[Freesurfer] MRI registration

[Zeynep Akalin Acar]

Hi all,

I'm trying to register two brain volumes using Freesurfer. I need to find a
mapping for each voxel of the MR image to the reference image. I tried using
mri_register with the option -vf as the wiki documentation suggests that it
outputs a vector field. Instead it expects a variance volume. The surface
registrations do not work for me either, because they don't include a
mapping of inner points. I tried Talairach transformation, but, it is a
rigid registration, and I need a non-rigid registration.

Is there a tool in Freesurfer that can register two brain volumes with a
mapping of each voxel?

Thanks,

Zeynep.
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[Freesurfer] calculating the surface area of each region on Desikan template

[Zhangyuanchao]

hi, expert,
 
How could I obtain the surface area of each region on the Desikan template?
How can I obtain this area in both native space and the average template space?
In the surf folder of each subjects, I noticed there is lh.area file, what is 
meaning of this file? Do I need ?h.area for calculating the area of each region?
 
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Jan Drozd]

Hi Bruce,

Thanks for pointing this out to me about the RAM.

I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects simultaneously 
if each subject requires 2 to 3 Gb of RAM.  

Thanks,
John

Sent from my iPhone

On 2011-07-05, at 6:08 PM, Bruce Fischl  wrote:

> how much ram do you have? You'll need at least 2G/subject if not 3
> On Tue, 5 Jul 2011, John Drozd wrote:
> 
>> Hi Bruce,
>> Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.
>> Take care,
>> John
>> 2011/7/5 Bruce Fischl 
>>  Sorry, that won't help a single subject much, although there are
>>  options to run the hemis in parallel. You can run multiple
>>  subjects at the same time, which is what we usually do. Or you
>>  can use cuss
>> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
>> 
>>  Hi Bruce,
>> 
>>  Okay, thank you. I understand and can see that to do an
>>  accurate job, the pipeline must be complicated.
>>  I have eight processors on my linux desktop computer.
>>  Maybe some parts of recon-all are multi-threaded which
>>  could speed things up for me :-)
>> 
>>  Thank you,
>>  John
>> 
>>  2011/7/5 Bruce Fischl 
>>sorry, but the majority of the time is
>>required. We're working to speed things up,
>>but it is complicated software with multiple
>>nonlinear warps, segmentation procedures,
>>etc
>> Bruce
>> On Tue, 5 Jul 2011, John Drozd wrote:
>> 
>>  Hi Bruce and Pedro,
>> 
>>  Thank you both for sending me your
>>  suggestions. 
>>  Just to let you know, because my .dcm (dicom)
>>  files had a space and two dots
>>  in the filenames:
>>  (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
>>  (and using quotes around the file name or "\ "
>>  within the filename without
>>  the quotes did not work with recon-all),
>>  recon-all truncated the filename
>>  before the space as "2008_12_08.ek" feeding it
>>  to an mri_convert command and
>>  gave an error message.
>> 
>>  So I worked around this problem as follows: I
>>  converted the .dcm series to a
>>  nifti .nii volume using 3D Slicer, and then
>>  used mri_convert to convert the
>>  .nii format to .mgz format.  Then I ran
>>  recon-all on the .mgz formatted file
>>  and it is now running successfully.
>> 
>>  I see on the online tutorials and slides, that
>>  this process takes about 20
>>  hours. Is there a way to only run partial
>>  steps pertaining only to the
>>  cortical thickness? 
>> 
>>  Pedro also suggested that I go through the
>>  FreeSurferBeginnersGuide wiki
>>  which I am doing now. 
>> 
>>  Also, reading some mailing lists emails, I
>>  noticed that matlab can be used
>>  to analyze the cortical thickness statistiics,
>>  and also freesurfer comes
>>  with matlab scripts.  I will try these tools
>>  out as well.
>> 
>>  Thank you for your time,
>>  John
>> 
>>  On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
>>  
>>  wrote:
>>   recon-all \
>>  -i >  dicom series> \
>>  -s  \
>>  -sd >  folder in> \
>>  -all
>> 
>>   cheers
>>   Bruce
>> 
>>  On Tue, 5 Jul 2011, John Drozd wrote:
>> 
>>   Hi,
>> 
>>   I am running freesurfer on 64 bit Fedora
>>  10 linux.
>>   I am using version: 
>> 
>>   freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
>>   Can anyone point me to a reference web
>>  page listing what
>>   steps I need to
>>   type to process
>>   a series of MRI dicom slices and use
>>  FreeSurfer to measure
>>   cortical
>>   thickness for this dicom series?
>> 
>>   Thank you,
>>   John
>> 
>>   --
>>   John Drozd
>>   Post-Doctoral Fellow, Robarts Research
>>  Institute
>>   The University of Western Ontario
>>   London, ON, Canada
>>   http://publish.uwo.ca/~jdrozd2/index.htm
>>
>> 
>>  ___
>>  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.
>> 
>>  --
>>  John Drozd
>>  Post-Doctoral Fellow, Robarts Research

Re: [Freesurfer] stats on masked functional data

[Nick Schmansky]

mri_anatomical_stats will do that for you.
see mri_anatomical_stats --help

it would be something like:

mris_anatomical_stats -l ../label/lh.V1.label \
-t ./lh.beta.mgh \
-f lh.beta.stats \
my_subject_id lh


note that the column name will say 'ThickAvg' and 'ThickStd', which is
actually the avg/std for your beta.mgh input file.

n.



On Tue, 2011-06-28 at 16:54 -0400, Ritobrato Datta wrote:
> Hello All,
> 
> Looks like this question slipped through. 
> I have a functional beta value overlay as a .mgh file and a V1 label file and 
> I want to compute the average beta value within that mask for each subject. 
> 
> How do I do this ?
> 
> Thanks a lot
> 
> Ri
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> 
> 

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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

how much ram do you have? You'll need at least 2G/subject if not 3
On Tue, 5 
Jul 2011, John Drozd wrote:



Hi Bruce,

Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.

Take care,
John

2011/7/5 Bruce Fischl 
  Sorry, that won't help a single subject much, although there are
  options to run the hemis in parallel. You can run multiple
  subjects at the same time, which is what we usually do. Or you
  can use cuss



On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:

  Hi Bruce,

  Okay, thank you. I understand and can see that to do an
  accurate job, the pipeline must be complicated.
  I have eight processors on my linux desktop computer.
  Maybe some parts of recon-all are multi-threaded which
  could speed things up for me :-)

  Thank you,
  John

  2011/7/5 Bruce Fischl 
sorry, but the majority of the time is
required. We're working to speed things up,
but it is complicated software with multiple
nonlinear warps, segmentation procedures,
etc


Bruce



On Tue, 5 Jul 2011, John Drozd wrote:

  Hi Bruce and Pedro,

  Thank you both for sending me your
  suggestions. 
  Just to let you know, because my .dcm (dicom)
  files had a space and two dots
  in the filenames:
  (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
  (and using quotes around the file name or "\ "
  within the filename without
  the quotes did not work with recon-all),
  recon-all truncated the filename
  before the space as "2008_12_08.ek" feeding it
  to an mri_convert command and
  gave an error message.

