Re: [Freesurfer] measuring cortical thickness using FreeSurfer

[Pedro Paulo de Magalhães Oliveira Junior]

I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut
flag

I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that
took only 10% more time than one recon-all alone.

2011/7/6 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
> >> 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 Ontari

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] 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] 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
>   
> 
> 
> 
> ___
> 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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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] 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] 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
contains patient information, please contact the Partners Compliance
HelpLine at
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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] 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
>>
>>
>>
>>
> ___
> 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
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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] 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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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] 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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