>> So if everything is correct, I should see the same numbers
>> for all surfaces, but
>> since it's not the case, I should run recon again...
>>
>> Thanks,
>> Ji Won
>>
>> 2016-03-22 12:24 GMT-04:00 Bruce Fischl
>> :
>>   you can try recon-all -make all for that subject and
>> and see if it doesn
>

Re: [Freesurfer] Regarding: oblique view

[Dr Sampada Sinha]

Hello Bruce,

Thanks again for your prompt response. We have an official holiday here.
Will send the info on Thursday.

Thanks and regards,
Sampada
Predoctoral student
KGMU, Lko
India

On haveay, March 2016, Bruce Fischl  wrote:

> I see
>
> if you have defects that large you should look at the inflated.nofix
> surface to see what they are.
>
> What is your voxel resolution?
>
> cheers
> Bruce
>
> On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
>
> Thanks Bruce for your reply. I did run it thru' recon-all. It went for
>> more than 2
>> days and then exited with XL defect error (convex hull was more than
>> 14000 and vertex
>> size about 54000). So today I started by running the recon-all in parts.
>> I did not
>> find anything wrong with brainmask files after running autorecon1. I am
>> presently
>> running the autorecon-2 process. Will get back with the surf files when
>> this process
>> is over.
>> Thank you again for your reply and support.
>>
>> Kind regards,
>>
>> Sampada
>>
>> On Tuesday, March 22, 2016, Bruce Fischl 
>> wrote:
>>   sure. Have you tried running it through recon-all? It may work
>> fine
>>   On
>>   Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
>>
>>   > Thanks Bruce for your reply. The acquisition was oblique and the
>> voxel
>>   size doesn't
>>   > conform to the 1mm cube isotropic. I am trying to work on it and
>> figure
>>   out a
>>   > solution. However, if I am not, hope its okay to send you the
>> nifti
>>   image.
>>   > Thanks and regards,
>>   >
>>   > Sampada
>>   >
>>   >
>>   >
>>   > Rnday, March 20, 2016, Bruce Fischl 
>> wrote:
>>   >   what do you mean by "adding" an oblique angle? If you mean
>>   acquiring the
>>   >   data obliquely you should be fine as long as the voxels are
>> close
>>   to 1mm
>>   >   isotropic.
>>   >
>>   >   cheers
>>   >   Bruce
>>   >   On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
>>   >
>>   >   > Dear freesurfer experts,
>>   >   > Does adding an oblique angle during coronal or axial
>>   acquisitions of
>>   >   T1w
>>   >   > images lead to topographical errors during
>> mri_fix_topology
>>   process?
>>   >   >
>>   >   > Thanks and regards,
>>   >   >
>>   >   > Sampada
>>   >   >
>>   >   >
>>   >   >
>>   >   > --
>>   >   > Sampada Sinha
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   >
>>   >   ___
>>   >   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.
>>   >
>>   >
>>   >
>>   > --
>>   > Sampada Sinha
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   ___
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>>
>>
>>
>> --
>> Sampada Sinha
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>

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Re: [Freesurfer] mris_flatten error

[Bruce Fischl]

then you must not have cut the patch from those surfaces. The error is 
about a vertex # in the patch (147220), which is larger than the total 
number of vertices in those surfaces (144977), so it's out of bounds. How 
did you do the cutting?


On Tue, 22 Mar 2016, Ji Won Bang wrote:


Oh, I see.

When I run all of these surfaces, it gave me the exactly same numbers...

[jbang@cpu156 surf]$ mris_euler_number lh.inflated
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.white
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.pial
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.orig
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.sphere
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

total defect index = 0

Thanks,
Ji Won

2016-03-22 12:59 GMT-04:00 Bruce Fischl :
  no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not
  a surface - it's a scalar field over the surface. The ones that should be
  the same are:

  lh.inflated
  lh.white
  lh.pial
  lh.orig
  lh.sphere
  lh.sphere.reg



  and same for the rh (but different from the lh ones)

  cheers
  Bruce


  On Tue, 22 Mar 2016, Ji Won Bang wrote:

Dear. Bruce.

Thanks for your help.

When I tried:
mris_euler_number rh.inflated.K

It gave me:
nquads=15728644,  nvertices=574
ERROR: MRISread: file 'rh.inflated.K' has many more faces
than vertices!
Probably trying to use a scalar data file as a surface!

When I tried:
mris_euler_number lh.inflated

It gave me:
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0
holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

When I tried:
mris_euler_number rh.inflated

It gave me:
euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0
holes
  F =2V-4:  294364 = 294368-4 (0)
  2E=3F:    883092 = 883092 (0)

So if everything is correct, I should see the same numbers
for all surfaces, but
since it's not the case, I should run recon again...

Thanks,
Ji Won

2016-03-22 12:24 GMT-04:00 Bruce Fischl
:
      you can try recon-all -make all for that subject and
and see if it doesn
      anything. But run mris_euler_number on those surfaces
and see if they
      match. They should all have the same number of
faces/edges/vertices (for
      one hemisphere in the same subject)

      On Tue, 22 Mar 2016,
      Ji Won Bang wrote:

      > Dear. Bruce.
      >
      > Thank you for your advice.
      > I think I misunderstood what you meant.
      >
      > What I did is this.
      > I showed the contrast result on a surface by using
the command:
      > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh
-analysis retino
      -contrast HorVer
      >
      > Then I cut line, and then plane (occipital plane) and
save it(3d) as
      lh.oc.patch.3d
      > under $SUBJECTS_DIR/$SUBJECT/surf/
      >
      > I'm not sure if I regenerated the surface files
correctly but I believe
      I created the
      > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from
recon-all process.
      >
      >
      > Should I do something else to regenerate the surface?
      >
      > Thank you.
      >
 

Re: [Freesurfer] mris_flatten error

[Ji Won Bang]

Oh, I see.

When I run all of these surfaces, it gave me the exactly same numbers...

[jbang@cpu156 surf]$ mris_euler_number lh.inflated
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.white
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.pial
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.orig
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.sphere
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

total defect index = 0
[jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

total defect index = 0

Thanks,
Ji Won

2016-03-22 12:59 GMT-04:00 Bruce Fischl :