  So I worked around this problem as follows: I
  converted the .dcm series to a
  nifti .nii volume using 3D Slicer, and then
  used mri_convert to convert the
  .nii format to .mgz format.  Then I ran
  recon-all on the .mgz formatted file
  and it is now running successfully.

  I see on the online tutorials and slides, that
  this process takes about 20
  hours. Is there a way to only run partial
  steps pertaining only to the
  cortical thickness? 

  Pedro also suggested that I go through the
  FreeSurferBeginnersGuide wiki
  which I am doing now. 

  Also, reading some mailing lists emails, I
  noticed that matlab can be used
  to analyze the cortical thickness statistiics,
  and also freesurfer comes
  with matlab scripts.  I will try these tools
  out as well.

  Thank you for your time,
  John

  On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl
  
  wrote:
       recon-all \
              -i  \
              -s  \
              -sd  \
              -all


       cheers
       Bruce



  On Tue, 5 Jul 2011, John Drozd wrote:

       Hi,

       I am running freesurfer on 64 bit Fedora
  10 linux.
       I am using version: 
     
   freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
       Can anyone point me to a reference web
  page listing what
       steps I need to
       type to process
       a series of MRI dicom slices and use
  FreeSurfer to measure
       cortical
       thickness for this dicom series?

       Thank you,
       John

       --
       John Drozd
       Post-Doctoral Fellow, Robarts Research
  Institute
       The University of Western Ontario
       London, ON, Canada
       http://publish.uwo.ca/~jdrozd2/index.htm
        



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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.




  --
  John Drozd
  Post-Doctoral Fellow, Robarts Research
  Institute
  The University of Western Ontario
  London, ON, Canada
  http://publish.uwo.ca/~jdrozd2/index.htm
   





--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 




--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 


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Re: [Freesurfer] tracula bvecs problem

[Anastasia Yendiki]

Hi Franz - Which of the files that you sent us are the original files (the 
bvalfile and bvecfile from your dmrirc)? I could not find any files that 
had 33 lines among your attachments so I'm not sure what your input files 
look like.

Thanks,
a.y

On Tue, 5 Jul 2011, Franz Liem wrote:

> Hello again.
>
> I dug into the code and could locate the problem (I don't have a solution, 
> though. My coding skills are quite amateurish.) I think the problem somehow 
> lies in the format of my bvecs file.
>
> flip4fsl is not able to read it correctly:
> ---
> if (-e $inbvecs) then
>  echo "INFO: found $inbvecs, converting to FSL format"
>  if $fslflipx then
>set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
>  endif
>  cp /dev/null $outbvecs
>  foreach j (1 2 3)
>foreach k (1 2 3)
>  if ($order[$k] == $j) then
>printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print 
> sgn*$n}'` \
>>> $outbvecs
>printf '\n' >> $outbvecs
>  endif
>end
>  end
> endif
> ---
>
> I tried
> awk '{ print $1 }' bvecs (with my original bvecs file)
> this printed:
> 0
>
> This has something to do with the file's carriage return. I then produced a 
> new bvecs file by manually typing values into a new text file. Now awk '{ 
> print $1 }' bvecs  delivers one column with 33 lines.
>
>
> Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x 66; 
> see attachment).
> I don't really get how this printf  & awk command works.
>
> Any comments are very much appreciated.
> Franz
>
>
>
>
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi Bruce,

Thanks for the suggestion, Bruce. I'll run 8 different subjects at once.

Take care,
John

2011/7/5 Bruce Fischl 

> Sorry, that won't help a single subject much, although there are options to
> run the hemis in parallel. You can run multiple subjects at the same time,
> which is what we usually do. Or you can use cuss
>
>
>
> On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:
>
> Hi Bruce,
>
> Okay, thank you. I understand and can see that to do an accurate job, the
> pipeline must be complicated.
> I have eight processors on my linux desktop computer.
> Maybe some parts of recon-all are multi-threaded which could speed things
> up for me :-)
>
> Thank you,
> John
>
> 2011/7/5 Bruce Fischl < 
> fis...@nmr.mgh.harvard.edu>
>
>> sorry, but the majority of the time is required. We're working to speed
>> things up, but it is complicated software with multiple nonlinear warps,
>> segmentation procedures, etc
>>
>>
>> Bruce
>>
>>
>>
>> On Tue, 5 Jul 2011, John Drozd wrote:
>>
>>  Hi Bruce and Pedro,
>>>
>>> Thank you both for sending me your suggestions.
>>> Just to let you know, because my .dcm (dicom) files had a space and two
>>> dots
>>> in the filenames:
>>> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
>>> (and using quotes around the file name or "\ " within the filename
>>> without
>>> the quotes did not work with recon-all), recon-all truncated the filename
>>> before the space as "2008_12_08.ek" feeding it to an mri_convert command
>>> and
>>> gave an error message.
>>>
>>> So I worked around this problem as follows: I converted the .dcm series
>>> to a
>>> nifti .nii volume using 3D Slicer, and then used mri_convert to convert
>>> the
>>> .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted
>>> file
>>> and it is now running successfully.
>>>
>>> I see on the online tutorials and slides, that this process takes about
>>> 20
>>> hours. Is there a way to only run partial steps pertaining only to the
>>> cortical thickness?
>>>
>>> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
>>> which I am doing now.
>>>
>>> Also, reading some mailing lists emails, I noticed that matlab can be
>>> used
>>> to analyze the cortical thickness statistiics, and also freesurfer comes
>>> with matlab scripts.  I will try these tools out as well.
>>>
>>> Thank you for your time,
>>> John
>>>
>>> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>  recon-all \
>>> -i  \
>>> -s  \
>>> -sd  \
>>> -all
>>>
>>>
>>>  cheers
>>>  Bruce
>>>
>>>
>>>
>>> On Tue, 5 Jul 2011, John Drozd wrote:
>>>
>>>  Hi,
>>>
>>>  I am running freesurfer on 64 bit Fedora 10 linux.
>>>  I am using version:
>>>  freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0.
>>>  Can anyone point me to a reference web page listing what
>>>  steps I need to
>>>  type to process
>>>  a series of MRI dicom slices and use FreeSurfer to measure
>>>  cortical
>>>  thickness for this dicom series?
>>>
>>>  Thank you,
>>>  John
>>>
>>>  --
>>>  John Drozd
>>>  Post-Doctoral Fellow, Robarts Research Institute
>>>  The University of Western Ontario
>>>  London, ON, Canada
>>>   
>>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>>
>>>
>>>
>>>
>>> __**_
>>> 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.
>>>
>>>
>>>
>>>
>>> --
>>> John Drozd
>>> Post-Doctoral Fellow, Robarts Research Institute
>>> The University of Western Ontario
>>> London, ON, Canada
>>>  http://publish.uwo.ca/~**
>>> jdrozd2/index.htm
>>>
>>>
>>>
>>>
>
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> 
> http://publish.uwo.ca/~jdrozd2/index.htm
>
>
>


-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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T

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

Sorry, that won't help a single subject much, although there are options to run 
the hemis in parallel. You can run multiple subjects at the same time, which is 
what we usually do. Or you can use cuss



On Jul 5, 2011, at 5:11 PM, John Drozd  wrote:

