mris_anatomical_stats on more than one subject at a time?

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mris_flatten error

Elissa Ash

22 Mar 2016 22 Mar '16

8:03 p.m.

Dear experts,

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

Thanks, Elissa

-- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

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Bruce Fischl

22 Mar 22 Mar

8:44 p.m.

Hi Elissa

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

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

...

Dear experts,

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

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

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

Elissa Ash

9:20 p.m.

New subject: mris_anatomical_stats on more than one subject at a time?

Thanks Bruce

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

Thanks, Elissa

On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Elissa

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

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

...
Dear experts,

Is there any way to run the mris_anatomical_stats command on more than

one subject at

...
a time?

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

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bruce Fischl

9:23 p.m.

New subject: mris_anatomical_stats on more than one subject at a time?

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

On Tue, 22 Mar 2016, Elissa Ash wrote:

...

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

Thanks, Elissa

On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Elissa
  not really. What would you want it to do? There are tools for tabulating
  the output of mris_anatomical_stats across subjects, if that's what you
  are trying to do

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

  >
  > Dear experts,
  >
  > Is there any way to run the mris_anatomical_stats command on more than
  one subject at
  > a time?
  >
  > Thanks,
  > Elissa
  > --
  > Elissa Ash, MD, PhD
  > Director, Center for Memory and Attention Disorders
  > Department of Neurology
  > Tel Aviv Sourasky Medical Center
  >
  > 6 Weizmann St.
  > Tel Aviv 64239, Israel
  > 972-3-6973698
  > fax: 972-3-695-0365
  >
  >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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

Elissa Ash

9:26 p.m.

New subject: mris_anatomical_stats on more than one subject at a time?

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

On Tue, Mar 22, 2016 at 6:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

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

On Tue, 22 Mar 2016, Elissa Ash wrote:

...
Thanks Bruce I am calculating the thickness for a given ROI (rh.BA45.label) and

comparing it

...
across subjects and it is tedious to have to type in the command

separately each time

...
(~60 subjects). I was hoping that there was a way to input multiple

subjects at once.

...
That's it.

Thanks, Elissa

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

fischl@nmr.mgh.harvard.edu> wrote:

...
  Hi Elissa

  not really. What would you want it to do? There are tools for
tabulating

...
  the output of mris_anatomical_stats across subjects, if that's
what you

...
  are trying to do

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

  >
  > Dear experts,
  >
  > Is there any way to run the mris_anatomical_stats command on
more than

...
  one subject at
  > a time?
  >
  > Thanks,
  > Elissa
  > --
  > Elissa Ash, MD, PhD
  > Director, Center for Memory and Attention Disorders
  > Department of Neurology
  > Tel Aviv Sourasky Medical Center
  >
  > 6 Weizmann St.
  > Tel Aviv 64239, Israel
  > 972-3-6973698
  > fax: 972-3-695-0365
  >
  >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom
it is

...
addressed. If you believe this e-mail was sent to you in error and the

e-mail

...
contains patient information, please contact the Partners Compliance

HelpLine

...
at http://www.partners.org/complianceline . If the e-mail was sent to you

in error

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

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

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Bruce Fischl

9:28 p.m.

New subject: mris_anatomical_stats on more than one subject at a time?

something like:

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

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

cheers Bruce

On Tue, 22 Mar 2016, Elissa Ash wrote:

...

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

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

  On Tue, 22 Mar
  2016, Elissa Ash wrote:

  > Thanks Bruce
  > I am calculating the thickness for a given ROI (rh.BA45.label) and
  comparing it
  > across subjects and it is tedious to have to type in the command
  separately each time
  > (~60 subjects). I was hoping that there was a way to input multiple
  subjects at once.
  > That's it.
  >
  > Thanks,
  > Elissa
  >
  > On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu> wrote:
  >       Hi Elissa
  >
  >       not really. What would you want it to do? There are tools for
  tabulating
  >       the output of mris_anatomical_stats across subjects, if that's
  what you
  >       are trying to do
  >
  >       cheers
  >       Bruce
  >       On Tue, 22 Mar 2016, Elissa Ash wrote:
  >
  >       >
  >       > Dear experts,
  >       >
  >       > Is there any way to run the mris_anatomical_stats command on
  more than
  >       one subject at
  >       > a time?
  >       >
  >       > Thanks,
  >       > Elissa
  >       > --
  >       > Elissa Ash, MD, PhD
  >       > Director, Center for Memory and Attention Disorders
  >       > Department of Neurology
  >       > Tel Aviv Sourasky Medical Center
  >       >
  >       > 6 Weizmann St.
  >       > Tel Aviv 64239, Israel
  >       > 972-3-6973698
  >       > fax: 972-3-695-0365
  >       >
  >       >
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  > The information in this e-mail is intended only for the person to whom
  it is
  > addressed. If you believe this e-mail was sent to you in error and the
  e-mail
  > contains patient information, please contact the Partners Compliance
  HelpLine
  > at
  > http://www.partners.org/complianceline . If the e-mail was sent to you
  in error
  > but does not contain patient information, please contact the sender and
  > properly
  > dispose of the e-mail.
  >
  >
  >
  >
  > --
  > Elissa Ash, MD, PhD
  > Director, Center for Memory and Attention Disorders
  > Department of Neurology
  > Tel Aviv Sourasky Medical Center
  >
  > 6 Weizmann St.
  > Tel Aviv 64239, Israel
  > 972-3-6973698
  > fax: 972-3-695-0365
  >
  >
  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

Elissa Ash

9:33 p.m.

New subject: mris_anatomical_stats on more than one subject at a time?

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

Elissa

On Tue, Mar 22, 2016 at 6:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

something like:

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

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

cheers Bruce

On Tue, 22 Mar 2016, Elissa Ash wrote:

Thanks! I am a newbie so I think it would take me longer to learn how to

...
write the script then to just do it one at a time! :)

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

  > Thanks Bruce
  > I am calculating the thickness for a given ROI (rh.BA45.label) and
  comparing it
  > across subjects and it is tedious to have to type in the command
  separately each time
  > (~60 subjects). I was hoping that there was a way to input
multiple subjects at once. > That's it. > > Thanks, > Elissa > > On Tue, Mar 22, 2016 at 5:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > Hi Elissa > > not really. What would you want it to do? There are tools for tabulating > the output of mris_anatomical_stats across subjects, if that's what you > are trying to do > > cheers > Bruce > On Tue, 22 Mar 2016, Elissa Ash wrote: > > > > > Dear experts, > > > > Is there any way to run the mris_anatomical_stats command on more than > one subject at > > a time? > > > > Thanks, > > Elissa > > -- > > Elissa Ash, MD, PhD > > Director, Center for Memory and Attention Disorders > > Department of Neurology > > Tel Aviv Sourasky Medical Center > > > > 6 Weizmann St. > > Tel Aviv 64239, Israel > > 972-3-6973698 > > fax: 972-3-695-0365 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > > -- > Elissa Ash, MD, PhD > Director, Center for Memory and Attention Disorders > Department of Neurology > Tel Aviv Sourasky Medical Center > > 6 Weizmann St. > Tel Aviv 64239, Israel > 972-3-6973698 > fax: 972-3-695-0365 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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Bruce Fischl
Elissa Ash