Sorry, the disk that held that patch failed and we did not have a backup so not everything was restored. I just put this file there:

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_aver...

Copy it to $FREESURFER_HOME/bin. Let me know how it goes

On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

External Email - Use Caution

Thanks Bruce. The following is the command.

make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects subject1 subject2 subject3

And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

But I dont know how to apply the patch. Can you give some information about this?

Emanuel

On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Emanuel

you need to send us the full command you ran and output of it if you want us to be able to help you

cheers Bruce On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

    External Email - Use Caution

Hello!, I am getting the following error using the command make_average_subject

mri/norm.mgz: could not load norm volume from (null)

I have found this page with a path for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

But I dont know how to apply the path. Can you give some information about this?

Thanks!

Emanuel

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Hi Emanuel,

can you include the full command line and output?

cheers Bruce On Wed, 12 Dec 2018, Emanuel Alvaredo wrote:

External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface  file with the new one but  I have the same message error. ASeg Vox2RAS: ----------- -1.00000   0.00000   0.00000   128.00000;  0.00000   0.00000   1.00000  -128.00000;  0.00000  -1.00000   0.00000   128.00000;  0.00000   0.00000   0.00000   1.00000; mghRead(mri/norm.mgz, -1): could not open file

---

Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Thanks

Emanuel

On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: Sorry, the disk that held that patch failed and we did not have a backup so not everything was restored. I just put this file there:

  https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface

  Copy it to $FREESURFER_HOME/bin. Let me know how it goes


  On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

          External Email - Use Caution        

  Thanks Bruce. The following is the command.

make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects  subject1  subject2 subject3

And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

But I dont know how to apply the patch. Can you give some information about this?

Emanuel

On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Emanuel

  you need to send us the full command you ran and output of it if you want
  us to be able to help you

  cheers
  Bruce
  On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

  >
  >         External Email - Use Caution        
  >
  > Hello!, I am getting the following error using the
  command make_average_subject 
  >
  > mri/norm.mgz: could not load norm volume from (null)
  >
  > I have found this page with a path for de issue
  >
  >
  https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
  >
  > But I dont know how to apply the path. Can you give some information about
  this?
  >
  > Thanks!
  >
  >
  >
  > Emanuel
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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can you include the full terminal output?

On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:

External Email - Use Caution

Hello Bruce, thanks for your anwer. Sure. The command is

make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon Baez_Recon Bonilla_Recon

The output is in the attached file

Thanks!

Emanuel

On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Emanuel,

can you include the full command line and output?

cheers Bruce On Wed, 12 Dec 2018, Emanuel Alvaredo wrote:

    External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface file with the new one but I have the same message error. ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file

---

Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Thanks

Emanuel

On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: Sorry, the disk that held that patch failed and we did not have a backup so not everything was restored. I just put this file there:

  https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface

  Copy it to $FREESURFER_HOME/bin. Let me know how it goes


  On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

          External Email - Use Caution

  Thanks Bruce. The following is the command.

make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects subject1 subject2 subject3

And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

But I dont know how to apply the patch. Can you give some information about this?

Emanuel

On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Emanuel

  you need to send us the full command you ran and output of it if you want
  us to be able to help you

  cheers
  Bruce
  On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

  >
  >         External Email - Use Caution
  >
  > Hello!, I am getting the following error using the
  command make_average_subject
  >
  > mri/norm.mgz: could not load norm volume from (null)
  >
  > I have found this page with a path for de issue
  >
  >
  https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
  >
  > But I dont know how to apply the path. Can you give some information about
  this?
  >
  > Thanks!
  >
  >
  >
  > Emanuel
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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External Email - Use Caution

Hello Bruce, Greve and Emanuel,

I have an identical problem. Have you found a solution to this issue? I'm attaching my recon-all.log, as well, in case you need it.

Thank you! Marta

On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo ealvaredo@gmail.com wrote:

    External Email - Use Caution

Thanks Greve. The output is attached now.

Emanuel

On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

...

can you include the full terminal output?

On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:

    External Email - Use Caution

Hello Bruce, thanks for your anwer. Sure. The command is

*make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon Baez_Recon Bonilla_Recon*

The output is in the attached file

Thanks!

Emanuel

On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Emanuel,

can you include the full command line and output?

cheers Bruce On Wed, 12 Dec 2018, Emanuel Alvaredo wrote:

...

    External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface

file with the new one but I

...

have the same message error. ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file

---

Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2

17:16:02 UTC 2018 x86_64 x86_64

...

x86_64 GNU/Linux

Thanks

Emanuel

On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <

DGREVE@mgh.harvard.edu> wrote:

...

  Sorry, the disk that held that patch failed and we did not have

a backup so not

...

  everything was restored. I just put this file there:

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_aver...

...

  Copy it to $FREESURFER_HOME/bin. Let me know how it goes


  On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

          External Email - Use Caution

  Thanks Bruce. The following is the command.

make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects

subject1

...

subject2 subject3

And I made a mistake in may last mail. I use the word path instead of

patch

...

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

...

But I dont know how to apply the patch. Can you give some information

about this?

...

