[Freesurfer] Freeview Surface Loading View Center

[Mingjian He]

Hi,

When using Freeview to load a surface file without volume, how does 
Freeview set the initial view center and cursor position? I’ve checked mid 
point of xyz ranges, centroid of vertices, and median. None of these gives me 
the initial SurfaceRAS values when opening the surface with Freeview. 

Thank you! 

Best,
Alex 

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Re: [Freesurfer] aparcstats2table error

[Hoopes, Andrew]

Hi Devika, the python scripts (like aparcstats2table) in 6.0 unfortunately must 
be run with python2. Your error implies that the python in your PATH points to 
python3. You should make sure python points to a python2 version before running 
freesurfer. Sorry for the inconvenience.
Andrew


From:  on behalf of Devika K 

Reply-To: FS Help 
Date: Sunday, January 19, 2020 at 9:09 AM
To: FS Help 
Subject: Re: [Freesurfer] aparcstats2table error


External Email - Use Caution
I tried doing cortical parcellation using Destrieux atlas.  I ran the 
aparcstats2table command from the SUBJECTS_DIR directory containing all of the 
output from recon-all.
But I got an error, PFA. Do I need to run any other commands before running 
aparcstats2table command, I would be grateful if anyone could  help me to 
resolve this issue.

Many thanks in advance.
[Image removed by sender.]
Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu
Amrita Vishwa Vidyapeetham
Coimbatore, India

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Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29

[Bruce Fischl]

can you email us the full command line and screen output?
On Sun, 19 Jan 
2020, Devika K wrote:




External Email - Use Caution

 I tried  by specicying the subjects name, by following  the below command. 


aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas
thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl

But still I got the same error.

On Sun, Jan 19, 2020, 10:30 PM 
wrote:
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  Today's Topics:

     1. RES: Re:  freesurfer container - freeview error
        (marc...@hucff.ufrj.br)
     2. registration of dwi images (Sam W)
     3. Re: registration of dwi images (Yendiki, Anastasia)
     4. Project hippocampus to inflated 3D model? (Mohammad
  Rashid)
     5. Re: aparcstats2table error (Devika K)
     6. Re: Project hippocampus to inflated 3D model? (Bruce
  Fischl)
     7. Re: aparcstats2table error (Bruce Fischl)


  --

  Message: 1
  Date: Sat, 18 Jan 2020 15:05:15 -0300
  From: 
  Subject: [Freesurfer] RES: Re:  freesurfer container - freeview
  error
  To: Freesurfer support list 
  Message-ID: <5e2383f1.1c69fb81.cfdf5.5...@mx.google.com>
  Content-Type: text/plain; charset="us-ascii"

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  Message: 2
  Date: Sun, 19 Jan 2020 00:52:10 +0100
  From: Sam W 
  Subject: [Freesurfer] registration of dwi images
  To: Freesurfer support list 
  Message-ID:
         
  
  Content-Type: text/plain; charset="utf-8"

          External Email - Use Caution       

  Hello!
  I have run eddy on all my dwi images and then run bbregister
  using the
  first b0 image as the source image.
  The b0 image is now well aligned with the anatomical image but
  how can I
  apply the same transformation to all other dwi images in my
  dataset?

  After eddy correction I extracted the first b0 image
  (nodif.nii.gz) and run
  the bbregister command:
  bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg
  /home/samm/nodiffb2orig.dat --dti --init-fsl --o
  /home/samm/registered_b0.nii.gz

  Thanks!
  Sam
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  Message: 3
  Date: Sun, 19 Jan 2020 00:43:00 +
  From: "Yendiki, Anastasia" 
  Subject: Re: [Freesurfer] registration of dwi images
  To: Freesurfer support list 
  Message-ID:
         


  Content-Type: text/plain; charset="us-ascii"

  Hi Sam - You can use mri_vol2vol to apply the transformation
  that was saved in the registration file nodiffb2orif.dat to any
  volume that's in the same space as nodif.nii.gz.

  a.y
  
  From: freesurfer-boun...@nmr.mgh.harvard.edu
   on behalf of Sam W
  
  Sent: Saturday, January 18, 2020 6:52:10 PM
  To: Freesurfer support list 
  Subject: [Freesurfer] registration of dwi images


          External Email - Use Caution

  Hello!
  I have run eddy on all my dwi images and then run bbregister
  using the first b0 image as the source image.
  The b0 image is now well aligned with the anatomical image but
  how can I apply the same transformation to all other dwi images
  in my dataset?

  After eddy correction I extracted the first b0 image
  (nodif.nii.gz) and run the bbregister command:
  bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg
  /home/samm/nodiffb2orig.dat --dti --init-fsl --o
  /home/samm/registered_b0.nii.gz

  Thanks!
  Sam
  -- next part --
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URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/6
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  Messag

Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29

[Devika K]

External Email - Use Caution

 I tried  by specicying the subjects name, by following  the below command.


aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas
thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl

But still I got the same error.

