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Hello Everyone,
If you previously downloaded the Ubuntu VM via the
link,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67
- then without any modifications, it should contain both the previous
freesurfer 6.0.0 release and the 7.0.0 beta 1 release from
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Hi,
I was trying to get through the lazy symbol binding errors and I have disable
the SIP. I have the following errors, would you mind taking a look to see what
might goes wrong?
Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Running
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Hello Renxi,
You can try downloading and applying the FreeSurfer_6_0_0_Patch.zip file from
here,
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Dear FreeSurfer experts
I have used this script to start Freeview from within Matlab
fs=getenv('FREESURFER_HOME');
setenv('FS_QT_HOME',fullfile(fs,'lib','qt'));
setenv('QTLIBPATH',fullfile(fs,'lib','qt','lib'))
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Hi guys.
After recon-all, the /surf/?h.sphere.reg file implies a registration has
been performed to an "average" subject on a sphere. Can you please tell
me which subject this is? Is it SUBJECTS_DIR/fsaverage? If so, what is
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Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing
The error is after the command find_corresponding_center_FSformat
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Thanks Bruce.
On 13/05/2020 15:41, Bruce Fischl wrote:
Hi Ian
we don't register to an individual subject - we register to a
probabilistic atlas compiled from many subjects. The fsaverage
subjects were also generated from that data so they are in
This is a design problem that will not be solved by simply forcing
glmfit to run. I would remove that class and those subjectgs
On 5/13/2020 2:33 PM, Marina Fernández wrote:
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Thank you, Doug.
That makes sense.
Do you think in this case it is a good option
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Thank you, Doug.
That makes sense.
Do you think in this case it is a good option to add the flag --illcond to
run this analysis without getting an error? or is it better not to use the
variable apoe in these statistical analyzes?
What do you
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is the command line ok?
by running
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133 --o L-VP.mgz
mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz
I obtain
diffcount 0
> Il 12 maggio 2020 alle 0.53 std...@virgilio.it ha
Does it run under version 6? We are not really supporting lGI anymore,
but maybe we can get it to work
On 5/13/2020 4:24 PM, Angela Favaro wrote:
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Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification
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indeed. I would like to merge two regions and extract the fMRI time serie. if
no difference is there, somewhat is wrong. the L-VP file contains the same
information of ThalamicNuclei.v10.T1.
thanks
> Il 13 maggio 2020 alle 17.02 "Douglas N. Greve"
Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.
On 5/13/2020 5:57 PM, Angela Favaro wrote:
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Please find attached
Are you running this from recon-all? If so send the recon-all.log. If
from the command line, send the command-line and all terminal output
On 5/13/2020 5:28 PM, Angela Favaro wrote:
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Hi Doug!
yes, it run under version 6!
Please let me know if it is
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Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela
> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve
> ha scritto:
>
> Does it run under version 6? We are not really supporting
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Just following up to confirm that this issue persists in 7.1.0 in case anyone
has any ideas; I've tried everything I can think of at this point.
:(
From: TRISTAN J PAUTSCH
Sent: Friday, April 17, 2020 12:21 PM
To:
DICOMs may save each slice or each volume separately. This is not a problem per
se, it's just a format, but it suggests that something may have changed in the
protocol, which begs the question if other things changed in the protocol. I'd
start by checking the converted nifti (dmri/dwi.nii.gz)
It problably means that seg 8130 does not exist in the input mgz. Can
you confirm that it does?
On 5/13/2020 12:51 PM, std...@virgilio.it wrote:
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indeed. I would like to merge two regions and extract the fMRI time
serie. if no difference is there,
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In the FreeSurferColorLUT.txt 8130 is the left VM.
The volume is correctly calculated in the VM of the subject.
I have tried with:
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replaceonly 8126 8127 --o L-VA.mgz
mri_diff --po
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Thanks for sharing!
I just wanted to add: for those who want to create their own FreeSurfer Docker
Image, the Dockerfile from Neurovault is very helpful to get started:
https://github.com/NeuroVault/NeuroVault/blob/master/fs_docker/Dockerfile
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Hello FreeSurfer Developers.
I installed and setup freesurfer ubuntu 18VM following steps in the website
https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_win.
However, when I clicked green start button to run VM at the last step, it did
not go
Did you try specifying your xformed file as the argument to --cached-in ?
If that does not work, then transform the thickness in the native
surface,then run mris_preproc, then smooth with mris_fwhm
On 5/12/2020 11:37 PM, Xiaojiang Yang wrote:
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Hi Douglas,
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Hi teams,
After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing guid
in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer.
It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh:
command not found:
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using freeview
instead.
cheers
Bruce
On Wed, 13 May 2020, ZhangBo wrote:
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Hi teams,
After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing
guid in
You can also use tkmeditfv and tksurferfv. They take the
tkmedit/tksurfer arguments but run freeview
On 5/13/2020 11:48 AM, Bruce Fischl wrote:
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using
freeview instead.
cheers
Bruce
On Wed, 13 May 2020, ZhangBo wrote:
Hi Ian
we don't register to an individual subject - we register to a
probabilistic atlas compiled from many subjects. The fsaverage subjects
were also generated from that data so they are in register, but the actual
atlas is a .tif file that you can find as the target of mris_register in
The problem is that class 3 (smaleapoe) only has two members but you
have four covariates. When you use DODS, each class gets its own fit to
the data. In this case, class 3 is trying to solve for 5 unkowns (offset
+ 4 slopes) with only two data points.
On 5/13/2020 10:18 AM, Marina Fernández
That means there is no difference
On 5/13/2020 10:47 AM, std...@virgilio.it wrote:
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is the command line ok?
by running
mri_binarize --i ThalamicNuclei.v10.T1.mgz --replace-only 8130 8133
--o L-VP.mgz
mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz
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Hi Douglas,
I email you the fsgd file and I have also sent it through FTP.
Thank you for your attention.
Best regards,
Marina.
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