> no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not a
> surface - it's a scalar field over the surface. The ones that should be the
> same are:
>
> lh.inflated
> lh.white
> lh.pial
> lh.orig
> lh.sphere
> lh.sphere.reg
>
>
>
> and same for the rh (but different from the lh ones)
>
>
> cheers
> Bruce
>
>
> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>
> Dear. Bruce.
>>
>> Thanks for your help.
>>
>> When I tried:
>> mris_euler_number rh.inflated.K
>>
>> It gave me:
>> nquads=15728644,  nvertices=574
>> ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices!
>> Probably trying to use a scalar data file as a surface!
>>
>> When I tried:
>> mris_euler_number lh.inflated
>>
>> It gave me:
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>   F =2V-4:  289950 = 289954-4 (0)
>>   2E=3F:869850 = 869850 (0)
>>
>> When I tried:
>> mris_euler_number rh.inflated
>>
>> It gave me:
>> euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes
>>   F =2V-4:  294364 = 294368-4 (0)
>>   2E=3F:883092 = 883092 (0)
>>
>> So if everything is correct, I should see the same numbers for all
>> surfaces, but
>> since it's not the case, I should run recon again...
>>
>> Thanks,
>> Ji Won
>>
>> 2016-03-22 12:24 GMT-04:00 Bruce Fischl :
>>   you can try recon-all -make all for that subject and and see if it
>> doesn
>>   anything. But run mris_euler_number on those surfaces and see if
>> they
>>   match. They should all have the same number of faces/edges/vertices
>> (for
>>   one hemisphere in the same subject)
>>
>>   On Tue, 22 Mar 2016,
>>   Ji Won Bang wrote:
>>
>>   > Dear. Bruce.
>>   >
>>   > Thank you for your advice.
>>   > I think I misunderstood what you meant.
>>   >
>>   > What I did is this.
>>   > I showed the contrast result on a surface by using the command:
>>   > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis
>> retino
>>   -contrast HorVer
>>   >
>>   > Then I cut line, and then plane (occipital plane) and save it(3d)
>> as
>>   lh.oc.patch.3d
>>   > under $SUBJECTS_DIR/$SUBJECT/surf/
>>   >
>>   > I'm not sure if I regenerated the surface files correctly but I
>> believe
>>   I created the
>>   > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all
>> process.
>>   >
>>   >
>>   > Should I do something else to regenerate the surface?
>>   >
>>   > Thank you.
>>   >
>>   > Best,
>>   > Ji Won
>>   >
>>   >
>>   >
>>   >
>>   >
>>   > 2016-03-22 11:39 GMT-04:00 Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>:
>>   >   what surface did you recut it from? Can you run
>> mris_euler_number
>>   on that
>>   >   surface (presumably the inflated) and also on the
>> white/orig/pial
>>   >   surfaces? They should all have the same number of vertices,
>> but I
>>   suspect
>>   >   some of them won't, meaning that they need to be
>> regenerated.
>>   >
>>   >   cheers
>>   >   Bruce
>>   >
>>   >
>>   >
>>   >
>>   >   On Tue, 22 Mar 2016, Ji Won Bang wrote:
>>   >
>>   >   > Dear. Freesurfer experts.
>>   >   >
>>   >   > Hi. How are you?
>>   >   >
>>   >   > I'm trying to flatten the visual cortex using the command
>>   mris

[Freesurfer] PET voxelwise

[Elijah Mak]

Hi Freesurfer Community,

I am trying to run a vertex-wise analyses of PET data.

I have already performed bbregister. Next, I did mri_vol2surf for each
subject, left and right hemispheres.

for i in `cat subjects`; do mri_vol2surf --src
FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
FS6_${i}_MPRAGE_Neuro.nii/surf/lh.PETSurface.mgh --hemi lh --regheader
FS6_${i}_MPRAGE_Neuro.nii --projfrac 0.5 --interp nearest; done

Is this command correct? Visual inspection on freeview looks OK.

How may I derive the group average from these individual surfaces and
perform the mri_glmfit?

Any help will be greatly appreciated.

Best Wishes,
Eli
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Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

I see

if you have defects that large you should look at the inflated.nofix 
surface to see what they are.


What is your voxel resolution?

cheers
Bruce

On Tue, 22 Mar 2016, Dr Sampada Sinha wrote:


Thanks Bruce for your reply. I did run it thru' recon-all. It went for more 
than 2
days and then exited with XL defect error (convex hull was more than 14000 and 
vertex
size about 54000). So today I started by running the recon-all in parts. I did 
not
find anything wrong with brainmask files after running autorecon1. I am 
presently
running the autorecon-2 process. Will get back with the surf files when this 
process
is over.
Thank you again for your reply and support.

Kind regards, 

Sampada

On Tuesday, March 22, 2016, Bruce Fischl  wrote:
  sure. Have you tried running it through recon-all? It may work fine
  On
  Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

  > Thanks Bruce for your reply. The acquisition was oblique and the voxel
  size doesn't
  > conform to the 1mm cube isotropic. I am trying to work on it and figure
  out a
  > solution. However, if I am not, hope its okay to send you the nifti
  image.
  > Thanks and regards,
  >
  > Sampada
  >
  >
  >
  > Rnday, March 20, 2016, Bruce Fischl  wrote:
  >       what do you mean by "adding" an oblique angle? If you mean
  acquiring the
  >       data obliquely you should be fine as long as the voxels are close
  to 1mm
  >       isotropic.
  >
  >       cheers
  >       Bruce
  >       On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
  >
  >       > Dear freesurfer experts,
  >       > Does adding an oblique angle during coronal or axial
  acquisitions of
  >       T1w
  >       > images lead to topographical errors during mri_fix_topology
  process?
  >       >
  >       > Thanks and regards,
  >       >
  >       > Sampada
  >       >
  >       >
  >       >
  >       > --
  >       > Sampada Sinha
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       >
  >       ___
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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
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  >       e-mail
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  >
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  >
  >
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Re: [Freesurfer] Regarding: oblique view

[Dr Sampada Sinha]

Thanks Bruce for your reply. I did run it thru' recon-all. It went for more
than 2 days and then exited with XL defect error (convex hull was more than
14000 and vertex size about 54000). So today I started by running the
recon-all in parts. I did not find anything wrong with brainmask files
after running autorecon1. I am presently running the autorecon-2 process.
Will get back with the surf files when this process is over.

Thank you again for your reply and support.

Kind regards,

Sampada

On Tuesday, March 22, 2016, Bruce Fischl  wrote:

> sure. Have you tried running it through recon-all? It may work fine
> On
> Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
>
> > Thanks Bruce for your reply. The acquisition was oblique and the voxel
> size doesn't
> > conform to the 1mm cube isotropic. I am trying to work on it and figure
> out a
> > solution. However, if I am not, hope its okay to send you the nifti
> image.
> > Thanks and regards,
> >
> > Sampada
> >
> >
> >
> > Rnday, March 20, 2016, Bruce Fischl  > wrote:
> >   what do you mean by "adding" an oblique angle? If you mean
> acquiring the
> >   data obliquely you should be fine as long as the voxels are close
> to 1mm
> >   isotropic.
> >
> >   cheers
> >   Bruce
> >   On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
> >
> >   > Dear freesurfer experts,
> >   > Does adding an oblique angle during coronal or axial
> acquisitions of
> >   T1w
> >   > images lead to topographical errors during mri_fix_topology
> process?
> >   >
> >   > Thanks and regards,
> >   >
> >   > Sampada
> >   >
> >   >
> >   >
> >   > --
> >   > Sampada Sinha
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   >
> >   ___
> >   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.
> >
> >
> >
> > --
> > Sampada Sinha
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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Re: [Freesurfer] mris_flatten error

[Bruce Fischl]

no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not 
a surface - it's a scalar field over the surface. The ones that should be 
the same are:


lh.inflated
lh.white
lh.pial
lh.orig
lh.sphere
lh.sphere.reg



and same for the rh (but different from the lh ones)

cheers
Bruce


On Tue, 22 Mar 2016, Ji Won Bang wrote:


Dear. Bruce.

Thanks for your help.

When I tried:
mris_euler_number rh.inflated.K

It gave me:
nquads=15728644,  nvertices=574
ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

When I tried:
mris_euler_number lh.inflated

It gave me:
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:    869850 = 869850 (0)

When I tried:
mris_euler_number rh.inflated

It gave me:
euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes
  F =2V-4:  294364 = 294368-4 (0)
  2E=3F:    883092 = 883092 (0)

So if everything is correct, I should see the same numbers for all surfaces, but
since it's not the case, I should run recon again...