On Sun, Jan 19, 2020, 10:30 PM 
wrote:

> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>1. RES: Re:  freesurfer container - freeview error
>   (marc...@hucff.ufrj.br)
>2. registration of dwi images (Sam W)
>3. Re: registration of dwi images (Yendiki, Anastasia)
>4. Project hippocampus to inflated 3D model? (Mohammad Rashid)
>5. Re: aparcstats2table error (Devika K)
>6. Re: Project hippocampus to inflated 3D model? (Bruce Fischl)
>7. Re: aparcstats2table error (Bruce Fischl)
>
>
> --
>
> Message: 1
> Date: Sat, 18 Jan 2020 15:05:15 -0300
> From: 
> Subject: [Freesurfer] RES: Re:  freesurfer container - freeview error
> To: Freesurfer support list 
> Message-ID: <5e2383f1.1c69fb81.cfdf5.5...@mx.google.com>
> Content-Type: text/plain; charset="us-ascii"
>
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200118/ff64f6b3/attachment-0001.html
>
> --
>
> Message: 2
> Date: Sun, 19 Jan 2020 00:52:10 +0100
> From: Sam W 
> Subject: [Freesurfer] registration of dwi images
> To: Freesurfer support list 
> Message-ID:
> <
> cafyehvvrxw-p0vwvqeia_fmnurmavmsb9wts3zdhlgfvzhc...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Hello!
> I have run eddy on all my dwi images and then run bbregister using the
> first b0 image as the source image.
> The b0 image is now well aligned with the anatomical image but how can I
> apply the same transformation to all other dwi images in my dataset?
>
> After eddy correction I extracted the first b0 image (nodif.nii.gz) and run
> the bbregister command:
> bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg
> /home/samm/nodiffb2orig.dat --dti --init-fsl --o
> /home/samm/registered_b0.nii.gz
>
> Thanks!
> Sam
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/ca86b4c2/attachment-0001.html
>
> --
>
> Message: 3
> Date: Sun, 19 Jan 2020 00:43:00 +
> From: "Yendiki, Anastasia" 
> Subject: Re: [Freesurfer] registration of dwi images
> To: Freesurfer support list 
> Message-ID:
> <
> bl0pr04mb483326316f9b4242f271210f8a...@bl0pr04mb4833.namprd04.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Sam - You can use mri_vol2vol to apply the transformation that was
> saved in the registration file nodiffb2orif.dat to any volume that's in the
> same space as nodif.nii.gz.
>
> a.y
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sam W <
> samf...@gmail.com>
> Sent: Saturday, January 18, 2020 6:52:10 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] registration of dwi images
>
>
> External Email - Use Caution
>
> Hello!
> I have run eddy on all my dwi images and then run bbregister using the
> first b0 image as the source image.
> The b0 image is now well aligned with the anatomical image but how can I
> apply the same transformation to all other dwi images in my dataset?
>
> After eddy correction I extracted the first b0 image (nodif.nii.gz) and
> run the bbregister command:
> bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg
> /home/samm/nodiffb2orig.dat --dti --init-fsl --o
> /home/samm/registered_b0.nii.gz
>
> Thanks!
> Sam
> -- next part --
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200

Re: [Freesurfer] aparcstats2table error

[Bruce Fischl]

Hi Devika

In the future can you include the text of the command and the output in 
your email instead of a screenshot? That will make our job easier.


Try specifying which subjects you want processed explicitly with 
--subjects


cheers
Bruce

On Sun, 19 Jan 
2020, Devika K wrote:




External Email - Use Caution

I tried doing cortical parcellation using Destrieux atlas.  I ran the
aparcstats2table command from the SUBJECTS_DIR directory containing all of
the output from recon-all.
But I got an error, PFA. Do I need to run any other commands before running
aparcstats2table command, I would be grateful if anyone could  help me to
resolve this issue.

Many thanks in advance.[cleardot.gif]
Regards
Devika K
Research Scholar, Dept of EEE
e: k_dev...@cb.students.amrita.edu
Amrita Vishwa Vidyapeetham
Coimbatore, India


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Re: [Freesurfer] Project hippocampus to inflated 3D model?

[Bruce Fischl]

Hi Mohammad

you can use mri_tessellate or mri_mc to build a mesh model of the 
hippocampus from the aseg if you want, then use mris_inflate on it. You 
will lose internal structure though.


cheers
Bruce
On Sun, 19 Jan 2020, Mohammad Rashid 
wrote:




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Hello,

I have had success projecting regions such as the entorhinal region to an
inflated 3D model. But I can't seem to do the same for hippocampi. I
wouldn't need any hippocampal subfields, just projecting the hippocampus as
a whole would be useful. Is there perhaps a particular file used for this
that I am missing?

Any help is appreciated,
Mohammad Rashid

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