External Email - Use Caution
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-request@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-owner@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
(marcosm@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: <marcosm@hucff.ufrj.br>
Subject: [Freesurfer] RES: Re: freesurfer container - freeview error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5e2383f1.1c69fb81.cfdf5.57cf@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 <samfmri@gmail.com>
Subject: [Freesurfer] registration of dwi images
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFYEHVvrxw-P0VWvqeiA_fMnUrMavmSb9wts3zDhLGFVZHC2ow@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 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] registration of dwi images
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BL0PR04MB483326316F9B4242F271210F8A330@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Sam W <samfmri@gmail.com>
Sent: Saturday, January 18, 2020 6:52:10 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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/20200119/64bf5201/attachment-0001.html
------------------------------
Message: 4
Date: Sun, 19 Jan 2020 02:35:22 +0000
From: Mohammad Rashid <17mrr6@queensu.ca>
Subject: [Freesurfer] Project hippocampus to inflated 3D model?
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<YTXPR0101MB0990C9B2C52A93B6DEDFAE43E7330@YTXPR0101MB0990.CANPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
External Email - Use Caution
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/c73c92f1/attachment-0001.html
------------------------------
Message: 5
Date: Sun, 19 Jan 2020 19:36:43 +0530
From: Devika K <devikakuttala@gmail.com>
Subject: Re: [Freesurfer] aparcstats2table error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CA+m7eQEvrwLAmdCt6Oo+X9-78OtP1=ouBWqYXim15mn3DrK_xA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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.
Regards
Devika K
Research Scholar, Dept of EEE
e: k_devika@cb.students.amrita.edu
Amrita Vishwa Vidyapeetham
Coimbatore, India
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/fe6bf01e/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2020-01-19 16-06-48.png
Type: image/png
Size: 226736 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/fe6bf01e/attachment-0001.png
------------------------------
Message: 6
Date: Sun, 19 Jan 2020 11:33:22 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Project hippocampus to inflated 3D model?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.2001191132410.4818@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
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:
>
> ????????External Email - Use Caution????????
>
> 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
>
>
------------------------------
Message: 7
Date: Sun, 19 Jan 2020 11:38:26 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aparcstats2table error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.2001191137270.4818@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
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_devika@cb.students.amrita.edu
> Amrita Vishwa Vidyapeetham
> Coimbatore, India
>
>
>
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 191, Issue 29
*******************************************