> Hi Bruce,
> 
> Okay, thank you. I understand and can see that to do an accurate job, the 
> pipeline must be complicated.
> I have eight processors on my linux desktop computer. 
> Maybe some parts of recon-all are multi-threaded which could speed things up 
> for me :-)
> 
> Thank you,
> John
> 
> 2011/7/5 Bruce Fischl 
> sorry, but the majority of the time is required. We're working to speed 
> things up, but it is complicated software with multiple nonlinear warps, 
> segmentation procedures, etc
> 
> 
> Bruce
> 
> 
> 
> On Tue, 5 Jul 2011, John Drozd wrote:
> 
> Hi Bruce and Pedro,
> 
> Thank you both for sending me your suggestions. 
> Just to let you know, because my .dcm (dicom) files had a space and two dots
> in the filenames:
> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
> (and using quotes around the file name or "\ " within the filename without
> the quotes did not work with recon-all), recon-all truncated the filename
> before the space as "2008_12_08.ek" feeding it to an mri_convert command and
> gave an error message.
> 
> So I worked around this problem as follows: I converted the .dcm series to a
> nifti .nii volume using 3D Slicer, and then used mri_convert to convert the
> .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file
> and it is now running successfully.
> 
> I see on the online tutorials and slides, that this process takes about 20
> hours. Is there a way to only run partial steps pertaining only to the
> cortical thickness? 
> 
> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
> which I am doing now. 
> 
> Also, reading some mailing lists emails, I noticed that matlab can be used
> to analyze the cortical thickness statistiics, and also freesurfer comes
> with matlab scripts.  I will try these tools out as well.
> 
> Thank you for your time,
> John
> 
> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl 
> wrote:
>  recon-all \
> -i  \
> -s  \
> -sd  \
> -all
> 
> 
>  cheers
>  Bruce
> 
> 
> 
> On Tue, 5 Jul 2011, John Drozd wrote:
> 
>  Hi,
> 
>  I am running freesurfer on 64 bit Fedora 10 linux.
>  I am using version: 
>  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
>  Can anyone point me to a reference web page listing what
>  steps I need to
>  type to process
>  a series of MRI dicom slices and use FreeSurfer to measure
>  cortical
>  thickness for this dicom series?
> 
>  Thank you,
>  John
> 
>  --
>  John Drozd
>  Post-Doctoral Fellow, Robarts Research Institute
>  The University of Western Ontario
>  London, ON, Canada
>  http://publish.uwo.ca/~jdrozd2/index.htm
>   
> 
> 
> 
> ___
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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.
> 
> 
> 
> 
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>  
> 
> 
> 
> 
> 
> -- 
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>  
> 
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Re: [Freesurfer] gyrification Index of a label

[Nick Schmansky]

and to further this, i added a section on the wiki page on how to use
qdec to perform a surface-based lgi analysis.  basically, you just do
this:

To perform a vertex-wise analysis in QDEC of the lgi surface data, first
sample the results to the average template subject 'fsaverage': 

recon-all -s my_subject_id -qcache -measure pial_lgi

Do this for each of the subjects in your group. 

Then to include 'pial_lgi' as a measure in the 'measures' menu selector
in the QDEC Design tab, create a file named .Qdecrc in your
$SUBJECTS_DIR/qdec directory containing this text: 

MEASURE1 = pial_lgi

This will allow a surface-based group GLM analysis of the lgi measure.
You would select 'pial_lgi' in the measures menu (where you will
normally find 'thickness' as the default). 

N.



On Tue, 2011-07-05 at 22:56 +0200, Marie Schaer wrote:
> Hi Ritobrato,
> 
> Nick already answered your query. Just a small add: the gold standard to use 
> local gyrification index is to compute vertex-wise analyses rather than 
> parcel-wise comparisons. Indeed, lGI at each point already quantifies the 
> gyrification in the surrounding region. As a result, the average lGI in a 
> given cortical region will also reflect to some (minimal) extent the 
> gyrification in the neighboring gyral regions. 
>  
> Hope it helps,
> 
> Marie
> 
> On Jul 5, 2011, at 10:47 PM, Nick Schmansky wrote:
> 
> > this command can be used:
> > 
> > mri_segstats --annot my_subject_id lh aparc \
> >  --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi \
> >  --sum lh.aparc.pial_lgi.stats
> > 
> > i've updated the lGI wiki page to include this as well.
> > 
> > n.
> > 
> > 
> > On Tue, 2011-07-05 at 14:15 -0400, Ritobrato Datta wrote:
> >> Hi All,
> >> 
> >> I have run
> >> 
> >> recon-all -s  -localGI
> >> 
> >> Now I want to get the gyrification Index of a particular label. Is there a 
> >> way to do that ?
> >> 
> >> Please let me know 
> >> 
> >> Thanks
> >> 
> >> Ri
> >> 
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> 
> >> 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> > 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
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi Bruce,

Okay, thank you. I understand and can see that to do an accurate job, the
pipeline must be complicated.
I have eight processors on my linux desktop computer.
Maybe some parts of recon-all are multi-threaded which could speed things up
for me :-)

Thank you,
John

2011/7/5 Bruce Fischl 

> sorry, but the majority of the time is required. We're working to speed
> things up, but it is complicated software with multiple nonlinear warps,
> segmentation procedures, etc
>
>
> Bruce
>
>
>
> On Tue, 5 Jul 2011, John Drozd wrote:
>
>  Hi Bruce and Pedro,
>>
>> Thank you both for sending me your suggestions.
>> Just to let you know, because my .dcm (dicom) files had a space and two
>> dots
>> in the filenames:
>> (e.g. "2008_12_08.ek -0035-0001-1.dcm" )
>> (and using quotes around the file name or "\ " within the filename without
>> the quotes did not work with recon-all), recon-all truncated the filename
>> before the space as "2008_12_08.ek" feeding it to an mri_convert command
>> and
>> gave an error message.
>>
>> So I worked around this problem as follows: I converted the .dcm series to
>> a
>> nifti .nii volume using 3D Slicer, and then used mri_convert to convert
>> the
>> .nii format to .mgz format.  Then I ran recon-all on the .mgz formatted
>> file
>> and it is now running successfully.
>>
>> I see on the online tutorials and slides, that this process takes about 20
>> hours. Is there a way to only run partial steps pertaining only to the
>> cortical thickness?
>>
>> Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
>> which I am doing now.
>>
>> Also, reading some mailing lists emails, I noticed that matlab can be used
>> to analyze the cortical thickness statistiics, and also freesurfer comes
>> with matlab scripts.  I will try these tools out as well.
>>
>> Thank you for your time,
>> John
>>
>> On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl 
>> wrote:
>>  recon-all \
>> -i  \
>> -s  \
>> -sd  \
>> -all
>>
>>
>>  cheers
>>  Bruce
>>
>>
>>
>> On Tue, 5 Jul 2011, John Drozd wrote:
>>
>>  Hi,
>>
>>  I am running freesurfer on 64 bit Fedora 10 linux.
>>  I am using version:
>>  freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0.
>>  Can anyone point me to a reference web page listing what
>>  steps I need to
>>  type to process
>>  a series of MRI dicom slices and use FreeSurfer to measure
>>  cortical
>>  thickness for this dicom series?
>>
>>  Thank you,
>>  John
>>
>>  --
>>  John Drozd
>>  Post-Doctoral Fellow, Robarts Research Institute
>>  The University of Western Ontario
>>  London, ON, Canada
>>  
>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>
>>
>>
>>
>> __**_
>> 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.
>>
>>
>>
>>
>> --
>> John Drozd
>> Post-Doctoral Fellow, Robarts Research Institute
>> The University of Western Ontario
>> London, ON, Canada
>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>
>>
>>
>>


-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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Re: [Freesurfer] gyrification Index of a label

[Marie Schaer]

Hi Ritobrato,

Nick already answered your query. Just a small add: the gold standard to use 
local gyrification index is to compute vertex-wise analyses rather than 
parcel-wise comparisons. Indeed, lGI at each point already quantifies the 
gyrification in the surrounding region. As a result, the average lGI in a given 
cortical region will also reflect to some (minimal) extent the gyrification in 
the neighboring gyral regions. 
 
