measuring cortical thickness using FreeSurfer

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John Drozd

5 Jul 2011 5 Jul '11

12:14 p.m.

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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Pedro Paulo de Magalhães Oliveira Junior

5 Jul 5 Jul

12:34 p.m.

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

On Tue, Jul 5, 2011 at 13:14, John Drozd john.drozd@gmail.com 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.

Bruce Fischl

1:18 p.m.

recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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

John Drozd

4:29 p.m.

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 -0035-0001-00001.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 fischl@nmr.mgh.harvard.eduwrote:

...

recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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 http://publish.uwo.ca/%7Ejdrozd2/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

Bruce Fischl

4:39 p.m.

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 -0035-0001-00001.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 fischl@nmr.mgh.harvard.edu wrote: recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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

5:11 p.m.

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 fischl@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 -0035-0001-00001.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 fischl@nmr.mgh.harvard.edu wrote: recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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<http://publish.uwo.ca/%7Ejdrozd2/index.htm>
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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 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 http://publish.uwo.ca/%7Ejdrozd2/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

Bruce Fischl

5:29 p.m.

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 john.drozd@gmail.com 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 fischl@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 -0035-0001-00001.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 fischl@nmr.mgh.harvard.edu wrote: recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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 Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm

John Drozd

5:36 p.m.

Hi Bruce,

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

Take care, John

2011/7/5 Bruce Fischl fischl@nmr.mgh.harvard.edu

...

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 john.drozd@gmail.com 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 < fischl@nmr.mgh.harvard.edu fischl@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 -0035-0001-00001.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 <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote: recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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/%7Ejdrozd2/index.htm>
http://publish.uwo.ca/~**jdrozd2/index.htm

______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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/%7Ejdrozd2/index.htm 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/%7Ejdrozd2/index.htm 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

Bruce Fischl

6:08 p.m.

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 fischl@nmr.mgh.harvard.edu 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 john.drozd@gmail.com 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 <fischl@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 -0035-0001-00001.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
  <fischl@nmr.mgh.harvard.edu>
  wrote:
       recon-all \
              -i <one slice in the anatomical
  dicom series> \
              -s <subject id that you make up> \
              -sd <directory to put the subject
  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 Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm

John Jan Drozd

6 Jul 6 Jul

12:52 a.m.

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 fischl@nmr.mgh.harvard.edu 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 fischl@nmr.mgh.harvard.edu 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 john.drozd@gmail.com 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 <fischl@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 -0035-0001-00001.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
 <fischl@nmr.mgh.harvard.edu>
 wrote:
      recon-all \
             -i <one slice in the anatomical
 dicom series> \
             -s <subject id that you make up> \
             -sd <directory to put the subject
 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


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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

Pedro Paulo de Magalhães Oliveira Junior

11:48 a.m.

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 john.drozd@gmail.com

...

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 fischl@nmr.mgh.harvard.edu 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 fischl@nmr.mgh.harvard.edu 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 john.drozd@gmail.com 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 fischl@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 -0035-0001-00001.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 fischl@nmr.mgh.harvard.edu wrote: recon-all \ -i <one slice in the anatomical dicom series> \ -s <subject id that you make up> \ -sd <directory to put the subject 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 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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participants (4)

Bruce Fischl
John Drozd
John Jan Drozd
Pedro Paulo de Magalhães Oliveira Junior