Thanks,
Ji Won

2016-03-22 12:24 GMT-04:00 Bruce Fischl :
  you can try recon-all -make all for that subject and and see if it doesn
  anything. But run mris_euler_number on those surfaces and see if they
  match. They should all have the same number of faces/edges/vertices (for
  one hemisphere in the same subject)

  On Tue, 22 Mar 2016,
  Ji Won Bang wrote:

  > Dear. Bruce.
  >
  > Thank you for your advice.
  > I think I misunderstood what you meant.
  >
  > What I did is this.
  > I showed the contrast result on a surface by using the command:
  > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
  -contrast HorVer
  >
  > Then I cut line, and then plane (occipital plane) and save it(3d) as
  lh.oc.patch.3d
  > under $SUBJECTS_DIR/$SUBJECT/surf/
  >
  > I'm not sure if I regenerated the surface files correctly but I believe
  I created the
  > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process.
  >
  >
  > Should I do something else to regenerate the surface?
  >
  > Thank you.
  >
  > Best,
  > Ji Won
  >
  >
  >
  >
  >
  > 2016-03-22 11:39 GMT-04:00 Bruce Fischl :
  >       what surface did you recut it from? Can you run mris_euler_number
  on that
  >       surface (presumably the inflated) and also on the white/orig/pial
  >       surfaces? They should all have the same number of vertices, but I
  suspect
  >       some of them won't, meaning that they need to be regenerated.
  >
  >       cheers
  >       Bruce
  >
  >
  >
  >
  >       On Tue, 22 Mar 2016, Ji Won Bang wrote:
  >
  >       > Dear. Freesurfer experts.
  >       >
  >       > Hi. How are you?
  >       >
  >       > I'm trying to flatten the visual cortex using the command
  mris_flatten
  >       (freesurfer
  >       > version 5.3.0).
  >       >
  >       > The command line is:
  >       > mris_flatten -w 0 -distances 12 7
  >       $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
  >       > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
  >       >
  >       > The error I get is:
  >       > using write iterations = 0
  >       > sampling 7 neighbors out to a distance of 12 mm
  >       > reading patch
  >       /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d
  with
  >       > 27964 vertices (19.0% of total)
  >       > MRISreadPatch: bad vertex # (147220) found in patch file
  >       > No such file or directory
  >       >
  >       > Previously, Bruce advised me to recut it, so I deleted the
  >       lh.oc.patch.3d and recut
  >       > it. However, freesurfer gives me the same error message...
  >       >
  >       > Could you please help me fix it?
  >       >
  >       > Thank you so much.
  >       >
  >       > Best,
  >       > Ji Won
  >       >
  >       >
  > ___
  > 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.
  >
  >
  >
  

Re: [Freesurfer] mris_flatten error

[Ji Won Bang]

Dear. Bruce.

Thanks for your help.

When I tried:
mris_euler_number rh.inflated.K

It gave me:
nquads=15728644,  nvertices=574
ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

When I tried:
mris_euler_number lh.inflated

It gave me:
euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
  F =2V-4:  289950 = 289954-4 (0)
  2E=3F:869850 = 869850 (0)

When I tried:
mris_euler_number rh.inflated

It gave me:
euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes
  F =2V-4:  294364 = 294368-4 (0)
  2E=3F:883092 = 883092 (0)

So if everything is correct, I should see the same numbers for all
surfaces, but since it's not the case, I should run recon again...

Thanks,
Ji Won

2016-03-22 12:24 GMT-04:00 Bruce Fischl :

> you can try recon-all -make all for that subject and and see if it doesn
> anything. But run mris_euler_number on those surfaces and see if they
> match. They should all have the same number of faces/edges/vertices (for
> one hemisphere in the same subject)
>
> On Tue, 22 Mar 2016,
> Ji Won Bang wrote:
>
> > Dear. Bruce.
> >
> > Thank you for your advice.
> > I think I misunderstood what you meant.
> >
> > What I did is this.
> > I showed the contrast result on a surface by using the command:
> > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> -contrast HorVer
> >
> > Then I cut line, and then plane (occipital plane) and save it(3d) as
> lh.oc.patch.3d
> > under $SUBJECTS_DIR/$SUBJECT/surf/
> >
> > I'm not sure if I regenerated the surface files correctly but I believe
> I created the
> > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process.
> >
> >
> > Should I do something else to regenerate the surface?
> >
> > Thank you.
> >
> > Best,
> > Ji Won
> >
> >
> >
> >
> >
> > 2016-03-22 11:39 GMT-04:00 Bruce Fischl :
> >   what surface did you recut it from? Can you run mris_euler_number
> on that
> >   surface (presumably the inflated) and also on the white/orig/pial
> >   surfaces? They should all have the same number of vertices, but I
> suspect
> >   some of them won't, meaning that they need to be regenerated.
> >
> >   cheers
> >   Bruce
> >
> >
> >
> >
> >   On Tue, 22 Mar 2016, Ji Won Bang wrote:
> >
> >   > Dear. Freesurfer experts.
> >   >
> >   > Hi. How are you?
> >   >
> >   > I'm trying to flatten the visual cortex using the command
> mris_flatten
> >   (freesurfer
> >   > version 5.3.0).
> >   >
> >   > The command line is:
> >   > mris_flatten -w 0 -distances 12 7
> >   $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
> >   > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
> >   >
> >   > The error I get is:
> >   > using write iterations = 0
> >   > sampling 7 neighbors out to a distance of 12 mm
> >   > reading patch
> >   /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with
> >   > 27964 vertices (19.0% of total)
> >   > MRISreadPatch: bad vertex # (147220) found in patch file
> >   > No such file or directory
> >   >
> >   > Previously, Bruce advised me to recut it, so I deleted the
> >   lh.oc.patch.3d and recut
> >   > it. However, freesurfer gives me the same error message...
> >   >
> >   > Could you please help me fix it?
> >   >
> >   > Thank you so much.
> >   >
> >   > Best,
> >   > Ji Won
> >   >
> >   >
> > ___
> > 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] Using digital tablet pen

[Lilla Zollei]

Hi Mahmoud,

At the below link you will find some suggestions / settings that we use 
with our Cintiq tablet:


https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewSegmentations
"Segmenting using a Cintiq tablet or display"

Best, Lilla

On Tue, 22 Mar 2016, Mahmoud wrote:


Dear Experts,

I was wondering if someone could share with me and others the experience using 
digital tablet pen and those sort of things instead of mouse to edit and touch 
the images especially the masks.
I appreciate your help.

Thank you!
Mahmoud

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Re: [Freesurfer] mris_flatten error

[Bruce Fischl]

you can try recon-all -make all for that subject and and see if it doesn 
anything. But run mris_euler_number on those surfaces and see if they 
match. They should all have the same number of faces/edges/vertices (for 
one hemisphere in the same subject)

On Tue, 22 Mar 2016, 
Ji Won Bang wrote:

> Dear. Bruce.
> 
> Thank you for your advice.
> I think I misunderstood what you meant.
> 
> What I did is this.
> I showed the contrast result on a surface by using the command:
> tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast 
> HorVer
> 
> Then I cut line, and then plane (occipital plane) and save it(3d) as 
> lh.oc.patch.3d
> under $SUBJECTS_DIR/$SUBJECT/surf/
> 
> I'm not sure if I regenerated the surface files correctly but I believe I 
> created the
> surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process.
> 
> 
> Should I do something else to regenerate the surface?
> 
> Thank you.
> 
> Best,
> Ji Won
> 
> 
> 
> 
> 
> 2016-03-22 11:39 GMT-04:00 Bruce Fischl :
>   what surface did you recut it from? Can you run mris_euler_number on 
> that
>   surface (presumably the inflated) and also on the white/orig/pial
>   surfaces? They should all have the same number of vertices, but I 
> suspect
>   some of them won't, meaning that they need to be regenerated.
>
>   cheers
>   Bruce
> 
> 
> 
>
>   On Tue, 22 Mar 2016, Ji Won Bang wrote:
>
>   > Dear. Freesurfer experts.
>   >
>   > Hi. How are you?
>   >
>   > I'm trying to flatten the visual cortex using the command mris_flatten
>   (freesurfer
>   > version 5.3.0).
>   >
>   > The command line is:
>   > mris_flatten -w 0 -distances 12 7
>   $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
>   > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
>   >
>   > The error I get is:
>   > using write iterations = 0
>   > sampling 7 neighbors out to a distance of 12 mm
>   > reading patch
>   /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with
>   > 27964 vertices (19.0% of total)
>   > MRISreadPatch: bad vertex # (147220) found in patch file
>   > No such file or directory
>   >
>   > Previously, Bruce advised me to recut it, so I deleted the
>   lh.oc.patch.3d and recut
>   > it. However, freesurfer gives me the same error message...
>   >
>   > Could you please help me fix it?
>   >
>   > Thank you so much.
>   >
>   > Best,
>   > Ji Won
>   >
>   >
> ___
> 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] mris_flatten error

[Ji Won Bang]

Dear. Bruce.