Hope it helps,

Marie

On Jul 5, 2011, at 10:47 PM, Nick Schmansky wrote:

> this command can be used:
> 
> mri_segstats --annot my_subject_id lh aparc \
>  --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi \
>  --sum lh.aparc.pial_lgi.stats
> 
> i've updated the lGI wiki page to include this as well.
> 
> n.
> 
> 
> On Tue, 2011-07-05 at 14:15 -0400, Ritobrato Datta wrote:
>> Hi All,
>> 
>> I have run
>> 
>> recon-all -s  -localGI
>> 
>> Now I want to get the gyrification Index of a particular label. Is there a 
>> way to do that ?
>> 
>> Please let me know 
>> 
>> Thanks
>> 
>> Ri
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
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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 
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> properly
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Re: [Freesurfer] gyrification Index of a label

[Nick Schmansky]

this command can be used:

mri_segstats --annot my_subject_id lh aparc \
  --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi \
  --sum lh.aparc.pial_lgi.stats

i've updated the lGI wiki page to include this as well.

n.


On Tue, 2011-07-05 at 14:15 -0400, Ritobrato Datta wrote:
> Hi All,
> 
> I have run
> 
> recon-all -s  -localGI
> 
> Now I want to get the gyrification Index of a particular label. Is there a 
> way to do that ?
> 
> Please let me know 
> 
> Thanks
> 
> Ri
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 

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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

sorry, but the majority of the time is required. We're working to speed 
things up, but it is complicated software with multiple nonlinear warps, 
segmentation procedures, etc


Bruce



On Tue, 5 Jul 2011, John Drozd wrote:


Hi Bruce and Pedro,

Thank you both for sending me your suggestions. 
Just to let you know, because my .dcm (dicom) files had a space and two dots
in the filenames:
(e.g. "2008_12_08.ek -0035-0001-1.dcm" )
(and using quotes around the file name or "\ " within the filename without
the quotes did not work with recon-all), recon-all truncated the filename
before the space as "2008_12_08.ek" feeding it to an mri_convert command and
gave an error message.

So I worked around this problem as follows: I converted the .dcm series to a
nifti .nii volume using 3D Slicer, and then used mri_convert to convert the
.nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file
and it is now running successfully.

I see on the online tutorials and slides, that this process takes about 20
hours. Is there a way to only run partial steps pertaining only to the
cortical thickness? 

Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
which I am doing now. 

Also, reading some mailing lists emails, I noticed that matlab can be used
to analyze the cortical thickness statistiics, and also freesurfer comes
with matlab scripts.  I will try these tools out as well.

Thank you for your time,
John

On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl 
wrote:
  recon-all \
         -i  \
         -s  \
         -sd  \
         -all


  cheers
  Bruce



On Tue, 5 Jul 2011, John Drozd wrote:

  Hi,

  I am running freesurfer on 64 bit Fedora 10 linux.
  I am using version: 
  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
  Can anyone point me to a reference web page listing what
  steps I need to
  type to process
  a series of MRI dicom slices and use FreeSurfer to measure
  cortical
  thickness for this dicom series?

  Thank you,
  John

  --
  John Drozd
  Post-Doctoral Fellow, Robarts Research Institute
  The University of Western Ontario
  London, ON, Canada
  http://publish.uwo.ca/~jdrozd2/index.htm
   



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e-mail
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--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 


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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi Bruce and Pedro,

Thank you both for sending me your suggestions.
Just to let you know, because my .dcm (dicom) files had a space and two dots
in the filenames:
(e.g. "2008_12_08.ek -0035-0001-1.dcm" )
(and using quotes around the file name or "\ " within the filename without
the quotes did not work with recon-all), recon-all truncated the filename
before the space as "2008_12_08.ek" feeding it to an mri_convert command and
gave an error message.

So I worked around this problem as follows: I converted the .dcm series to a
nifti .nii volume using 3D Slicer, and then used mri_convert to convert the
.nii format to .mgz format.  Then I ran recon-all on the .mgz formatted file
and it is now running successfully.

I see on the online tutorials and slides, that this process takes about 20
hours. Is there a way to only run partial steps pertaining only to the
cortical thickness?

Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki
which I am doing now.

Also, reading some mailing lists emails, I noticed that matlab can be used
to analyze the cortical thickness statistiics, and also freesurfer comes
with matlab scripts.  I will try these tools out as well.

Thank you for your time,
John

On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl wrote:

> recon-all \
>-i  \
>-s  \
>-sd  \
>-all
>
>
> cheers
> Bruce
>
>
>
> On Tue, 5 Jul 2011, John Drozd wrote:
>
>  Hi,
>>
>> I am running freesurfer on 64 bit Fedora 10 linux.
>> I am using version:  freesurfer-Linux-centos4_x86_**64-stable-pub-v4.3.0.
>> Can anyone point me to a reference web page listing what steps I need to
>> type to process
>> a series of MRI dicom slices and use FreeSurfer to measure cortical
>> thickness for this dicom series?
>>
>> Thank you,
>> John
>>
>> --
>> John Drozd
>> Post-Doctoral Fellow, Robarts Research Institute
>> The University of Western Ontario
>> London, ON, Canada
>> http://publish.uwo.ca/~**jdrozd2/index.htm
>>
>>
>>
>>
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>
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> 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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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Re: [Freesurfer] tracula bvecs problem

[rspriti]

Hi Franz,

Sorry I just saw your previous email now. The problem could be due to the
variable decimal places you've used in your input bvecs file. I've
modified your bvecs file from the previous email to 3 decimal places
constantly for all the gradient values (See Attached!!). Can you check to
see if this solves the problem?

