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by running
mri_diff --po mri/ThalamicNuclei.v10.T1.mgz L-VP.mgz
I obtain
diffcount 0
> Il 11 maggio 2020 alle 19.18 "Douglas N. Greve" ha
> scritto:
>
> Try running this to see if there is a difference
> mri_diff --po
Hi All, I regret to inform you that we are recalling 7.0.0 because we
found some small issues with the way that conforming step was being
performed. The conforming step takes your input volume and converts it
to 256x256x256 1mm and converts the type to UCHAR (8 bit). When
converting to UCHAR,
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is there a way to visualize the changes in thickness, area, and volume between
the 2 timepoints (cortical and subcortical)? I was under the impression that
running mri_preproc would aloow me to visualize change in cortical thickness bt
the 2
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Thanks for the reply Doug.
I'm looking for the same number of verts as the *subject* - maybe it's
as simple as I should be registering the subjects *to* the FS average
subject? But the problem is that I want the points in subject space,
not
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Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd
like a little bit of guidance as I am slightly confused about some of the
outputs of freesurfer.
I have a preprocessed nifti EPI image in
Just call your thickness file some other name, eg,
lh.xformed.thickness.mgz, the just specify --meas xformed.thickness.mgz
On 5/11/2020 3:52 PM, Xiaojiang Yang wrote:
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Thank you Douglas!
If I apply my transform to both the healthy controls and the patient,
For thickness, you can look at the difference (or percent difference).
You would use freeview (or tksurferfv, which is a frontend for
freeview). When you run mris_preproc, you can specify that you want it
to compute the (percent) difference, or you can do it with the
multi-frame output of
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Thank you Douglas!
If I apply my transform to both the healthy controls and the patient, I
guess I would lose the convenience of using mri_glmfit, which eventually
loses the convenience of using mri-glmfit-sim (I don't care not
using mri_glmfit, but I
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Hi FreeSurfer Experts,
We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the
.xdebug_tkmedit file, it outputs the following error:
"Tcl_Init returned 1: Can't find a usable init.tcl in the following
directories:
Thank you
OK, I can try
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, May 11, 2020 2:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Hippocampus {Disarmed}
Can you get the coords by loading the
Can you get the coords by loading the segmentation in freeview and
clicking on what you want the corners to be?
On 5/11/2020 2:42 PM, Del Re, Elisabetta wrote:
The voxels are boxes
In coronal we have been using the uncus to divide in anterior vs
posterior.
The voxels are boxes
In coronal we have been using the uncus to divide in anterior vs posterior.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, May 11, 2020 2:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
And how do you want to define your voxel? As a bounding box around a
particular structure (or structures)? Which ones?
On 5/11/2020 2:12 PM, Del Re, Elisabetta wrote:
Hi Douglas,
basically yes.
Thank you so much,
Elisabetta
Hi Douglas,
basically yes.
Thank you so much,
Elisabetta
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, May 11, 2020 1:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Hippocampus {Disarmed}
I'm
Hi Alex,
That command just downloads the fs_install_mcr script into your freesurfer
directory. These are two separate steps. Once downloaded, you can run
fs_install_mcr R2012b
as you would normally.
best
Andrew
From: on behalf of "Lab of Autism and
Developmental Neuroscience, Lab of Autism
Ian, it seems like you want two different things. When you run
mri_surf2surf, it gives you an output that has the same number of
vertices as the target which would allow you to do the one-to-one
comparison that you want to do. But at the same time, there seems to be
a problem with having the
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Thanks Tim.
I'd like a set of points on the surface to compare across subjects,
where there are the same number of points for each subject and they're
roughly in the same "physiological position" on each subject. So again,
if on my atlas I have a
It is probably more up-to-date to run
bbregister --help
On 5/9/2020 1:10 PM, Bruce Fischl wrote:
https://surfer.nmr.mgh.harvard.edu/fswiki/bbregister
On Sat, 9 May 2020, Amar Shukla wrote:
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Dear Sir,
Thank you for valuable information, do we have any link
Is what about topological defects? There is not an error listed in the
log file but it should have continued to run (this would not have
anything to do with any topo defects). There could be a topo defect in
the area outside of the skull that is labeled as cortex. In any event,
you should fix
It depends on what you are trying to do with the statistic. But at first
glance, I would guess that it is not since the statistic (mean and
stddev) will be a mixture of across subjects and time points. It will be
hard to interpret
On 5/8/2020 2:22 PM, Nasiriavanaki, Zahra wrote:
> Hi
I guess you could apply your transform to both the healthy controls and
to your patient, can then create an FSGD file with two classes as before
but no continuous variable. Then just have a contrast that computes the
diff between the patient and the mean of the controls.
On 5/8/2020 11:49 AM,
On 5/10/2020 12:24 PM, Safi Ullah . wrote:
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Dear Freesurfer,
*Q.1*: The colors of FreeSurferColorLUT.txt corresponds to which mgz file?
I wanted to extract Substancia-Nigra but with reference to a
conversion, held in 2019,
Try running this to see if there is a difference
mri_diff --po ThalamicNuclei.v10.T1.mgz Left-Ventroposterior.mgz
Sometimes it is not easy to see a difference that is just a few voxels
On 5/11/2020 3:02 AM, std...@virgilio.it wrote:
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By visualizing the
I'm still not sure what you are asking for. Do you want coordinates for
your MRS voxels for each subject?
On 5/11/2020 12:53 PM, Del Re, Elisabetta wrote:
I'm trying to recreate the same freesurfer subdivision during MRS
acquisition of 2 voxels for anterior and posterior hippocampus. I am
I'm trying to recreate the same freesurfer subdivision during MRS acquisition
of 2 voxels for anterior and posterior hippocampus. I am trying to find a way
to be consistent and recreate the two big freesurfer anterior/posterior voxels.
I am looking for suggestions
Dera Elisabetta,
Can you please give us some more detail on what you mean by “I am trying to
translate the same subdivision to MRI acquisition for spectroscopy purposes.”?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
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I'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg
/home/ian/lh_reg.white --streg
Uuummm this is funny. A directory “hippoSF_T1_v21_left” should have been
created under tmp, but it isn’t there. Are you sure you have writing
permissions for the subject directory?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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Can anyone please help me out which OS will be suitable for using
freesurfer from now onwards.
Regards:
Rahul Sharma
Research Scholar
NIT Silchar (Assam)
9827834360
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Dear Freesurfer team,
I have analyzed the anterior/posterior hippocampus successfully utilizing FS6.0.
I am trying to translate the same subdivision to MRI acquisition for
spectroscopy purposes.
Do you have suggestions?
Thank you very much,
regards,
Elisabetta
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The registration registers the meshes, but it does not alter the number of
vertices in them. There is no 1-to-1 correspondence between the vertices of the
2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
> On May 11, 2020 at
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By visualizing the output by freeview, I found that it was the same of
ThalamicNuclei.v10.T1.mgz.
Thanks
> Il 11 maggio 2020 alle 2.19 Bruce Fischl < fis...@nmr.mgh.harvard.edu
> mailto:fis...@nmr.mgh.harvard.edu > ha scritto:
>
>
> Hi
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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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Dear List,
I installed version 7 into a directory named 'freesurfer' where there are
already Verion 6 and Version 7(beta) is installed.
My OS is 'Ubuntu_FS_600_700b1_TutorialData'
"/usr/local/freesurfer/6.0.0-1"
"/usr/local/freesurfer/7.0.0-0.1b1"
So
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