Thank you for your advice.
I think I misunderstood what you meant.

What I did is this.
I showed the contrast result on a surface by using the command:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast HorVer

Then I cut line, and then plane (occipital plane) and save it(3d) as
lh.oc.patch.3d under $SUBJECTS_DIR/$SUBJECT/surf/

I'm not sure if I regenerated the surface files correctly but I believe I
created the surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all
process.


Should I do something else to regenerate the surface?

Thank you.

Best,
Ji Won





2016-03-22 11:39 GMT-04:00 Bruce Fischl :

> what surface did you recut it from? Can you run mris_euler_number on that
> surface (presumably the inflated) and also on the white/orig/pial
> surfaces? They should all have the same number of vertices, but I suspect
> some of them won't, meaning that they need to be regenerated.
>
> cheers
> Bruce
>
>
>
>
> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>
> > Dear. Freesurfer experts.
> >
> > Hi. How are you?
> >
> > I'm trying to flatten the visual cortex using the command mris_flatten
> (freesurfer
> > version 5.3.0).
> >
> > The command line is:
> > mris_flatten -w 0 -distances 12 7
> $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
> > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
> >
> > The error I get is:
> > using write iterations = 0
> > sampling 7 neighbors out to a distance of 12 mm
> > reading patch
> /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with
> > 27964 vertices (19.0% of total)
> > MRISreadPatch: bad vertex # (147220) found in patch file
> > No such file or directory
> >
> > Previously, Bruce advised me to recut it, so I deleted the
> lh.oc.patch.3d and recut
> > it. However, freesurfer gives me the same error message...
> >
> > Could you please help me fix it?
> >
> > Thank you so much.
> >
> > Best,
> > Ji Won
> >
> >
> ___
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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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Re: [Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Hi Doug,

Thanks for your response. What I'm trying to do is to get each voxel's
times course in structural space and I was under the impression that
mri_vol2vol --mov func.nii would be the right way to go. Would you please
let me know what the best way would be to do this?

best,
Ehsan,.


On Wed, Mar 16, 2016 at 11:27 PM, Douglas Greve 
wrote:

> that's going to create a pretty big volume as it will map your functional
> time course to a 256^3 float volume. If you have 100 time points, then that
> will be about 7G.
>
> On 3/16/16 3:27 PM, Ehsan Tadayon wrote:
>
> Hi Bruce,
>
> Thanks for your response. I'm using :
>
> freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS
> X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm
> using:
>
> mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o
> func.anat.nii.gz
>
> Thanks in advance for your help.
>
> best regards,
> Ehsan.
>
>
>
>
> On Tue, Mar 15, 2016 at 11:49 PM, Bruce Fischl  > wrote:
>
>> Hi Ehsan
>>
>> We need the full command line and screen output and also what your
>> hardware and software environments are to help you. Certainly sounds like
>> you ran out of memory though
>>
>> Cheers
>> Bruce
>>
>> > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon <
>> ehsan.tadayo...@gmail.com> wrote:
>> >
>> > Ehsan
>>
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Re: [Freesurfer] mris_flatten error

[Bruce Fischl]

what surface did you recut it from? Can you run mris_euler_number on that 
surface (presumably the inflated) and also on the white/orig/pial 
surfaces? They should all have the same number of vertices, but I suspect 
some of them won't, meaning that they need to be regenerated.

cheers
Bruce




On Tue, 22 Mar 2016, Ji Won Bang wrote:

> Dear. Freesurfer experts.
> 
> Hi. How are you?
> 
> I'm trying to flatten the visual cortex using the command mris_flatten 
> (freesurfer
> version 5.3.0).
> 
> The command line is:
> mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
> $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
> 
> The error I get is:
> using write iterations = 0
> sampling 7 neighbors out to a distance of 12 mm
> reading patch /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d 
> with
> 27964 vertices (19.0% of total)
> MRISreadPatch: bad vertex # (147220) found in patch file
> No such file or directory
> 
> Previously, Bruce advised me to recut it, so I deleted the lh.oc.patch.3d and 
> recut
> it. However, freesurfer gives me the same error message...
> 
> Could you please help me fix it?
> 
> Thank you so much.
> 
> Best,
> Ji Won
> 
>
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[Freesurfer] mris_flatten error

[Ji Won Bang]

Dear. Freesurfer experts.

Hi. How are you?

I'm trying to flatten the visual cortex using the command mris_flatten
(freesurfer version 5.3.0).

The command line is:
mris_flatten -w 0 -distances 12 7
$SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
$SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat

The error I get is:
using write iterations = 0
sampling 7 neighbors out to a distance of 12 mm
reading patch /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d
with 27964 vertices (19.0% of total)
MRISreadPatch: bad vertex # (147220) found in patch file
No such file or directory

Previously, Bruce advised me to recut it, so I deleted the lh.oc.patch.3d
and recut it. However, freesurfer gives me the same error message...

Could you please help me fix it?

Thank you so much.

Best,
Ji Won
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Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

[Morten Sejer Hansen]

Hi Bruce,

Again, thank you for the quick response!

I will be looking forward to the upgrade then.

Kind regards

Morten

-Oprindelig meddelelse-
Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce Fischl
Sendt: 22. marts 2016 16:16
Til: Freesurfer support list
Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are 
not reported

Hi Morten

not yet. The STN is on our list of things to segment (as is the SN), although 
both will likely require good T2* (or maybe T2) weighted images.

cheers
Bruce
On
Tue, 22 Mar 2016, Morten Sejer Hansen wrote:

> Dear Bruce,
>
> Thank you for your quick and precise answer.
>
> One last question. Is it possible to segment the Nucl. Subthalamicus? It is a 
> subcortical anatomical structure, and is a part of the basal ganglia. It is 
> not included in the output following the command:
>
> asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all
> 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume
> --tablefile Subcortical.txt
>
>
> Kind regards
>
> Morten
>
>
> -Oprindelig meddelelse-
> Fra: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce
> Fischl
> Sendt: 22. marts 2016 14:02
> Til: Freesurfer support list
> Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra
> volumes are not reported
>
> Hi Morten
>
> the insula you should be able to get out of the cortical labels in the 
> various *.annot files. The substantia nigra we don't segment at the moment, 
> and I suspect it would be hard to do so from only a T1-weighted scan.
>
> cheers
> Bruce
> On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:
>
>>
>> Dear Experts,
>>
>>
>>
>> I am interested in retrieving the volume of the insula and substantia
>> nigra from T1W structural scans converted to nii.gz files. All scans
>> have undergone the recon-all process without error.
>>
>> I have seen volume estimations of Insula and substantia nigra
>> performed in several studies, but I can’t seem to figure out how I retrieve 
>> these volumes.
>>
>>
>>
>> I ran the command:
>>
>>
>>
>> asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all
>> 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume
>> --tablefile Subcortical.txt
>>
>>
>>
>> SUBJECTS_DIR : /Applications/freesurfer/subjects
>>
>> Parsing the .stats files
>>
>> Building the table..
>>
>> Writing the table to Subcortical.txt
>>
>>
>>
>> following this I get at fine output with several volume estimation of
>> subcortical structures, but without the Insula (left and right), and
>> without the substantia nigra (left and right).
>>
>>
>>
>> I tried to run the same command on “Bert”, and ended up with the same
>> result (with the insula and substania nigra still missing). I also
>> tried to add the
>>
>>
>>
>> --all-segs
>>
>>
>>
>> But without any change in the output.
>>
>>
>>
>> On the
>> FreeSurferColorLUT(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutori
>> a
>> l/AnatomicalROI/FreeSurferColorL
>> UT) I can see that the structures I am interested in have the
>> following numbers: 19, 27, 55 and 59.
>>
>>
>>
>> Could you provide me answers on how to extract the volumes of the
>> insula and substantia nigra?
>>
>>
>>
>> Thanks a lot!
>>
>>
>>
>> Kind regards
>>
>>
>>
>> Morten Sejer Hansen
>>
>>
>>
>>
>>
>>
>>
>> Morten Sejer Hansen
>>
>> MD
>> Direct: + 45 26373611
>>
>> Mail: morten.sejer.han...@regionh.dk / morten.sejer.han...@dadlnet.dk
>>
>> Department of anaesthesiology 4231
>>
>> Centre of head and orthopaedics
>>
>> Copenhagen University Hospital, Rigshospitalet
>>
>> Blegdamsvej 9
>> 2100 Copenhagen
>>
>>
>>
>> Tel: +45 35 45 35 45
>> Web: www.regionh.dk
>>
>> This e-mail and any attachment may contain confidential and
>> privileged material intended for the addressee only. If you are not
>> the addressee, you are notified that no part of the e-mail or any
>> attachment may be disclosed, copied or distributed, and that any
>> other action related to this e-mail or attachment is strictly
>> prohibited, and may be unlawful. If you have received this e-mail by error, 
>> please notify the sender immediately by return e-mail, and delete this 
>> message.
>>
>>
>>
>>
>> _
>> _
>> ___
>>
>>
>> Denne e-mail indeholder fortrolig information. Hvis du ikke er den
>> rette modtager af denne e-mail eller hvis du modtager den ved en
>> fejltagelse, beder vi dig venligst informere afsender om fejlen ved
>> at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme 
>> uden at videresende eller kopiere den.
>>
>>
>
> 
>
>
> Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette 
> modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder 
> vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. 
> Samtidig bed

Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

[Bruce Fischl]

Hi Morten

not yet. The STN is on our list of things to segment (as is the SN), 
although both will likely require good T2* (or maybe T2) weighted images.


cheers
Bruce
On 
Tue, 22 Mar 2016, Morten Sejer Hansen wrote:



Dear Bruce,

Thank you for your quick and precise answer.

One last question. Is it possible to segment the Nucl. Subthalamicus? It is a 
subcortical anatomical structure, and is a part of the basal ganglia. It is not 
included in the output following the command:

asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all 
4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt


Kind regards

Morten


-Oprindelig meddelelse-
Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce Fischl
Sendt: 22. marts 2016 14:02
Til: Freesurfer support list
Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are 
not reported

Hi Morten

the insula you should be able to get out of the cortical labels in the various 
*.annot files. The substantia nigra we don't segment at the moment, and I 
suspect it would be hard to do so from only a T1-weighted scan.

cheers
Bruce
On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:



Dear Experts,



I am interested in retrieving the volume of the insula and substantia
nigra from T1W structural scans converted to nii.gz files. All scans
have undergone the recon-all process without error.

I have seen volume estimations of Insula and substantia nigra
performed in several studies, but I can’t seem to figure out how I retrieve 
these volumes.



I ran the command:



asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all
3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume
--tablefile Subcortical.txt



SUBJECTS_DIR : /Applications/freesurfer/subjects

Parsing the .stats files

Building the table..

Writing the table to Subcortical.txt



following this I get at fine output with several volume estimation of
subcortical structures, but without the Insula (left and right), and
without the substantia nigra (left and right).



I tried to run the same command on “Bert”, and ended up with the same
result (with the insula and substania nigra still missing). I also
tried to add the



--all-segs



But without any change in the output.



On the
FreeSurferColorLUT(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutoria
l/AnatomicalROI/FreeSurferColorL
UT) I can see that the structures I am interested in have the
following numbers: 19, 27, 55 and 59.



Could you provide me answers on how to extract the volumes of the
insula and substantia nigra?



Thanks a lot!



Kind regards



Morten Sejer Hansen







Morten Sejer Hansen

MD
Direct: + 45 26373611

Mail: morten.sejer.han...@regionh.dk / morten.sejer.han...@dadlnet.dk

Department of anaesthesiology 4231

Centre of head and orthopaedics

Copenhagen University Hospital, Rigshospitalet

Blegdamsvej 9
2100 Copenhagen



Tel: +45 35 45 35 45
Web: www.regionh.dk

This e-mail and any attachment may contain confidential and privileged
material intended for the addressee only. If you are not the
addressee, you are notified that no part of the e-mail or any
attachment may be disclosed, copied or distributed, and that any other
action related to this e-mail or attachment is strictly prohibited,
and may be unlawful. If you have received this e-mail by error, please notify 
the sender immediately by return e-mail, and delete this message.




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Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

[Morten Sejer Hansen]

Dear Bruce,

Thank you for your quick and precise answer.

One last question. Is it possible to segment the Nucl. Subthalamicus? It is a 
subcortical anatomical structure, and is a part of the basal ganglia. It is not 
included in the output following the command:

asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all 
4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt


Kind regards

Morten


-Oprindelig meddelelse-
Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne af Bruce Fischl
Sendt: 22. marts 2016 14:02
Til: Freesurfer support list
Emne: Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are 
not reported

Hi Morten

the insula you should be able to get out of the cortical labels in the various 
*.annot files. The substantia nigra we don't segment at the moment, and I 
suspect it would be hard to do so from only a T1-weighted scan.

cheers
Bruce
On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:

