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Thanks!
Mark
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461
Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu
This email m
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Yes, Great! That is what I want to see!
El 18 de jul. de 2019 15:50 -0300, Greve, Douglas N.,Ph.D.
, escribió:
> depends on what you want in the end. You can do that analysis, but
> p-values will be meaningless. Do you just want the difference between
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All my script is based on tksurfer derived commande. Is this possible to
parametrize freeview by command lines with as many options than tksurfer,
and then save snap in one script?
Please give me some information on how to set properly "Color Wheel" Co
depends on what you want in the end. You can do that analysis, but
p-values will be meaningless. Do you just want the difference between
the subject and the group mean? If so, that will work. It should also
give you z-values if that is of intereest
On 7/18/19 2:33 PM, m s wrote:
>
> Ext
In freeview, you can use :overlay_color=colorscale,settings
maybe Ruopeng can weigh in on exactly what to set them to to get the
colorwheel
Are you also looking to have freeview snap pictures for you?
On 7/18/19 11:57 AM, Matthieu VANHOUTTE wrote:
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> Sorry not to be
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Hello Freesurfer experts!
I need to compare one patient to a group of controls and I wanted to know
which is the best way to do this.
Is it correct to do it with group analysis when 1 group only has one
patient, thus no stdev, and the other group (contr
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Firstly I used the command line to extract whole cc, mri_vol2label --c
aseg.auto.mgz --id 192 --l cc.label. Then, I tried to get the labels of the
subregions of cc using the command, mri_vol2label --c cc.mgz --id 251 --l
cc1.label.
Please find the attac
please send the command line and full terminal output
On 7/18/2019 12:27 PM, Sadia Sheikh wrote:
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Thanks for your response.
I tried mri_vol2label initially but I was facing this error. error: found no
voxels matching id 192. The problem is with my given comma
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Thanks for your response.
I tried mri_vol2label initially but I was facing this error. error: found
no voxels matching id 192. The problem is with my given command or this
command is not possible for corpus callosum? Please find the attached
output of t
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Dear Freesurfer experts,
May I ask how to create a slice delay file for slice timing in fsfast? Is
there an example? The slice order of my data is [33:-2:1 32:-2:2], how
could I convert this vector to time fraction of TR? I have checked the help
inform
When you run mri_surfcluster, save an output cluster number (--ocn)
output, then feed that into mri_segstats.
On 7/18/19 11:44 AM, Mark Wagshul wrote:
>
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>
> Hi. I have a question about cluster size determination within Freesurfer.
>
> We are running linear
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Hi. I have a question about cluster size determination within Freesurfer.
We are running linear mixed model on our Freesurfer generated volume data over
the left and right cortex parcellations, and would like to look at cluster size
at the p < 0.01
you can try mri_vol2label
On 7/17/19 11:16 PM, Sadia Sheikh wrote:
>
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>
> Hello Bruce
>
> I don't have much experience in Freesurfer and I want to get the
> labels of CC. Is there any other way to get corpus callosum labels or
> voxels without using Matlab?
There is a program called tksurferfv that runs freeview but takes all
the same command line args as tksurfer
On 7/18/19 10:56 AM, Bruce Fischl wrote:
> Hi Matthieu
>
> tksurfer has been deprecated for years. Is there a reason you can't
> switch to freeview?
>
> cheers
> Bruce
> On Thu, 18 Jul 201
Hi Matthieu
tksurfer has been deprecated for years. Is there a reason you can't
switch to freeview?
cheers
Bruce
On Thu, 18 Jul 2019, Matthieu VANHOUTTE wrote:
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>
> Dear experts,
>
> I use tksurfer in command line to generate multiple faces images of
> overl
Hi Cristian
it's not so much the difference in voxel size as it is the thickness and
anisotropy of your FLAIR voxels. You would be much better off getting 1mm
iso which would have comparable SNR to what you have now. You can try it,
but the 3.5mm slice thickness will probably mess stuff up
s
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Dear experts,
I use tksurfer in command line to generate multiple faces images of
overlays on the fsaverage surface.
Graphically it is possible via freeview to set the color scale of the
overlay with "Color Wheel" setting. I searched into the tksufe
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Hi Bronwyn,
assuming that you have specified the contrasts and done the F-tests already,
you will have some output from from the 'lme_mass_F' function. Let's say this
output is called 'F_lhstats'. This matlab structure has a field called 'df', so
yo
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I understand.
Thanks for your response, Feifei!
Bruce Fischl 于2019年7月16日周二 下午10:09写道：
> Hi Feifei
>
> we don't compute thickness using the method introudced by (MacDonald et
> al.2000). For that you can look at either our 1999 NeuroImage pair of
>
Dear Freesurfer experts,
I want to improve pial reconstruction by using FLAIR images in the pial
reconstruction (freesurfer v6.0).
Ø recon-all -subject subjectname -FLAIR /path/to/FLAIR_volume -FLAIRpial
-autorecon3
T1 was acquired in a 3T Phillips scanner with a isometric voxel size of
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