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Yes, I set the FreeSurfer home environment and added the license file to that
folder. It is Word readable.
Sarah
> On Nov 20, 2018, at 12:03 PM, Greve, Douglas N.,Ph.D.
> wrote:
>
> did you put it in $FREESURFER_HOME/.license ? Is it
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Hello,
Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum?
Thank you so much in advance for your help!
Best,
Da-yea
--
Disclaimer:
The materials in this
On 11/20/18 1:37 PM, Song, Da-Yea wrote:
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Hello,
I had a question regarding the aseg.stats and was hoping to get some help.
1. How is the TotalGray calculated? On the wiki page it mentioned that it
is the sum of lhCortex + rhCortex + SubCortGray +
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Hello Freesurfers,
Can anyone help with a licensing issue I have? I downloaded Freesurfer the
other day with a brand new license and got the following message: “ERROR:
Invalid FreeSurfer license key was found in license file”. I tried getting a
new
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Hello Sarah,
If you can bring up a terminal with your freesurfer environment set, then
please try the following commands, i.e.,
$ cd $FREESURFER_HOME
$ cat $FS_LICENSE
output deleted
Without posting the contents of your license, I think the
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Thank you for pointing that out! I took another look and was able to get the
following;
TotalGray (from the aseg.stats) = 751765.612392
298534.487540 (lhCortex) + 287682.124852 (rhCortex) + 58860.00
(SubCortGray) + 52358.1
did you put it in $FREESURFER_HOME/.license ? Is it world-readable?
On 11/20/18 2:38 PM, Sarah Haigh wrote:
> External Email - Use Caution
>
> Hello Freesurfers,
>
> Can anyone help with a licensing issue I have? I downloaded Freesurfer the
> other day with a brand new license and got
No, it does not.
On 11/20/18 3:54 PM, Song, Da-Yea wrote:
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Hello,
Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum?
Thank you so much in advance for your help!
Best,
Da-yea
Disclaimer:
The
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Dear Freesurfer experts,
I would like to run surface based paired t test of PET data on surface. For
every subject I have visit pre treatment and post treatment. I tried to follow
the instructions here
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Dear FreeSurfer Developers,
I have the most recent version of FreeSurfer installed on a MacOS Mojave
(10.14) and as I was running recon-all, I received the following error
message:
"Assertion failed at line 742 in file templates/CachedArray.cc
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Hi Sarah,
I would just move that file aside (rename it to something that is not
license.txt) and follow the instructions on the wiki to generate another
license.txt file. Then you could check it again with the previous
commands.
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Hi FS experts and users
I found two middle frontal cortex in thickness, with different prefix. So what
is the difference?
Another question: Can I get the thickness of hippocampus and amygdala?
Thanks.
Rujing
2018-11-21
charujing123
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Hi,
I ran the code and the license appeared, but no email address or numbers. These
were the first few lines:
FreeSurfer Software License Agreement ("Agreement")
Version 1.0 (February 2011)
Is this wrong? The rwx settings look
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Thank you! This seemed to work. I got my email address and the numbers this
time in the license. Not sure what happened there. Good check.
Sarah
On Nov 20, 2018, at 3:46 PM, fsbuild
mailto:fsbu...@contbay.com>> wrote:
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Thanks, Douglas!
I found subcort.mask.mgz there, that should work (subcortical mask in MNI
space)!
Best,
Chao-Gan
On Wed, Nov 21, 2018 at 12:45 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> The masking is not done as part of the
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Hi Douglas,
Thanks for the response. Yes, I confirm that the file
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
view it in freeview. Any other possible errors?
Also, would you mind elaborating how to use permutation to
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Hi
The following code worked.
for asubject in /home/vivek/Downloads/freesurfer/subjects/*.nii; do
recon-all -s ${asubject%.nii} -i $asubject -all -qcache; done
Thank you.
On Tue, Nov 20, 2018 at 12:19 PM Vivek Sharma
wrote:
> I have a folder, lets
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Hi, what is difference between 'lh_G_Ins_lg_cent_ins_volume' and
'lh_G_insular_short_volume'. Are these both insula?
Thanks.
Rujing
2018-11-21
charujing123 ___
Freesurfer mailing list
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Thanks Douglas, I've attached here the output from mri_glmfit-sim
--glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces
--debug
Could you clarify how to use permutation to correct for MC for LGI? (as
in what to enter for command
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Hello Freesurfer Developers,
I have a general question about how to analyse a certain combination of data. I
have an independent variable that contains voxel-wise data and I have a
dependent variable that contains vertex-wise cortical thickness
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Dear Douglas,
When doing --3spaces, is there a default subcortical mask in MNI space
provided by freesurfer? Where is it stored?
Thanks,
Chao-Gan
On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
>
>
> On
in csh it would be something like
setenv SUBJECTS_DIR
foreach fname ($dir/*.nii)
set fonly=${f:t}
set fnoext=${f:r}
recon-all -i $fname -s $fnoext -all
end
On Tue, 20 Nov 2018, Vivek Sharma wrote:
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I have a folder, lets name
oh, that was from your example. -i should be the full path to
the input volume *or* one file in the correct dicom series. -s
is something you choose to uniquely identify that subject's recon-all
outputs
cheers
Bruce
On Tue, 20 Nov 2018, Vivek Sharma wrote:
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The masking is not done as part of the correction for mult comp but when you
run mri_glmfit. When you run it on a volume, you have to specify the mask, so
the mask depends upon your application. For fsfast, the mask in
$FREESURFER_HOME/subjects/fsaverage/mri.2mm is used.
On 11/20/18 4:57 AM,
wow, I have no idea. Can you send us the .nii file and we will try? What
machine is it failing on and does it print any error messages during
conversion? Can you send us the full command line and terminal output of
the mri_convert command that fails?
cheers
Bruce
On Tue, 20 Nov 2018, Batuhan
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Dear FreeSurfer developers,
I am trying to segment the cortex of my subjects into multiple layers and am
trying several approaches.
I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and
it works perfectly.
I am also
can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
exists and that you have read permission to it? Eg, can you load it with
freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
On 11/20/18 8:25 AM, C.P.E. Rollins wrote:
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Hi Inês
nibabel should be able to read freesurfer images directly (thanks to Satra!
I think):
http://nipy.org/nibabel/reference/nibabel.freesurfer.html
cheers
Bruce
On Tue, 20 Nov
2018, Borges Pereira Ines Isabel wrote:
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Dear FreeSurfer
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As you said, you can load FreeSurfer data (both the surface files and volume
data) with the respective nibabel functions, i.e., read_geometry and
read_morph_data. The ?h.pial and ?h.white files are surface meshes, so
read_geometry would apply.
I'm
Yes, I agree. Going to the volume irreversibly reduces the resolution and
would have to be very highres to have a hope of representing more than
two compartments.
cheers
Bruce
On Tue, 20 Nov 2018, ts...@rcmd.org wrote:
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As you said, you can load
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Hello,
I had a question regarding the aseg.stats and was hoping to get some help.
1. How is the TotalGray calculated? On the wiki page it mentioned that it
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried
calculating
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