Thanks,
Priti


> Hello again.
>
> I dug into the code and could locate the problem (I don't have a solution,
> though. My coding skills are quite amateurish.) I think the problem
> somehow lies in the format of my bvecs file.
>
>  flip4fsl is not able to read it correctly:
> ---
> if (-e $inbvecs) then
>   echo "INFO: found $inbvecs, converting to FSL format"
>   if $fslflipx then
> set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
>   endif
>   cp /dev/null $outbvecs
>   foreach j (1 2 3)
> foreach k (1 2 3)
>   if ($order[$k] == $j) then
> printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print
> sgn*$n}'` \
> >> $outbvecs
> printf '\n' >> $outbvecs
>   endif
> end
>   end
> endif
> ---
>
> I tried
> awk '{ print $1 }' bvecs (with my original bvecs file)
> this printed:
> 0
>
> This has something to do with the file's carriage return. I then produced
> a new bvecs file by manually typing values into a new text file. Now awk
> '{ print $1 }' bvecs  delivers one column with 33 lines.
>
>
> Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x
> 66; see attachment).
> I don't really get how this printf  & awk command works.
>
> Any comments are very much appreciated.
> Franz
>
>
>
>
> Am 05.07.2011 um 15:19 schrieb Franz Liem:
>
>> Dear Freesurfers.
>>
>> I am trying to run trac-all on one subject and have a problem with the
>> bvecs file at the -prep stage.
>> After dtifit is started an error massage occurs: Error: bvecs and bvals
>> don't have the same number of entries.
>> I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at
>> the -corr stage (-corr alone finishes without error).
>>
>> My input file is one 4d .nii.gz file (with a total of 33 images, with
>> the first being a b0 image).
>>
>> (I have attached the files from the dmri folder)
>>
>> The dmri/bvecs file only contains:
>> 0,000
>> 0,000
>> 0,000
>>
>> The original bvecs contains 3 columns and 33 lines.
>>
>> The dmri/bvals seems to be ok (1 column and 33 lines).
>>
>> eddy_correct processes 33 files (dmri/dwi_tmp ... dmri/dwi_tmp0032).
>>
>> I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although
>> the recon was done with 5.0.0, but I guess this not important at this
>> stage, is it?)
>>
>>
>> ***
>> My Configuration File:
>>
>> set dtroot = $SUBJECTS_DIR/DTI
>> set subjlist = (s02x)
>>
>> set dcmroot = $SUBJECTS_DIR/DTI
>> set dcmlist = (s02x/dti4d.nii.gz)
>>
>> set bvalfile = /Users/.../DTI/bvals/bvals
>> set bvecfile = /Users/.../DTI/bvals/bvecs
>> set nb0 = 1
>>
>> set doeddy = 1
>> set dorotbvecs = 1
>> set thrbet = 0.3
>> set doregflt = 1
>> set doregbbr = 0
>> ***
>>
>>
>> Thanks,
>> Franz
>>
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modified_bvecs
Description: Binary data
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[Freesurfer] gyrification Index of a label

[Ritobrato Datta]

Hi All,

I have run

recon-all -s  -localGI

Now I want to get the gyrification Index of a particular label. Is there a way 
to do that ?

Please let me know 

Thanks

Ri

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Re: [Freesurfer] tracula bvecs problem

[rspriti]

Hi Franz,

Please refer to the following page:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Specifically Step7.2 for the format in which bvals/bvecs files should be
given as an input.

If your input bvals/bvecs are in the right format flip4fsl should not give
you an error.

Also if you can send us your original bvecs and bvals file (before any
flipping is done) we can take a look to make sure it is in the right
format.

-Priti

> Hello again.
>
> I dug into the code and could locate the problem (I don't have a
solution,
> though. My coding skills are quite amateurish.) I think the problem
somehow lies in the format of my bvecs file.
>
>  flip4fsl is not able to read it correctly:
> ---
> if (-e $inbvecs) then
>   echo "INFO: found $inbvecs, converting to FSL format"
>   if $fslflipx then
> set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
>   endif
>   cp /dev/null $outbvecs
>   foreach j (1 2 3)
> foreach k (1 2 3)
>   if ($order[$k] == $j) then
> printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k
'{print
> sgn*$n}'` \
> >> $outbvecs
> printf '\n' >> $outbvecs
>   endif
> end
>   end
> endif
> ---
>
> I tried
> awk '{ print $1 }' bvecs (with my original bvecs file)
> this printed:
> 0
>
> This has something to do with the file's carriage return. I then
produced
> a new bvecs file by manually typing values into a new text file. Now awk
'{ print $1 }' bvecs  delivers one column with 33 lines.
>
>
> Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x
66; see attachment).
> I don't really get how this printf  & awk command works.
>
> Any comments are very much appreciated.
> Franz
>
>
>
>
> Am 05.07.2011 um 15:19 schrieb Franz Liem:
>
>> Dear Freesurfers.
>> I am trying to run trac-all on one subject and have a problem with the
bvecs file at the -prep stage.
>> After dtifit is started an error massage occurs: Error: bvecs and bvals
don't have the same number of entries.
>> I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at
the -corr stage (-corr alone finishes without error).
>> My input file is one 4d .nii.gz file (with a total of 33 images, with
the first being a b0 image).
>> (I have attached the files from the dmri folder)
>> The dmri/bvecs file only contains:
>> 0,000
>> 0,000
>> 0,000
>> The original bvecs contains 3 columns and 33 lines.
>> The dmri/bvals seems to be ok (1 column and 33 lines).
>> eddy_correct processes 33 files (dmri/dwi_tmp ...
dmri/dwi_tmp0032).
>> I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although
the recon was done with 5.0.0, but I guess this not important at this
stage, is it?)
>> ***
>> My Configuration File:
>> set dtroot = $SUBJECTS_DIR/DTI
>> set subjlist = (s02x)
>> set dcmroot = $SUBJECTS_DIR/DTI
>> set dcmlist = (s02x/dti4d.nii.gz)
>> set bvalfile = /Users/.../DTI/bvals/bvals
>> set bvecfile = /Users/.../DTI/bvals/bvecs
>> set nb0 = 1
>> set doeddy = 1
>> set dorotbvecs = 1
>> set thrbet = 0.3
>> set doregflt = 1
>> set doregbbr = 0
>> ***
>> Thanks,
>> Franz
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it is
>> addressed. If you believe this e-mail was sent to you in error and the
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HelpLine at
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Re: [Freesurfer] fieldsign problems

[Bruce Fischl]

no, it's definitely not normal. Do you see any error messages? Can you 
explain exactly what you did?
On Tue, 5 Jul 2011, Michelle Umali wrote:

> Hi All,
> I am running a retinotopy analysis, and when I look at the fieldsign
> image all I see are a bunch of red and blue speckles.
>
> Is this normal?
>
> Thanks.
> Michelle
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[Freesurfer] fieldsign problems

[Michelle Umali]

Hi All,
I am running a retinotopy analysis, and when I look at the fieldsign
image all I see are a bunch of red and blue speckles.

Is this normal?

Thanks.
Michelle
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Re: [Freesurfer] tracula bvecs problem

[Franz Liem]

Hello again.

I dug into the code and could locate the problem (I don't have a solution, 
though. My coding skills are quite amateurish.) I think the problem somehow 
lies in the format of my bvecs file.

 flip4fsl is not able to read it correctly:
---
if (-e $inbvecs) then
  echo "INFO: found $inbvecs, converting to FSL format"
  if $fslflipx then
set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"`
  endif
  cp /dev/null $outbvecs
  foreach j (1 2 3)
foreach k (1 2 3)
  if ($order[$k] == $j) then
printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print 
sgn*$n}'` \
>> $outbvecs
printf '\n' >> $outbvecs
  endif
end
  end
endif
---

I tried
awk '{ print $1 }' bvecs (with my original bvecs file)
this printed:
0

This has something to do with the file's carriage return. I then produced a new 
bvecs file by manually typing values into a new text file. Now awk '{ print $1 
}' bvecs  delivers one column with 33 lines.


Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x 66; see 
attachment).
I don't really get how this printf  & awk command works.