>
> Dear Experts,
>
>
>
> I am interested in retrieving the volume of the insula and substantia
> nigra from T1W structural scans converted to nii.gz files. All scans
> have undergone the recon-all process without error.
>
> I have seen volume estimations of Insula and substantia nigra
> performed in several studies, but I can’t seem to figure out how I retrieve 
> these volumes.
>
>
>
> I ran the command:
>
>
>
> asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all
> 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume
> --tablefile Subcortical.txt
>
>
>
> SUBJECTS_DIR : /Applications/freesurfer/subjects
>
> Parsing the .stats files
>
> Building the table..
>
> Writing the table to Subcortical.txt
>
>
>
> following this I get at fine output with several volume estimation of
> subcortical structures, but without the Insula (left and right), and
> without the substantia nigra (left and right).
>
>
>
> I tried to run the same command on “Bert”, and ended up with the same
> result (with the insula and substania nigra still missing). I also
> tried to add the
>
>
>
> --all-segs
>
>
>
> But without any change in the output.
>
>
>
> On the
> FreeSurferColorLUT(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutoria
> l/AnatomicalROI/FreeSurferColorL
> UT) I can see that the structures I am interested in have the
> following numbers: 19, 27, 55 and 59.
>
>
>
> Could you provide me answers on how to extract the volumes of the
> insula and substantia nigra?
>
>
>
> Thanks a lot!
>
>
>
> Kind regards
>
>
>
> Morten Sejer Hansen
>
>
>
>
>
>
>
> Morten Sejer Hansen
>
> MD
> Direct: + 45 26373611
>
> Mail: morten.sejer.han...@regionh.dk / morten.sejer.han...@dadlnet.dk
>
> Department of anaesthesiology 4231
>
> Centre of head and orthopaedics
>
> Copenhagen University Hospital, Rigshospitalet
>
> Blegdamsvej 9
> 2100 Copenhagen
>
>
>
> Tel: +45 35 45 35 45
> Web: www.regionh.dk
>
> This e-mail and any attachment may contain confidential and privileged
> material intended for the addressee only. If you are not the
> addressee, you are notified that no part of the e-mail or any
> attachment may be disclosed, copied or distributed, and that any other
> action related to this e-mail or attachment is strictly prohibited,
> and may be unlawful. If you have received this e-mail by error, please notify 
> the sender immediately by return e-mail, and delete this message.
>
>
>
>
> __
> ___
>
>
> Denne e-mail indeholder fortrolig information. Hvis du ikke er den
> rette modtager af denne e-mail eller hvis du modtager den ved en
> fejltagelse, beder vi dig venligst informere afsender om fejlen ved at
> bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at 
> videresende eller kopiere den.
>
>




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[Freesurfer] Using digital tablet pen

[Mahmoud]

Dear Experts,

I was wondering if someone could share with me and others the experience
using digital tablet pen and those sort of things instead of mouse to edit
and touch the images especially the masks.
I appreciate your help.

Thank you!
Mahmoud
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[Freesurfer] Surface based analysis using FA maps

[Alshikho, Mohamad J.]

Dear FS experts,

I would like to run surface based analysis using FA maps. I am not exactly sure 
that what I am doing is totally right specially step 2 . I used the following 
commands:


1.   I registered the FA maps to T1 using the command:  bbregister --s bert 
--mov dtifit_FA.nii --bold --init-fsl --reg  reg.dat

2.   I concatenated the subject's FA maps using the command :  mris_preproc 
-target fsaverage -hemi lh -iv .bert1/dtifit_FA.nii reg.dat -iv 
bert2/dtifit_FA.nii reg.dat  --projfrac 0.5 --out lh.FA.mgz

3.   Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex 
--sval  lh.FA.mgz --tval lh.FA_5mm.mgz

4.   Then GLM analysis using mri_glmfit

5.   Correction for multiple comparison mri_glmfit-sim



Kindly, are these steps correct? I used the previous steps to do surface based 
analysis using PET images and it worked very well. While for the FA maps it 
seems that there is something wrong and I can't figure out what it is!


I highly appreciate any input on this!


Best,
Mohamad
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[Freesurfer] mri_glmfit-sim ( cluster wise analysis)

[Alshikho, Mohamad J.]

Dear FS experts,
I ran cortical thickness analysis as previously explained in Wiki :

Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

My data is previously cached so I ran the command : mris_preproc --fsgd 
gender_age.fsgd  --cache-in thickness.fwhm10.fsaverage  --target fsaverage 
--hemi lh  --out lh.gender_age.thickness.10.mgh
GLM analysis: mri_glmfit  --y lh.gender_age.thickness.10.mgh  --fsgd 
gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx  --surf fsaverage lh  
--cortex  --glmdir lh.gender_age.glmdir
Correction for multiple comparison  mri_glmfit-sim  --glmdir 
lh.gender_age.glmdir  --cache 4 neg  --cwp  0.05  --2spaces

In order to do cluster-wise correction for multiple comparisons, I ran the 
command "mri_glmfit-sim" (step3). This command is calling, internally, the 
command "mri_surfcluster" as follow:

mdline mri_surfcluster --in lh//2G0C/sig.mgh --csd 
/usr/local/freesurfer/stable5_3_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd
 --mask lh//mask.mgh --cwsig lh//2G0C/cache.th13.pos.sig.cluster.mgh --vwsig 
lh//2G0C/cache.th13.pos.sig.voxel.mgh --sum 
lh//2G0C/cache.th13.pos.sig.cluster.summary --ocn 
lh//2G0C/cache.th13.pos.sig.ocn.mgh --oannot 
lh//2G0C/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf 
lh//2G0C/cache.th13.pos.pdf.dat --cwpvalthresh 0.05 --o 
lh//2G0C/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white


Kindly, I have the following questions:


1.   How the command mri_surfcluster choose the fwhm=?? for the flag "csd" 
. In the previous command it shows fwhm=15. Is this depends on how much I am 
smoothing in the previous steps?

2.   What is purpose of using the flag Bonferroni in the previous command

3.   If we are doing cluster wise correction, what is theexact usage of the 
flag "--vwsig" ?


Thanks for your patience !
Looking forward to learn from you


Mohamad
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Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1 qform or sform are valid

[Douglas Greve]

To check whether the orientation is correct, you can view it in freeview 
or tkmedit. When you click on the axial view it should show up axially, 
etc. Though you cannot tell whether it is left-right reversed this way. 
You cannot feed it a matrix, but you can specify the direction cosines 
on the mri_convert command line (-iid, -ijd, -ikd). You'll have to play 
with it a bit. You can also try giving it an orientation string instead. 
if you run mri_convert without any options, then it will give you lots 
of documentation.


On 3/20/16 8:44 PM, Reema Jayakar wrote:

Hello FS list subscribers,

Is there a way to manually feed FS with NIfTI-1 qform or sform 
information? Or correctly add this information to the original .nii 
files? My sense of the problem is that there is a problem with the 
header information in my .nii files and FS cannot tell what is 
anterior, posterior, left, right.


That said, I am very new to FS and my interpretation of the error 
could be wrong. So I am laying out the details below (recon-all.log is 
also attached to this email):


  * When I try to run recon-all there are no output images/files
generated and the message I get is that the Talairach transform
failed
  * When I try to run autorecon1 an autorecon2 with the "-notal check"
flag, FS does not give me any error message and proceeds with
generating output. However, I can visually see (via brainmask.mgz)
that oreintations are messed up (e.g., tried to register coronal
orientation on top of sagittal orientation)
  * This problem only occurs with .nii files from a particular study
that came out of a specific scanner. All my other data are running
through FS smoothly, which is why I think there is some problem
with the .nii files
  * Also, when I view my raw .nii images in FSL view none of the usual
orientation markers are visible to me, which again suggest that
they may be missing?
  * Unfortunately, I do not currently have the original .dcm files
available as this is a multi-site archival study


Any help you can provide to resolve this issue would be really 
appreciated!


Thank you,
Reema



--
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu 



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Re: [Freesurfer] Create a surface overlay with statistic results using AAL ROI

[Douglas Greve]

There is not an easy way to do this. You'd have to make an annotation 
from the AAL. Possible, but not easy.


On 3/21/16 3:54 PM, carolina.mr wrote:

Hi all,
I have some statistical results for AAL 90 coordinates (correlation 
coefficients from network measurements x clinical data).
I would like to create an overlay to visualize in FreeSurfer standard 
(fsaverage) space, showing the areas with positive and negative 
correlations (and the scale / power of correlation, i.e. beta-value, 
for each area).
Is it possible using FreeSurfer tools? If it is possible, how should I 
produce a .txt file to be read in FreeSurfer.

