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Hi Anastasia,
Nope, I don't actually get any output and/or log file.
Regards,
Heidi Foo
On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia
wrote:
> Hi Heidi - The config file that you sent looked fine to me. What is the
> trac-all command line th
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Hello Anastasia,
Please find attached the trac-all log.
Thanks for your help,
Vinny
On Wed, Sep 19, 2018 at 8:44 PM Yendiki, Anastasia
wrote:
> Hi Vinny - This error is during the diffusion-to-structural registration.
> Can you send the entire log
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Dear Freesurfer experts,
I need to transform a bunch of MNI coordinates of fiber tracts to native space.
I have already done the follow steps:
(1)intra-subject registration (register the individual's low-b diffusion to
T1images using bbregister )
Hi Vinny - This error is during the diffusion-to-structural registration. Can
you send the entire log file (scripts/trac-all.log)?
Best,
a.y
On Sep 19, 2018 8:39 PM, Vinny K wrote:
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Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I g
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Hi,
I am using 'freesurfer-linux-centos6_x86_64-dev-20180902-a7bb8b4.
I get the following error when running the command: trac-all -prep -c
dmrirc.
Any help would be greatly appreciated.
Thanks,
Vinny
/home/Vinit/freesurfer/subjects/diffusion/Subj
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Dear Bram,
According recon-all help "If a subject has enlarged ventricles due to
atrophy, include the -bigventricles
flag with the -autorecon2 stage in order to prevent surfaces extending into
the ventricle regions. The flag directly affects the binary
Do the raw images look like that too?
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Matthew Grecsek mailto:m...@grecsek.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, September 19, 2018 at 4:07 PM
To: Freesurfer support list
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Yes, a part of the brain appears missing. See attached screenshot.
I did not use a configuration file, I simply accepted all defaults and
kicked off the process with -s and -i flags.
Re: [Freesurfer] Fr
It is hard to say. While a p-value changing from .02 to .2 seems like a
lot, it does not really take much change in the values. I would look at
the CVs for the individual subjects both in cross and long and see which
ones are causing the change. My experience is that long is much better
than cr
You'll still need to have WM at about 110 or else FS will fail.
On 09/19/2018 02:48 PM, Raquib Ridwan wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I would like to know if intensity normalization(not bias field
> correction) so that white-matter is ~110 and gm is ~60 is necessary
>
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Hi,
I would like to know if intensity normalization(not bias field correction)
so that white-matter is ~110 and gm is ~60 is necessary for freesurfer
segmentation. Will intensity normalization using other methods still work
for freesurfer segmentation?
>
>> Thanks a lot for your support,
>>
>> Yacila
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>> Url
s I get when I try to
> follow the examples of recon-all
>
> Thanks a lot for your support,
>
> Yacila
> -- next part --
> A non-text attachment was scrubbed...
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> Desc: F
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Hi,
I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
version of FreeSurfer.
I used cross-sectional pipeline to identify ROIs (from Desikan atlas) with
significant difference in cortical volume (CV) between controls and *patients
(s
Hi Matt – It looks like some sort of registration issue. When you display the
FA map (dmri/dtifit_FA) and structural segmentation in diffusion space
(label/diff/aparc+aseg), do they look fine? Is there any part of the brain that
is cut off from any of the images? Also, can you attach your config
Not sure what is going on there. Is that really the only thing that gets
printed out? Run recon-all with -debug as the first option. Capture and
send us the terminal output (ie, the stuff that gets printed to the
screen). Also, please make sure to include previous correspondence in
your email s
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Dear Freesurfer experts,
Please find in the attachment a file with the errors I get when I try to follow
the examples of recon-all
Thanks a lot for your support,
Yacila{\rtf1\ansi\ansicpg1252\cocoartf1561\cocoasubrtf600
{\fonttbl\f0\fnil\fcharset0
Hi Yacila
can you send us the full command line and screen output of whatever you
ran?
thanks
Bruce
On Wed, 19 Sep 2018, Yacila Isabela Deza Araujo wrote:
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Hello,
I just started with Freesurfer and got the following error during the call of
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Dear Freesurfer experts,
I need to transform a bunch of MNI coordinates of fiber tracts to native space.
I have already registered my subjects to cvs_avg35_inMNI152 using
mri_cvs_register. How can I transform the MNI coordinates back into the native
Yes - if you've used the -bigventricles flag, you should always include it with
the recon-all command.
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Matthieu Vanhoutte
Sent: Tuesday, September 18, 2018 12:45:23 PM
To: Freesurfer support list
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Hello,
I just started with Freesurfer and got the following error during the call of
the command recon-all
If: missing file name
I should say that other commands work well. I looked for the error and it seems
that it is a change in the script. I ins
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Job description:
Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most
comprehensive birth cohort study over the world. The GUSTO mothers were
recruited during pregnancy between 2009 and 2010. We have followed the
GUSTO family since then
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Job description:
Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most
comprehensive birth cohort study over the world. The GUSTO mothers were
recruited during pregnancy between 2009 and 2010. We have followed the
GUSTO family since then
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