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Thanks Bruce.
I had to increase the angular search range in the affine part to get it to work.
Cheers,
Chris.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bruce Fischl
Sent: Monday, 17 September 2018 11:49 PM
To: Freesurfer support li
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Hello Freesurfer developers and subscribers,
I'm attempting to run brain segmentation with low resolution mri(thickness
~= 7mm) for EEG analysis. I know that this is very low resolution to get
good quality results. However, I think the low quality resu
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Hi Anastasia,
It seems like I do. Could the problem be the config.txt?
Thanks!
Best Regards,
Heidi Foo
On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:
> Hi Heidi – Do you have write permission to create the ou
Hi Kambiz
sounds like something is wrong with the nifti file. Have you tried
running mri_convert directly on the dicom files?
cheers
Bruce
On Mon, 17 Sep 2018, Kambiz
Tavabi wrote:
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Greetings,
I am having trouble converting flash volumes (nii.g
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Greetings,
I am having trouble converting flash volumes (nii.gz) to mgz type using
mri_convert. I used dcm2nii to unpack original DICOM files and subsequently
the command mri_convert flash5.nii.gz flash5.mgz fails with...
niiRead(): bad number of dimens
Hi Rebecca
if you upload a subject we will take a look. Can you also send an image of
what you think the problem area is? You can also try the hippocampal
subfield code as it may improve things
cheers
Bruce
On Mon, 17 Sep 2018, Rebecca
Ray wrote:
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I am working on MRIs with a single time point.
FreeSurfer appears to over estimate the hippocampus in 99% of the cases. I
have attempted to correct the segmentation but after running autorecon2 and
autorecon3 it did not make the changes that I made.
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Hi Freesurfer devs,
Just a simple question, it´s possible make the thalamic nuclei segmentation
using as input a simple T2 image as additional scan or by contrary, is
always required use as input a more specific scan such as the FGATIR or a
DBS scan.
Did you look at the results of the registration to make sure that they
are ok? But you probably don't need to run the registration anyway since
the surfaces are in the T1.mgz space anyway. How are you verifying that
the efield is properly aligned to the T1.mgz? Is it also 1mm^3 and
256^3? Doe
Hi Heidi – Do you have write permission to create the output directory
/data_int/heidi/forHeidi/Preprocessed?
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Heidi Emmanuel Foo
mailto:heidifo...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.ha
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Hi Freesurfer Experts,
I was wondering if you have had time to look at my data to correct my midline
problems? Many of my subjects have this problem.
Best regards,
Maxime
De : Maxime Perron
Envoyé : 13 septe
Hi Chris
you need to give us more information. What commands did you run? What was
their output? Also, if you can send images of what you think is incorrect
that might also be helpful
cheers
Bruce
On Mon, 17 Sep 2018, Chris Adamson wrote:
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Frees
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Dear Prof. Fischl,
Sorry for the lack of clarity. I used bbregister to generate a registration.dat
file. I used simnibs to calculate the Efield distribution and this has the
option to convert the Efield mesh files to .nii files. So I registered the h
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