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I am using freesurfer 5.3.0 (unfortunately this is the version I have to
use) and I am encountering an error in the process. I have attached the
recon-all.log file. Any pointers to identify the error would be very
helpful,
Thank you,
Michele
Tue Oct 6
gt; My guess is it is a problem with the install of the MNI tools. Does it run
> all the way through on other subjects? What happens when you run this
> command?
>
> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
>
>
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Hello all,
I am trying to run Tracula for one of my subjects and after creating the
configuration file I run trac-all -prep -c /path/to/config/file
but I am getting this error:
FSLDIR: Undefined variable.
I have run the SetUpFreeSurfer.sh script and ec
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solved it, turns out symlinks don't like relative paths (which I was using
in the config file for tracula), changing those to absolute paths tracula
finished with no errors
On Fri, 6 Nov 2020 at 11:38, Michele Valotti
wrote:
> Hi all,
>
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Dear Freesurfer Team,
I am trying to run recon-all on a test scan, but I am getting this error:
Error opening ./tmp.mri_nu_correct.mni.6973/nu1.mnc
mincRead(): error reading volume from file
./tmp.mri_nu_correct.mni.6973/nu1.mnc
(logs attached)
I jus
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Hi all,
I am running a test of long FS on some subjects to see if I can improve the
segmentation accuracy compared to cross FS. The aparc+aseg.mgz output of
long FS, however, is not aligned with the original timepoint structural
scan, but rather to the
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Hi all,
I am running long FreeSurfer and after successfully testing it on my local
machine I tried to run it on a server (which should however have the same
FreeSurfer version and setup), but I am getting this error
mri_convert ./tmp.mri_nu_correct.mni
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attached is the log for the run, the version of mri_convert is the same
version on my local machine (where the command runs) and in the cloud
instance
On Fri, 5 Feb 2021 at 18:02, Michele Valotti
wrote:
> Hi all,
> I am running long FreeSurf
t;
> It’s possible there’s another install of MNI that’s interfering with the
> freesurfer one.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
lt environment?
>
>
>
> MNI_DIR
>
> MINC_BIN_DIR
>
> MINC_LIB_DIR
>
>
>
> It’s possible there’s another install of MNI that’s interfering with the
> freesurfer one.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu &
t;
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Thursday, February 11, 2021 at 11:02 AM
> *To: *Freesurfer support list
> *Subject: *Re: [Frees
can figure it out for sure.
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Michele Valotti <
> michele.valo...@gmail.com>
> *Date: *Thursday, February 11, 2021 at 12:07 PM
> *
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Hi all,
I was wondering if anyone had a chance to look at the log to shed some
light on this mystery error, or if more info or a different log are needed.
Thank you,
Michele
On Fri, 12 Feb 2021 at 10:05, Michele Valotti
wrote:
> Hi Andrew,
>
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Dear Freesurfer experts,
Should I expect Freesurfer 7 to significantly improve segmentation of the
Temporal Lobe when compared to Freesurfer 6? I often see sub-optimal
segmentation of this region in Freesurfer 6 and I am wondering if an
upgrade to 7 w
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