Any comments are very much appreciated.
Franz





bvecs
Description: Binary data

Am 05.07.2011 um 15:19 schrieb Franz Liem:

> Dear Freesurfers.
> 
> I am trying to run trac-all on one subject and have a problem with the bvecs 
> file at the -prep stage.
> After dtifit is started an error massage occurs: Error: bvecs and bvals don't 
> have the same number of entries.
> I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at the 
> -corr stage (-corr alone finishes without error).
> 
> My input file is one 4d .nii.gz file (with a total of 33 images, with the 
> first being a b0 image).
> 
> (I have attached the files from the dmri folder)
> 
> The dmri/bvecs file only contains:
> 0,000
> 0,000
> 0,000
> 
> The original bvecs contains 3 columns and 33 lines.
> 
> The dmri/bvals seems to be ok (1 column and 33 lines).
> 
> eddy_correct processes 33 files (dmri/dwi_tmp ... dmri/dwi_tmp0032).
> 
> I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although the 
> recon was done with 5.0.0, but I guess this not important at this stage, is 
> it?)
> 
> 
> ***
> My Configuration File:
> 
> set dtroot = $SUBJECTS_DIR/DTI
> set subjlist = (s02x)
> 
> set dcmroot = $SUBJECTS_DIR/DTI
> set dcmlist = (s02x/dti4d.nii.gz)
> 
> set bvalfile = /Users/.../DTI/bvals/bvals
> set bvecfile = /Users/.../DTI/bvals/bvecs
> set nb0 = 1
> 
> set doeddy = 1
> set dorotbvecs = 1
> set thrbet = 0.3
> set doregflt = 1
> set doregbbr = 0
> ***
> 
> 
> Thanks,
> Franz
> 
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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Bruce Fischl]

recon-all \
-i  \
-s  \
-sd  \
-all


cheers
Bruce


On Tue, 5 Jul 2011, John Drozd wrote:


Hi,

I am running freesurfer on 64 bit Fedora 10 linux.
I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
Can anyone point me to a reference web page listing what steps I need to
type to process
a series of MRI dicom slices and use FreeSurfer to measure cortical
thickness for this dicom series?

Thank you,
John

--
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
 


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Re: [Freesurfer] Matlab and FS

[Bruce Fischl]

Hi Carolina,

the thickness in each region can be obtained either from the aparc.stats 
file or in matlab by loading the thickness using read_curv.m and the 
various label files with read_label.m. Make sure to account for the indices 
being one-based in the return from read_curv.m, but zero-based in the 
label.

cheers
Bruce


On 
Tue, 5 Jul 2011, Carolina Valencia wrote:

> Hello FS'users,
> 
> I'm trying to do an histogram of cortical thickness for 2 cases in matlab,
> but the problem is that I have Installed matlab in a computer (windows) and
> FS in another one (ubuntu)
> Can I configure something to use the FS commands in matlab in order to
> obtain some graphs?
> And also, where can I find the cortical thickness in each regions (Brodmann
> areas, gyrus or sulci) of the brain in order to compare a normal patient
> with a patiwnt who has a cortical dysplasia ?
> 
> Thanks a lot for your help,
> 
> Carolina
> 
> 
>
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Re: [Freesurfer] Matlab and FS

[jorge luis]

 
Hi Carolina
 
There is a directory freesurfer/matlab which contains several matlab-based 
scripts for reading and writing (after modified) surface- and volume-based data 
generated in freesurfer. 
Transport files from Linux to Windows will be tedious and things may not work 
properly, therefore, I recommend you to install Matlab for Linux or you can try 
with Octave (a kind of GNU Matlab for Linux).
 
Cheers 
Jorge

--- El mar, 5/7/11, Carolina Valencia  escribió:


De: Carolina Valencia 
Asunto: [Freesurfer] Matlab and FS
Para: freesurfer@nmr.mgh.harvard.edu
Fecha: martes, 5 de julio, 2011 17:39


Hello FS'users,

I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but 
the problem is that I have Installed matlab in a computer (windows) and FS in 
another one (ubuntu)
Can I configure something to use the FS commands in matlab in order to obtain 
some graphs?
And also, where can I find the cortical thickness in each regions (Brodmann 
areas, gyrus or sulci) of the brain in order to compare a normal patient with a 
patiwnt who has a cortical dysplasia ?

Thanks a lot for your help,

Carolina


-Adjunto en línea a continuación-


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Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Pedro Paulo de Magalhães Oliveira Junior]

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

On Tue, Jul 5, 2011 at 13:14, John Drozd  wrote:

> Hi,
>
> I am running freesurfer on 64 bit Fedora 10 linux.
> I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
> Can anyone point me to a reference web page listing what steps I need to
> type to process
> a series of MRI dicom slices and use FreeSurfer to measure cortical
> thickness for this dicom series?
>
> Thank you,
> John
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
> http://publish.uwo.ca/~jdrozd2/index.htm
>
>
>
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> is
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> properly
> dispose of the e-mail.
>
>
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[Freesurfer] measuring cortical thickness using FreeSurfer

[John Drozd]

Hi,

I am running freesurfer on 64 bit Fedora 10 linux.
I am using version:  freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0.
Can anyone point me to a reference web page listing what steps I need to
type to process
a series of MRI dicom slices and use FreeSurfer to measure cortical
thickness for this dicom series?

Thank you,
John

-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
http://publish.uwo.ca/~jdrozd2/index.htm
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[Freesurfer] Tksurfer Time Course Correlation

[Tyler Blazey]

Hi,

I have a couple of questions about Tksurfer's time course correlation option. 
First, what type of correlation does it show? Does it use Pearson's r or 
something else? Second, is there any way to get the same output from the 
command line? From previous list discussions, it looks like it might be 
possible using a Tcl script, but I am looking for more of a standard unix/linux 
command.

Thanks for any help,

- Tyler



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[Freesurfer] Matlab and FS

[Carolina Valencia]

Hello FS'users,

I'm trying to do an histogram of cortical thickness for 2 cases in matlab,
but the problem is that I have Installed matlab in a computer (windows) and
FS in another one (ubuntu)
Can I configure something to use the FS commands in matlab in order to
obtain some graphs?
And also, where can I find the cortical thickness in each regions (Brodmann
areas, gyrus or sulci) of the brain in order to compare a normal patient
with a patiwnt who has a cortical dysplasia ?

Thanks a lot for your help,

Carolina
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Re: [Freesurfer] Thickness measurements stats

[Bruce Fischl]

I can't say whether it's the best way, but it should be relatively unbiased

On Tue, 5 Jul 2011, Ignacio Letelier 
wrote:



Then, and finally is this method the best way to determine whether exist any
cortical thickness anomaly, I mean, to use a normal  control acquisition as
comparisson?

Thanks in advance
Ignacio.
2011/7/5 Bruce Fischl 
  Hi Ignacio,

  the thickness is definitely affected by factors such as sequence
  type, field strength and acquisition parameters (not to mention
  age, maybe gender, etc...) so I think you need to acquire your
  own control(s) on a matched acquisition.

  cheers.
  Bruce


 On Tue, 5 Jul 2011, Ignacio Letelier wrote:

  Hi Bruce,

  Otherwise, is it possible to simply compare my T1 brain
  acquisition  (with
  dysplasia suspicion) with a 'normal template' (which maybe
  bert) to
  determine whether there exist any  anomaly in the cortical
  thickness ? and,
  is it possible to visualize these potential differences
  using a color map
  scaling?