Kind regards,
Carolina


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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

[Douglas Greve]

try now

On 3/21/16 10:24 PM, Bharadwaj, Pradyumna - (prad) wrote:
> Hi Doug,
>
> Could you please upload epidewarp.fsl for FSL 5.x once again.
>
> Thanks!
> -Prad
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, March 1, 2016 12:39 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>
> try now
>
> On 03/01/2016 02:16 PM, Versace, Amelia wrote:
>> Hi,
>>
>> I am having the same issue.
>>
>> Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
>>
>> Thanks a lot, Amelia
>>
>> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
>> Greve
>> *Sent:* Wednesday, February 10, 2016 10:58 PM
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>>
>> what is your command line? I think there is a rescaling in which it
>> expcts the phase to be 0-2048 (or 4096) as this is how it comes of the
>> (siemens) scanner. Could that be the problem?
>>
>> On 2/10/16 10:40 PM, Joseph Dien wrote:
>>
>>  I ran into the same issue:
>>
>>  FSLVersion 5.0.4
>>
>>  FSLVerMaj 5
>>
>>  FSL Version is 5.0.4, must be 3.X or 4.X
>>
>>  I downloaded the epidewarp.fsl script from the suggested ftp site
>>  and replaced the existing script.  It did indeed fix the version
>>  incompatibility with FSL 5.x.
>>
>>  I ran into a new problem where it was aborting.  After some
>>  trouble shooting and looking over the documentation, I realized
>>  that —-epi is a required input without which the script crashes
>>  (or is it supposed to be optional but there is a bug in the script?).
>>
>>  After including it, it ran much further but then aborted with the
>>  following error:
>>
>>  ERROR: input phase image exceeds allowable phase range.
>>
>>  Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>>
>>  This is consistent with the documentation.  I’m not sure why the
>>  phase image exceeds the range though.
>>
>>  It ran without problems with SPM’s FieldMap Toolbox and it is from
>>  a standard Siemen’s scanner sequence (two magnitude files and one
>>  phase difference file).
>>
>>  Do I just divide the values by two with something like fslmaths
>>  since it seems to have exactly double the required range?
>>
>>  Joe
>>
>>  On Nov 26, 2014, at 21:36, Douglas Greve
>>  mailto:gr...@nmr.mgh.harvard.edu>>
>>  wrote:
>>
>>
>>  It is there again. I don't know what the status if it  is in
>>  terms of the version. Try it and let me know
>>  doug
>>
>>  On 11/25/14 4:34 PM, Morgan Hough wrote:
>>
>>  Hi Doug,
>>
>>  Could you put the epidewarp.fsl script back on your ftp
>>  site? I don’t see it at the link in the archives:
>>
>>  
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>>
>>  BTW, is the script updated in some way for 5.x or can I
>>  can the old script just be changed to accept 5.x version
>>  numbers.
>>
>>  Cheers,
>>
>>  -Morgan
>>
>>  ___
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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.
>>
>>  
>> 
>>
>>  Joseph Dien, PhD
>>
>>  Senior Research Scientist
>>
>>  Maryland Neuroimaging Center
>>
>>  University of Maryland, College Park
>>
>>  E-mail: jdie...@mac.com 
>>  Cell Phone: 202-297-8117
>>  http://joedien.com
>>
>>
>>
>>
>>
>>  ___
>>
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>>
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>>
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>>
>>
>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Cente

Re: [Freesurfer] extracting pial surface area numbers...

[Douglas Greve]

That number is the mean vertex area, so to get the total area for each 
subject multiply that number by the number of vertices in the cluster.


On 3/21/16 2:29 PM, Karl Liu wrote:


Dear FS team,


My question is how I should extract the measure of pial surface area 
from a significant cluster after group-analysis. I performed 
statistical analysis in QDEC, choosing pial surface area as the 
measure. I found a significant cluster. Now I would to extract the 
surface area of this cluster from each subject, so that I can plot the 
group means.  But the numbers I got from the 
"cache.th20.neg.y.ocn.dat" file are quite small (mean centered at ~1). 
I am wondering how I should get the correct numbers from each subject.



thank you in advance


Karl



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Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

[Z K]

Hello Sampada,

Because of significant changes in the code, we halted development of the 
beta release I sent you last year. We will be publishing a new beta 
release soon (week-ish) but in the meantime, if you want the latest 
"dev" version of the freesurfer you can downlownd it from our Download site:

   https://surfer.nmr.mgh.harvard.edu/fswiki/Download


On 03/22/2016 10:29 AM, Dr Sampada Sinha wrote:
> Thanks  Bruce. I was sent the link for dev version by Zeke last year.
> It's working on Linux platform. But, I am not able to download or
> install it on Mac.
>
> Thanks and kind regards,
>
> Sampada
>
> On Tuesday, March 22, 2016, Bruce Fischl  > wrote:
>
> Hi Sampada
>
> V6 is not out yet, although we are actively (frantically?) working
> on it.
>
> cheers
> Bruce
> On
> Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
>
>  > Dear freesurfer experts,
>  >
>  > I am trying to do hippocampal subfields segmentation on Mac. I
> will greatly
>  > appreciate if freesurfer 6.0 version link is forwarded to me.
>  >
>  > With thanks and regards,
>  >
>  > Sampada
>  > Pre-doctoral student
>  > KGMU, Lucknow
>  > India
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
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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.
>
>
>
> --
> Sampada Sinha
>
>
>
>
>
>
>
> */
> /*
>
>
>
>
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Re: [Freesurfer] Regarding: oblique view

[Bruce Fischl]

sure. Have you tried running it through recon-all? It may work fine
On 
Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

> Thanks Bruce for your reply. The acquisition was oblique and the voxel size 
> doesn't
> conform to the 1mm cube isotropic. I am trying to work on it and figure out a
> solution. However, if I am not, hope its okay to send you the nifti image.
> Thanks and regards,
> 
> Sampada
> 
> 
> 
> Rnday, March 20, 2016, Bruce Fischl  wrote:
>   what do you mean by "adding" an oblique angle? If you mean acquiring the
>   data obliquely you should be fine as long as the voxels are close to 1mm
>   isotropic.
>
>   cheers
>   Bruce
>   On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
>
>   > Dear freesurfer experts,
>   > Does adding an oblique angle during coronal or axial acquisitions of
>   T1w
>   > images lead to topographical errors during mri_fix_topology process?
>   >
>   > Thanks and regards,
>   >
>   > Sampada
>   >
>   >
>   >
>   > --
>   > Sampada Sinha
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   ___
>   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.
> 
> 
> 
> --
> Sampada Sinha
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

[Dr Sampada Sinha]

Thanks  Bruce. I was sent the link for dev version by Zeke last year. It's
working on Linux platform. But, I am not able to download or install it on
Mac.

Thanks and kind regards,

Sampada

On Tuesday, March 22, 2016, Bruce Fischl  wrote:

> Hi Sampada
>
> V6 is not out yet, although we are actively (frantically?) working on it.
>
> cheers
> Bruce
> On
> Tue, 22 Mar 2016, Dr Sampada Sinha wrote:
>
> > Dear freesurfer experts,
> >
> > I am trying to do hippocampal subfields segmentation on Mac. I will
> greatly
> > appreciate if freesurfer 6.0 version link is forwarded to me.
> >
> > With thanks and regards,
> >
> > Sampada
> > Pre-doctoral student
> > KGMU, Lucknow
> > India
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
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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.
>
>

-- 
Sampada Sinha
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Re: [Freesurfer] Regarding: oblique view

[Dr Sampada Sinha]

Thanks Bruce for your reply. The acquisition was oblique and the voxel size
doesn't conform to the 1mm cube isotropic. I am trying to work on it and
figure out a solution. However, if I am not, hope its okay to send you the
nifti image.

