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Hi,
Thank you for your email. Sorry about that. Here they are.
Best regards,
Julia
> 27 okt. 2020 kl. 00:17 skrev Hoopes, Andrew :
>
> Hi Julia,
> I think you might have forgotten to attach the logs :)
> Andrew
>
> On 10/25/20, 11:55 AM,
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Hello Freesurfer Developers,
I have some questions about why the first step of PETSurfer needs to create
gtmseg.mgz segmentation.
I noticed that the differences between gtmseg.mgz and aseg.mgz are the
gtmseg.mgz has a higher resolution and also
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I am double checking so the command is trac-all -prep -c /path/to/configuration
file- is that what you meant?
Thanks,
Oshadi
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent:
Hi Julia,
I think you might have forgotten to attach the logs :)
Andrew
On 10/25/20, 11:55 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Julia Lam" wrote:
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Hi Andrew,
Thank you for your reply. Updating freesurfer solved
Hi James,
It sounds like your target filesystem does not support symlinks? The answer to
your question depends on how you are actually copying data, and you should
probably contact your IT about this, but if you’re using rsync to move recons,
you can supply the --copy-links flag to transform
Not sure, cortical thickness maybe?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 11:57 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] please help me
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thank Bruce
I read several articles
What goes after "-c" in the trac-all command should be the configuration file,
not the nifti file.
From: Shanika Jayakody
Sent: Monday, October 26, 2020 5:01 PM
To: Yendiki, Anastasia
Subject: Fw: Tracula error: run list is longer than subject list
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Hi Anastasia
Thanks for your reply.
That file was a Dicom but it was named as "IM_0017". Anyways I tried with the
extension (renamed the file too as IM_007.dcm)
Just to see if there is a different outcome, I ran trac-all on another subject
too but
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Dear Freesurfer team,
I have been trying to extract local gyrification index in a dataset according
to a label which I have created.
1) First of all, I extracted lGI as per DKT areas, which one is lGI value in
the ?h.pial_lgi.stats file (derived on
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Hello,
Sorry for the rapid follow up email, I just noticed I left some personal
contact information on the previous email.
Could you please remove my signature from the archives?
Thank you so much.
Sincerely,
James Park
From:
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Hello Antonin,
I’ve found a few posts that seem to indicate you can upgrade as well as
downgrade the kernel (and its dependent packages) by editing the
/etc/apt/sources.list to point to the Ubuntu distribution you want (and then
running update,
Glad to hear; thanks for sharing! It’s nice to see success stories here and
there among all the questions
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: AmirHussein Abdolalizadeh
Date: Sunday, October 25, 2020 at 06:33
Hi Cat - The FA/MD/RD/AD at a specific voxel comes from first fitting a tensor
to the intensity values of all the DWIs at that voxel and then finding the
eigenvalues of the tensor at that voxel. The tracts work like ROIs - the
FA/MD/RD/AD values are averaged over all the voxels in a tract.
Hi Zhen - We do not have a date for the next FreeSurfer release yet. The code
for the infant stream has been merged into the main TRACULA code base, but
there is some work still to be done to finalize the new atlas that we've been
working on. In the meantime, you can try running the infant T1
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Dear experts,
I use to have a perfectly working freesurfer installation on my Ubuntu
18.04 LTS machine, until that doomsday where I installed updates as
recommended by ubuntu itself.
Now, each time I run freeview, I get the following error:
Aborted
Hi Ileana - You can set the "pathlist" to include a specific set of pathways.
In the example config file the pathlist includes all 18 pathways, but you can
change it, e.g., to only include the rh ones:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
That said, TRACULA doesn't use the
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Hi Anastasia
Thanks again for helping with troubleshooting the error- I was wondering if you
have any suggestions for me to try.
I have also tried running TRACULA on freesurfer tutorial data but get the same
error
Best regards,
Oshadi
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From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Monday, October 19, 2020 8:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error: run list is longer
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Hi Anastasia,
Thank you so much for your reply.
I omitted a very important information. I am working with left hemisphere
stroke data. On a visual check I see that recon all worked well on all the
participants (big and small lesions). Although trac
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Hi,
I am using FS 7.1.0. After running the surface thickness GLM analysis
I get one cluster after correction for multiple comparison showing a
significant group difference. I want to make a plot illustrating this
group difference. However, when using
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Sorry I had to re-posted this since since it quickly moved down the
list without an answer
Julian Macoveanu Thu, 22 Oct 2020 00:59:50 -0700
Hi,
I am using FS 7.1.0. After running the surface thickness GLM analysis
I get one cluster after correction
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