Emanuel

On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl <

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

...

  Hi Emanuel

  you need to send us the full command you ran and output of it if

you want

...

  us to be able to help you

  cheers
  Bruce
  On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

  >
  >         External Email - Use Caution
  >
  > Hello!, I am getting the following error using the
  command make_average_subject
  >
  > mri/norm.mgz: could not load norm volume from (null)
  >
  > I have found this page with a path for de issue
  >
  >

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

...

  >
  > But I dont know how to apply the path. Can you give some

information about

...

  this?
  >
  > Thanks!
  >
  >
  >
  > Emanuel
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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External Email - Use Caution

Hello Bruce, Doug and Emanuel,

I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded the development version and tried that, but neither procedures fixed the problem.

In the meantime, my father-in-law took a week and fixed the script and now it runs smoothly and finishes without error. The following code segment of the make_average_subject file needed to be fixed:

*Erroneous code segment: * … if($DoSurfaces && $DoVolumes) then set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg) echo $cmd $cmd if($status) exit 1; endif …

*New, corrected code segment: *

if($DoSurfaces && $DoVolumes) then *#set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)* * set cmd = (recon-all -s $average_subject -nuintensitycor -gcareg -canorm -careg -calabel -cortribbon -aparc2aseg)* echo $cmd $cmd if($status) exit 1; endif …

The code that is highlighted with red and a hashtag is what caused the script to exit with errors. The one below that (highlighted with green) is the fixed line of code that finishes without errors.

The patched make_average_subject file is also attached. Feel free to use it.

Best, Marta (and my father-in-law)

On Tue, Jan 22, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

This has been fixed in our development version. I can give you a new script or you can try this: cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI! ln -s orig.mgz norm.mgz Then re-run make_average_subject

On 12/14/18 1:43 PM, Emanuel Alvaredo wrote:

...

    External Email - Use Caution

Thanks Greve. The output is attached now.

Emanuel

On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

 can you include the full terminal output?

On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:

...

        External Email - Use Caution

Hello Bruce, thanks for your anwer. Sure. The command is

*make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
Bartley_Recon Baez_Recon Bonilla_Recon*

The output is in the attached file

Thanks!

Emanuel


On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
wrote:

    Hi Emanuel,

    can you include the full command line and output?

    cheers
    Bruce
    On Wed, 12 Dec 2018,
    Emanuel Alvaredo wrote:

    >
    >         External Email - Use Caution
    >
    > Thanks for your answer Douglas. I replaced the
    make_average_surface  file with the new one but  I
    > have the same message error.
    > ASeg Vox2RAS: -----------
    > -1.00000   0.00000   0.00000   128.00000;
    >  0.00000   0.00000   1.00000  -128.00000;
    >  0.00000  -1.00000   0.00000   128.00000;
    >  0.00000   0.00000   0.00000   1.00000;
    > mghRead(mri/norm.mgz, -1): could not open file
    > -------------------------
    >
    > Labeling Slice
    > relabeling unlikely voxels in interior of white matter
    > mri/norm.mgz: could not load norm volume from (null)
    >
    > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP
    Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64
    > x86_64 GNU/Linux
    >
    > Thanks
    >
    > Emanuel
    >
    >
    > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D.
    <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:
    >       Sorry, the disk that held that patch failed and we
    did not have a backup so not
    >       everything was restored. I just put this file there:
    >
    >

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_aver...

...

...

    >
    >       Copy it to $FREESURFER_HOME/bin. Let me know how it goes
    >
    >
    >       On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
    >
    >               External Email - Use Caution
    >
    >       Thanks Bruce. The following is the command.
    >
    >  make_average_subject --out avgsubjectPRUEBAESTASIEmac
    --subjects  subject1
    > subject2 subject3
    >
    >
    > And I made a mistake in may last mail. I use the word path
    instead of patch
    >
    > I have found this page with a patch for de issue
    >
    >

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

...

...

    >
    > But I dont know how to apply the patch. Can you give some
    information about this?
    >
    >
    > Emanuel
    >
    >
    > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl
    <fischl@nmr.mgh.harvard.edu
    <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
    >       Hi Emanuel
    >
    >       you need to send us the full command you ran and
    output of it if you want
    >       us to be able to help you
    >
    >       cheers
    >       Bruce
    >       On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
    >
    >       >
    >       >         External Email - Use Caution
    >       >
    >       > Hello!, I am getting the following error using the
    >       command make_average_subject
    >       >
    >       > mri/norm.mgz: could not load norm volume from (null)
    >       >
    >       > I have found this page with a path for de issue
    >       >
    >       >
    >

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008....

...

...

    >       >
    >       > But I dont know how to apply the path. Can you give
    some information about
    >       this?
    >       >
    >       > Thanks!
    >       >
    >       >
    >       >
    >       > Emanuel
    >       >
    >  >_______________________________________________
    >       Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >
    >
    >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >
    >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
    >
    >
    >_______________________________________________
    Freesurfer mailing list
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    <mailto:Freesurfer@nmr.mgh.harvard.edu>
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...

...

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
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Freesurfer@nmr.mgh.harvard.edu>

...

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