  Thanks in advance-

  Best regards.

  Ignacio.

  2011/7/3 Bruce Fischl 
       Hi Ignacio,

       I see. You could do that, but I don't think it will
  show what
       you want. There is a big geometric component to the
  thickness -
       crowns are thick and fund are thin - so at the very
  least you
       might try including mean curvature as a covariate.


  cheers
  Bruce

  On Fri, 1 Jul 2011, Ignacio Letelier wrote:

       Sorry I didn't realize since you have the same
  domain.

       Ok, Let's say I do know the mean cortical thickness
  value
       of a subject. Then
       is it possible know  what brain areas differ more
  from
       that mean value by
       using a color map visualization (I.e.  for example:
  red =
       higher deviations,
       deep blue = lower deviations)? So this way I can
  determine
       where there may
       exist some kind of dysplasia.

       Best regards.

       2011/7/1 Bruce Fischl 
            can you post this kind of thing so others can
  answer?
       I still
            don't understand though. stdv of what?


       On Fri, 1 Jul 2011, Ignacio Letelier wrote:

            Let's say I want to know if there is a way to
  know
       where
            is the highest stdv in the same subject, using a
       color map
            visualization in qdec or something?

            Best regards.

            2011/7/1 Bruce Fischl
  
                 Hi Ignacio

                 you mean different from the median in that
       subject?
            Easy enough to do in matlab, but we don't have
       anything
            out of the box to do it

                 cheers
                 Bruce

            On Fri, 1 Jul 2011, Ignacio Letelier wrote:

                 Hi forum

                 Is it possible to get statistical maps of 
       cortical
            thickness differences in the same subject? I.e.
  to
       know
            what areas differ most from the median


                 --
                 Ignacio




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[Freesurfer] correct mris_anatomical_stats syntax for lgi

[ZhiLiangLong]

Hi FS experts:
  I have run a group analysis with Local Gyrification Index (LGI) and obtained 
some statistical significant areas.Now I want to extract the information (lgi) 
of each area.Based on the QDec Group Analysis page, the following command is 
ran to examine cortical thickness:
 
 
mris_anatomical_stats -l rh.test.label -t rh.thickness -b -f
subject/stats/rh.test.stats subject rh
 
Is it possible that i can adjust this for lgi ? If so,would i just replace the 
rh.thickness above with rh.pial_lgi ?
 
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Re: [Freesurfer] Thickness measurements stats

[Ignacio Letelier]

Then, and finally is this method the best way to determine whether exist any
cortical thickness anomaly, I mean, to use a normal  control acquisition as
comparisson?

Thanks in advance
Ignacio.
2011/7/5 Bruce Fischl 

> Hi Ignacio,
>
> the thickness is definitely affected by factors such as sequence type,
> field strength and acquisition parameters (not to mention age, maybe gender,
> etc...) so I think you need to acquire your own control(s) on a matched
> acquisition.
>
> cheers.
> Bruce
>
>
>  On Tue, 5 Jul 2011, Ignacio Letelier wrote:
>
>  Hi Bruce,
>>
>> Otherwise, is it possible to simply compare my T1 brain acquisition  (with
>> dysplasia suspicion) with a 'normal template' (which maybe bert) to
>> determine whether there exist any  anomaly in the cortical thickness ?
>> and,
>> is it possible to visualize these potential differences using a color map
>> scaling?
>>
>> Thanks in advance-
>>
>> Best regards.
>>
>> Ignacio.
>>
>> 2011/7/3 Bruce Fischl 
>>  Hi Ignacio,
>>
>>  I see. You could do that, but I don't think it will show what
>>  you want. There is a big geometric component to the thickness -
>>  crowns are thick and fund are thin - so at the very least you
>>  might try including mean curvature as a covariate.
>>
>>
>> cheers
>> Bruce
>>
>> On Fri, 1 Jul 2011, Ignacio Letelier wrote:
>>
>>  Sorry I didn't realize since you have the same domain.
>>
>>  Ok, Let's say I do know the mean cortical thickness value
>>  of a subject. Then
>>  is it possible know  what brain areas differ more from
>>  that mean value by
>>  using a color map visualization (I.e.  for example: red =
>>  higher deviations,
>>  deep blue = lower deviations)? So this way I can determine
>>  where there may
>>  exist some kind of dysplasia.
>>
>>  Best regards.
>>
>>  2011/7/1 Bruce Fischl 
>>   can you post this kind of thing so others can answer?
>>  I still
>>   don't understand though. stdv of what?
>>
>>
>>  On Fri, 1 Jul 2011, Ignacio Letelier wrote:
>>
>>   Let's say I want to know if there is a way to know
>>  where
>>   is the highest stdv in the same subject, using a
>>  color map
>>   visualization in qdec or something?
>>
>>   Best regards.
>>
>>   2011/7/1 Bruce Fischl 
>>Hi Ignacio
>>
>>you mean different from the median in that
>>  subject?
>>   Easy enough to do in matlab, but we don't have
>>  anything
>>   out of the box to do it
>>
>>cheers
>>Bruce
>>
>>   On Fri, 1 Jul 2011, Ignacio Letelier wrote:
>>
>>Hi forum
>>
>>Is it possible to get statistical maps of
>>  cortical
>>   thickness differences in the same subject? I.e. to
>>  know
>>   what areas differ most from the median
>>
>>
>>--
>>Ignacio
>>
>>
>>
>>
>>   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] error using recon-all function

[Ryan Hutten]

Freesurfer experts,

I emailed last week with an error using recon-all. This problem has still
not been resolved. The summary of the problem should be shown below:

Thanks,
Ryan

On Fri, Jul 1, 2011 at 2:06 PM, Ryan Hutten <
ryanhutten2...@u.northwestern.edu> wrote:

>
>
> -- Forwarded message --
> From: Ryan Hutten 
> Date: Thu, Jun 30, 2011 at 1:34 PM
> Subject: Re: [Freesurfer] error using recon-all function
> To: Krish Subramaniam 
>
>
> Krish,
>
> under the $FREESURFER_HOME/bin directory, there is a file named avi2talxfm
>
> I copied the output of the command you sent me.
>
>
> tar -ztvf freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz | grep
> avi2tal
>  -rwxr-xr-x root/root  2087 2011-05-22 08:28 freesurfer/bin/avi2talxfm
>
>
> It looks like the file is there, but something is not working with it. Any
> ideas?
>
> Thanks,
> Ryan
>
>
> On Thu, Jun 30, 2011 at 12:53 PM, Krish Subramaniam <
> kr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Ryan
>>
>> We do bundle avi2talxfm in our distribution. Can you see that in
>> $FREESURFER_HOME/bin ?
>>
>> If you have the original freesurfer download file.. can you do a
>>
>>  tar -ztvf freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0.tar.gz |
>> grep avi2tal
>>
>> and see if it can find in the distribution ?
>>
>> Krish
>>
>>
>> On 06/30/2011 01:35 PM, Bruce Fischl wrote:
>>
>>> I assume you have to install it. Nick or Krish?
>>> On Thu, 30 Jun 2011, Ryan Hutten wrote:
>>>
>>>  Is this something that I can add manually to one of the files? Please
 let me know what steps I can take to correct this problem.