Thanks and regards,

Sampada



Rnday, March 20, 2016, Bruce Fischl  wrote:

> what do you mean by "adding" an oblique angle? If you mean acquiring the
> data obliquely you should be fine as long as the voxels are close to 1mm
> isotropic.
>
> cheers
> Bruce
> On Sun, 20 Mar 2016, Dr Sampada Sinha wrote:
>
> > Dear freesurfer experts,
> > Does adding an oblique angle during coronal or axial acquisitions of T1w
> > images lead to topographical errors during mri_fix_topology process?
> >
> > Thanks and regards,
> >
> > Sampada
> >
> >
> >
> > --
> > Sampada Sinha
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> ___
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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.
>
>

-- 
Sampada Sinha
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Re: [Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

[Bruce Fischl]

Hi Morten

the insula you should be able to get out of the cortical labels in the 
various *.annot files. The substantia nigra we don't segment at the 
moment, and I suspect it would be hard to do so from only a T1-weighted 
scan.


cheers
Bruce
On Tue, 22 Mar 2016, Morten Sejer Hansen wrote:



Dear Experts,

 

I am interested in retrieving the volume of the insula and substantia nigra 
from T1W
structural scans converted to nii.gz files. All scans have undergone the 
recon-all
process without error.

I have seen volume estimations of Insula and substantia nigra performed in 
several
studies, but I can’t seem to figure out how I retrieve these volumes.

 

I ran the command:

 

asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all
4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt

 

SUBJECTS_DIR : /Applications/freesurfer/subjects

Parsing the .stats files

Building the table..

Writing the table to Subcortical.txt

 

following this I get at fine output with several volume estimation of 
subcortical
structures, but without the Insula (left and right), and without the substantia 
nigra
(left and right).

 

I tried to run the same command on “Bert”, and ended up with the same result 
(with
the insula and substania nigra still missing). I also tried to add the

 

--all-segs

 

But without any change in the output.

 

On the 
FreeSurferColorLUT(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorL
UT) I can see that the structures I am interested in have the following 
numbers: 19,
27, 55 and 59.

 

Could you provide me answers on how to extract the volumes of the insula and
substantia nigra?

 

Thanks a lot!

 

Kind regards

 

Morten Sejer Hansen

 

 



Morten Sejer Hansen

MD
Direct: + 45 26373611

Mail: morten.sejer.han...@regionh.dk / morten.sejer.han...@dadlnet.dk

Department of anaesthesiology 4231

Centre of head and orthopaedics

Copenhagen University Hospital, Rigshospitalet

Blegdamsvej 9
2100 Copenhagen

 

Tel: +45 35 45 35 45
Web: www.regionh.dk

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Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

[Bruce Fischl]

Hi Sampada

V6 is not out yet, although we are actively (frantically?) working on it.

cheers
Bruce
On 
Tue, 22 Mar 2016, Dr Sampada Sinha wrote:

> Dear freesurfer experts,
> 
> I am trying to do hippocampal subfields segmentation on Mac. I will greatly
> appreciate if freesurfer 6.0 version link is forwarded to me.
> 
> With thanks and regards,
> 
> Sampada
> Pre-doctoral student
> KGMU, Lucknow
> India
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
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[Freesurfer] Asegstats2table: insula and Substantia nigra volumes are not reported

[Morten Sejer Hansen]

Dear Experts,

I am interested in retrieving the volume of the insula and substantia nigra 
from T1W structural scans converted to nii.gz files. All scans have undergone 
the recon-all process without error.
I have seen volume estimations of Insula and substantia nigra performed in 
several studies, but I can't seem to figure out how I retrieve these volumes.

I ran the command:

asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all 
4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt

SUBJECTS_DIR : /Applications/freesurfer/subjects
Parsing the .stats files
Building the table..
Writing the table to Subcortical.txt

following this I get at fine output with several volume estimation of 
subcortical structures, but without the Insula (left and right), and without 
the substantia nigra (left and right).

I tried to run the same command on "Bert", and ended up with the same result 
(with the insula and substania nigra still missing). I also tried to add the

--all-segs

But without any change in the output.

On the FreeSurferColorLUT 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT)
 I can see that the structures I am interested in have the following numbers: 
19, 27, 55 and 59.

Could you provide me answers on how to extract the volumes of the insula and 
substantia nigra?

Thanks a lot!

Kind regards

Morten Sejer Hansen




Morten Sejer Hansen
MD
Direct: + 45 26373611
Mail: morten.sejer.han...@regionh.dk / 
morten.sejer.han...@dadlnet.dk

Department of anaesthesiology 4231
Centre of head and orthopaedics
Copenhagen University Hospital, Rigshospitalet
Blegdamsvej 9
2100 Copenhagen

Tel: +45 35 45 35 45
Web: www.regionh.dk

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Re: [Freesurfer] "Bump" - Fwd: lGI value is aberrantly high and misalignment fix

[Marco Bucci]

Sorry, I forgot to mention
that I went back to the original line 51 of the Marie Schaer code in
"make_outer_surface".
No "fix" anymore.

Marco

2016-03-16 11:51 GMT+02:00 Marco Bucci :

> Dear all,
>
> I forward again my original post.
> I also attach the recon-all.log of one of the several faulty cases.
>
> I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0)
>  in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a
> and I have fixed the SearchProjectionOnPial.m.
>
> I also had to fix line 51 of make_outer_surface.m
> "v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the
> different orientation"
> with
> "v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4)
> vol.vox2ras1(3,4)-v(:,2)];"
> in order to use the image coordinate to fix surface orientation and
> alignment.
>
> If I would use the original line 51, the surface produced by recon -lgi
> results
> misaligned with the reference pial and image.
>
> My problems remains the aberrantly high lgI value in most of my subject
> images.
>
> Can you help me?
>
> Yours,
> Marco Bucci
>
>
> -- Forwarded message --
> From: Marco Bucci 
> Date: 2015-12-22 23:49 GMT+02:00
> Subject: Re: [Freesurfer] lGI value is aberrantly high
> To: "freesurfer@nmr.mgh.harvard.edu" 
>
>
> Dear all,
>
> I have a problem with the LGI module.
> At the step when the software computes the LGIs for the vertices,
> In one vertex the lGI results aberrantly high and the software exits
> with ERRORS.
>
> I tried the solution suggested by Marie Schaer to rereconstruct
> The images with "randomness"
> Recon-all -autorecon2-wm -randomness -autorecon3
>
> I tried this fix on two of my subjects
> With errors. Not all subject resulted
> Errors in the computation of the gyrification.
>
> Can you help me?
>
> Marco Bucci
> Turku Pet Center
>
> Sent from my iPhone
>
>
>
> --
> 
> Marco Bucci, PhD in
> Clinical Physiology and Nuclear Medicine
> Turku PET Centre
> Turku University Central Hospital (TUCH)
> PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland
> tel. +358 2 3132798
> fax. +358 2 2318191
> mobile: +358 40 6873976
> UTU e-mail: mar...@utu.fi
> 
>
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>
>


-- 

Marco Bucci, PhD in
Clinical Physiology and Nuclear Medicine
Turku PET Centre
Turku University Central Hospital (TUCH)
PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland
tel. +358 2 3132798
fax. +358 2 2318191
mobile: +358 40 6873976
UTU e-mail: mar...@utu.fi

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