External Email - Use Caution
Dear Yujing,
Thank you for your reply.
1. Confirmed I am running Freesurfer 6.0.
2. I am running both commands from within the individual subject directory
(ID=1003156). The parent folder contains several folders all labelled with
diffe
External Email - Use Caution
Responding to you off the list.
- R.
On Apr 21, 2022, at 15:08, Paul Wighton
wrote:External Email - Use
CautionHi Jacob,Can you provide
more details on how FreeSurfer was installed, how you are using the li
External Email - Use Caution
Dear R.,
I have already re-install FS and it worked.
Thanks for your attention!
Regards,
Krystal
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of krystaly
Sent: 22 April 2022 08:57:00
To: fsbuild; fre
External Email - Use Caution
Dear R.,
Thank you for your reply.
As per advise, I checked that my C drive still has 66.3 GB of free space.
Next, when I followed the instructions of how to disable Hyper-V, it has
already unchecked.
VM is still not working... Would you please hel
External Email - Use Caution
Hi Jacob,
Can you provide more details on how FreeSurfer was installed, how you are
using the license key and the errors you are receiving?
I just created a docker container with FreeSurfer v5.3.0-HCP (
https://secure-web.cisco.com/17NmBKDBeKQ2s5KCPv_
Hi Rebecca,
I’m trying to get more information to determine how it core dumped.
1. Can you confirm that you are running Freesurfer 6.0?
2. From which directory, did you run recon-all and dcmunpack?
3. Can you try dcmunpack by passing it full path to dicom directory?
Thanks.
Yujing
-
Can you provide the tkregisterfv command line and the terminal output?
On 4/21/2022 3:37 AM, Fritze, Stefan wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to computerecon-all -all -subjid XXX -qcache -3T, which works
fine with most of my study partici
basically, you should not have been using the beta version since it is a
beta version. hard to know what the differences were
On 4/20/2022 6:21 PM, Paul Wighton wrote:
External Email - Use Caution
Hi Matt,
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c was compiled
from t
Can you send your mri_gtmpvc command line?
On 4/20/2022 12:50 PM, Zhener Zhang wrote:
External Email - Use Caution
Hello,
I have a question regarding the way ROI-wise values are calculated
using PETSurfer.
We ran the PETSurfer pipeline with PVC=0 and noticed that a relatively
smal
HI Malav, did you create the subcortical mass? Have you separated the
hemispheres?
On 4/18/2022 4:48 PM, Malav Shah wrote:
External Email - Use Caution
Hi Dr. Greve,
I send a gentle reminder, in case the previous mail skipped your
attention.
with regards,
Malav
Yes, same command
On 4/17/2022 10:24 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Can someone confirm?
Thx.
Jim
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Alexopoulos,
Dimitrios
*Sent:* Tuesday, April 12, 2022 3:24 PM
*To:* Freesurfer support
I'm not sure. You can try just passing the skull stripped as input to
recon-all. The talairach transform will probably be off, but the rest
might work
On 4/17/2022 9:09 PM, Muhammed Görünen wrote:
External Email - Use Caution
Hi,
How can I run a recon process if I have just skull st
you need to add these flags again
On 4/16/2022 11:49 AM, VINCENT KOPPELMANS wrote:
External Email - Use Caution
I have made manual edits to a subject that was initially run with the
-FLAIR and -FLAIRpial input flags. When I want to rerun
freesurfer to implement these edits should I
Do you mean the difference between the d,m,h classes? If so, it would be
1 1 -1 -1 0 0 (rest all 0s)
1 1 0 0 -1 -1 ...
0 0 1 1 -1 -1 ...
On 4/14/2022 9:50 AM, David wrote:
External Email - Use Caution
Hi Freesurfer experts,
I'm very sorry to bother you, but I am very confused
Try using mris_expand, eg,
mris_expand lh.white -1 lh.subwhite
will create a surface 1mm into the WM
On 4/14/2022 7:50 AM, Lee Subin Kristine wrote:
External Email - Use Caution
Dear FreeSurfers,
I am interested in sampling values in the superficial white matter
(SWM) region, which i
in freeview, runsomethiing like
freeview -f rh.white:patch=rh.full.flat.patch.3d
The rh.white is just there to give freeview a full surfce to load. You
will only see your patch
On 4/14/2022 4:30 AM, Morgenroth Elenor wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I have
Yes, first line intercept, 2nd line slope
On 4/12/2022 3:44 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Hey! I'm resending this email because I think it got lost on the list.
Hello FreeSurfer Developers,
I'm extracting beta valuesfrom some analyzes and I would li
There is not an easy way to do this. Internally, there is a binary that
loads all the subjects then creates an average. You need some way to
create intermediate files, then combine them together, which we don't
support. Why do you want to create an average subject?
On 4/11/2022 9:54 AM, Marina
You don't have enough members in the classes to fit the model that you
have. Eg, class d has 4 members with which you are fitting an offset and
3 slopes leaving you with 0 degrees of freedom. You need to get more
subjects or change your model. btw, gender is usually modeled as a
discrete rather
Of course! Please let me know if you have any questions about the toolbox.
Best,
Iman
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fotiadis, Panagiotis
Sent: Thursday, April 21, 2022 12:32 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical depth at each cortical vox
External Email - Use Caution
Hi Iman,
That is extremely helpful, thank you very much (also the paper is a great read)!
Best,
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Aganj, Iman
Date: Thursday, April 21, 2022 at 12:06 PM
To: Freesurfer support list
S
Hi Panos,
You can do such a volumetric analysis using this toolbox:
Code: https://www.nitrc.org/projects/thickness
Paper: https://onlinelibrary.wiley.com/doi/epdf/10.1002/hbm.20740
You can apply the MLI_thickness function to the gray matter (soft or binary)
mask, which returns the layer thick
External Email - Use Caution
Hi FS experts,
I was wondering whether there was a way to assign each cortical voxel within
the T1w (volumetric) scan an index corresponding to its “cortical depth.” I
have essentially taken the cortical ribbon .mgz file, assigned each cortical
voxe
23 matches
Mail list logo