Can you try tkregisterfv ? The old tk tools are not supported any more.
tkregisterfv uses freeview
On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:
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Hi Isabelle,
It’s been a couple of years since I ran FreeSurfer on a Mac, but I
also have had this issue
If you have an LTA file, you can run
mris_apply_reg --lta lh.white your.lta lh.white.newcoords
On 3/16/2022 4:15 PM, Salar Dini, Elaheh wrote:
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Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate?
Something quite
The log might not be capturing all the standard error output. Run this
and send the output.log
recon-all -debug -s neo289e -segmentation -fill |& tee output.log
On 3/11/2022 3:19 PM, Alexopoulos, Dimitrios wrote:
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Yes it fails every time at the same spot.
Yes, just specify --regheader subjectname instead of a --reg
On 3/11/2022 9:34 AM, Jacoby, John wrote:
Hi all,
Usually when I want to map volume data to the fsaverage surface, I use
mri_vol2surf with a registration that transforms the volume into the
space of the subject's orig.mgz and with
Yes, oftentimes. You should not smooth the LGI. Also, I would strongly
suggest that you use permutation instead of mcz sim. For perm, the fwhm
won't matter.
On 3/10/2022 3:26 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
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I receive FWHM values
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Hi Anastatia – I didn’t know about orientLAS, thank you for that heads up!
I must have missed your recent reply to another user. I will see if I can find
that thread.
Thank you so much!
Kayti Thorn
(she/her)
Database Specialist
Medical University
Passing along this opening at the Carle Illinois Advanced Imaging Center on
behalf of Dr. Sheeba Arnold Anteraper:
https://www.ismrm.org/jobs/j07799.pdf
Anastasia.
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Hi Kayti - About the orientation, you can put your other maps in the same
orientation by running the orientLAS command on them.
About mri_binarize, did you see the response I just sent to another user? I
wonder if it's the same thing.
Anastasia.
From:
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Hi Anastasia,
Thank you so much! This is extremely helpful.
Quick follow up: If my non-dtifit maps are in a different orientation than the
dtifit maps (and other Tracula outputs), will I need to manually reorient my
non-dtifit maps?
On a related
Hi Elizabeth - This was a tricky one. My guess is that there's an error in what
comes right after the mri_binarize command, but the error doesn't get written
into the log file and is only shown on your terminal (I'm going to fix the
error logging aspect of this).
If my guess is right, the
Hi Bryna - I see that the error occurs in the corticospinal tract. Any change
the top or bottom of the brain is truncated in this subject's scan?
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Goeckner, Bryna
Sent: Thursday, March 17,
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Hi Nathan,
Thank you for your email. The problem is I cannot install an older macOS on my
computer at this time. Thank you for letting me know that you also had this
issue. Hopefully, there is a solution.
Have a lovely day,
isabelle
From:
Hi Jim - Thanks for pointing this out. I'll make sure to add $ANTSPATH before
every ants command. In the meantime, if you include $ANTSPATH in your own Unix
path, this should be enough for it to work.
Best,
Anastasia.
From:
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Hi Isabelle,
It’s been a couple of years since I ran FreeSurfer on a Mac, but I also have
had this issue before and it was due to the macOS. I don’t know if anything has
changed recently but if not then the only solution would be to try to install
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Hi, it loads the left inflated surface correctly.
Il giorno mer 16 mar 2022 alle ore 23:25 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:
> What happens if you run
> freeview -f
>
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