 Thanks,
 Ryan

 On Wed, Jun 29, 2011 at 1:22 PM, Bruce Fischl <
 fis...@nmr.mgh.harvard.edu> wrote:
  Nick: it looks like he's missing this command:


  tail ~/talairach_avi.log
  Reading: /usr/local/freesurfer/average/**
 711-2C_as_mni_average_305.**4dfp.ifh
  Writing: talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt

  start time Wed Jun 29 13:05:58 CDT 2011
  end time Wed Jun 29 13:06:19 CDT 2011

  mpr2mni305 success

  avi2talxfm orig.mgz /usr/local/freesurfer/average/**mni305.cor.mgz
 talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt
 transforms/talairach.auto.xfm
  avi2talxfm: Command not found.


 On Wed, 29 Jun 2011, Ryan Hutten wrote:

  I have attached the talairach_avi.log file.

  Thanks,
  Ryan

  On Wed, Jun 29, 2011 at 1:18 PM, Bruce Fischl <
 fis...@nmr.mgh.harvard.edu> wrote:
   Hi Ryan,

   what is in transforms/talairach_avi.log?

   cheers
   Bruce



  On Wed, 29 Jun 2011, Ryan Hutten wrote:

 > Hi,
 >
 > I am currently trying to use the recon-all function. It works fine on
 an older computer, but my group is attempting to get freesurfer up and
 running on
  a newer computer. The subject
  data is
 > located in a folder called 2645166 as shown in the following command.
 >
 > When I run the command:
 >
 > recon-all -s 2645166 -all
 >
 > I get the following error after the script runs for about a minute:
 >
 > ERROR: avi2talxfm failed, see transforms/talairach_avi.log
 > Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC
 2010 x86_64 x86_64 x86_64 GNU/Linux
 >
 >
 > The output of your bugr script gives:
 > FREESURFER_HOME: /usr/local/freesurfer
 >
 > Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
 >
 > RedHat release: Fedora release 14 (Laughlin)
 >
 > Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64
 >
 >
 > A brief internet search found nothing regarding this avi2talxfm
 function. Any suggestions and/or help would be greatly appreciated.
 >
 > Thanks,
 >
  __**_
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 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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  dispose of the e-mail.








>>
>
>
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Re: [Freesurfer] Thickness measurements stats

[Bruce Fischl]

Hi Ignacio,

the thickness is definitely affected by factors such as sequence type, 
field strength and acquisition parameters (not to mention age, maybe 
gender, etc...) so I think you need to acquire your own control(s) on a 
matched acquisition.


cheers.
Bruce

 On Tue, 5 Jul 2011, Ignacio Letelier wrote:


Hi Bruce,

Otherwise, is it possible to simply compare my T1 brain acquisition  (with
dysplasia suspicion) with a 'normal template' (which maybe bert) to
determine whether there exist any  anomaly in the cortical thickness ? and,
is it possible to visualize these potential differences using a color map
scaling?

Thanks in advance-

Best regards.

Ignacio.

2011/7/3 Bruce Fischl 
  Hi Ignacio,

  I see. You could do that, but I don't think it will show what
  you want. There is a big geometric component to the thickness -
  crowns are thick and fund are thin - so at the very least you
  might try including mean curvature as a covariate.


cheers
Bruce

On Fri, 1 Jul 2011, Ignacio Letelier wrote:

  Sorry I didn't realize since you have the same domain.

  Ok, Let's say I do know the mean cortical thickness value
  of a subject. Then
  is it possible know  what brain areas differ more from
  that mean value by
  using a color map visualization (I.e.  for example: red =
  higher deviations,
  deep blue = lower deviations)? So this way I can determine
  where there may
  exist some kind of dysplasia.

  Best regards.

  2011/7/1 Bruce Fischl 
       can you post this kind of thing so others can answer?
  I still
       don't understand though. stdv of what?


  On Fri, 1 Jul 2011, Ignacio Letelier wrote:

       Let's say I want to know if there is a way to know
  where
       is the highest stdv in the same subject, using a
  color map
       visualization in qdec or something?

       Best regards.

       2011/7/1 Bruce Fischl 
            Hi Ignacio

            you mean different from the median in that
  subject?
       Easy enough to do in matlab, but we don't have
  anything
       out of the box to do it

            cheers
            Bruce

       On Fri, 1 Jul 2011, Ignacio Letelier wrote:

            Hi forum

            Is it possible to get statistical maps of 
  cortical
       thickness differences in the same subject? I.e. to
  know
       what areas differ most from the median


            --
            Ignacio




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  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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Re: [Freesurfer] Fwd: freesurfer recon error

[Pedro Paulo de Magalhães Oliveira Junior]

Have you tried including the flag -cw256 with the recon-all command?


On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` wrote:

> Hi!,
>
> I am new to FreeSurfer and I am having some difficulty with the T1
> reconstruction. My MRI files were Par Rec and converted to nii. I
> successfully converted the nii file to mgz but had errors when running the
> recon -all command (see screen print attached). I have tried re-exporting
> the files in case there was an inital error at this stage but it returned
> the same error. I would appreciate any help with this.
>
> thanks
> Sarah
>
>
>
> ___
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>
>
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> 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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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] weird fieldsign image

[Michelle Umali]

Hi All,
I am running a retinotopy analysis, and when I look at the fieldsign  
image all I see are a bunch of red and blue speckles.

Is this normal?

I am trying to figure out the horizontal and vertical meridians and am  
not sure how to use the fieldsign image to do this. It's for my  
thesis, is there a basic manual on how to define V1/2 boundaries?

Thanks for your help.
Michelle

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[Freesurfer] tracula bvecs problem

[Franz Liem]

Dear Freesurfers.

I am trying to run trac-all on one subject and have a problem with the bvecs 
file at the -prep stage.
After dtifit is started an error massage occurs: Error: bvecs and bvals don't 
have the same number of entries.
I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at the 
-corr stage (-corr alone finishes without error).

My input file is one 4d .nii.gz file (with a total of 33 images, with the first 
being a b0 image).

(I have attached the files from the dmri folder)

The dmri/bvecs file only contains:
0,000
0,000
0,000

The original bvecs contains 3 columns and 33 lines.

The dmri/bvals seems to be ok (1 column and 33 lines).

eddy_correct processes 33 files (dmri/dwi_tmp ... dmri/dwi_tmp0032).

I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although the 
recon was done with 5.0.0, but I guess this not important at this stage, is it?)


***
My Configuration File:

set dtroot = $SUBJECTS_DIR/DTI
set subjlist = (s02x)

set dcmroot = $SUBJECTS_DIR/DTI
set dcmlist = (s02x/dti4d.nii.gz)

set bvalfile = /Users/.../DTI/bvals/bvals
set bvecfile = /Users/.../DTI/bvals/bvecs
set nb0 = 1

set doeddy = 1
set dorotbvecs = 1
set thrbet = 0.3
set doregflt = 1
set doregbbr = 0
***


Thanks,
Franz



bvals
Description: Binary data


bvecs
Description: Binary data


bvecs.norot
Description: Binary data


dwi_orig.mghdti.bvals
Description: Binary data


dwi_orig.mghdti.bvecs
Description: Binary data
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