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Dear Freesurfer experts,
I've tried to perform an autorecon1 for a patient's brain MRI(T1). There
are some dark regions in white matter areas. an error has occurred which
I've attached the corresponding log file here as well as the raw nii data.
I
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Dear Bruce,
I had a problem with bringing aseg.mgz into my subject space and you
recommend this command before:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz
which perfectly worked for me but now when I want to try it in
new
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Hi,
Thank you so much , it works.
BRG,
Nazanin
On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> if you want to mask the thickness, then use mri_mask
>
> On 10/10/2018 10:30
>
> On 10/07/2018 08:59 AM, N Saf wrote:
> >
> > External Email - Use Caution
> >
> > Dear Douglos,
> >
> > I did not understand how to use mri_label2label with the mask
> > option(there is srcmask options not mask alone !). I extract my label
> into labels (mri_annotation2label), then converting the label into a
> binary mask (mri_label2label with --mask option), then mri_binarize --i
> lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
>
>
> On 07/30/2018 01:47 AM, N Saf wrote:
> >
> >
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Dear Freesurfer Experts,
I wonder how can I show the cortical thickness surface on just one region
of my interest in Freeview. assume that I want to see the thickness
surface of one of the regions in DKTatlas. does it work if I make a binary
mask of
Dear experts,
I cut the inflated surface in tksurfer and obtain the flatten sheet by
mris_flatten but I can not load the $h.flaten.patch.3d not in freeview nor
in tksurfer it somehow collapse! my laptop is RAM:6G , core i5 , would you
please help me how can I see the 2D flatten sheet ??
many
thank you indeed.
On Mon, Jan 1, 2018 at 1:50 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Use tkmeditfv and tksurferfv and it will bring up freeview instead.
>
> On 12/26/17 4:17 AM, N Saf wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to view the
Dear FreeSurfer experts,
I am trying to view the Feat on volume and surface by following commands:
tkmedit bert orig.mgz -aux brain.mgz
-overlay ./fbert1.feat/stats/zstat1.nii.gz
-overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat
-fthresh 2.3 –fmax 4.3 -seg aparc+aseg.mgz
I, this:
>
> mri_convert -nth 1 .gca labels_gca.mgz
>
> would give you the highest prior label at each spot (and 2 would give you
> the prior)
>
> cheers
> Bruce
>
>
>
>
> On Mon, 30 Oct 2017, N Saf wrote:
>
> Dear Experts,
>> In the volume-based strea
Dear Experts,
In the volume-based stream, if I'm right the FreeSurfer does two
registration with MNI305 ,one affine and one nonlinear , is it possible to
perform the nonlinear registration somewhere else and then use the result
in FreeSurfer and run the rest of the analysis ?
thank's alot for
his entire calculation for you
>
> cheers
> Bruce
>
>
>
> On Thu, 28 Sep 2017, N Saf wrote:
>
> Dear FreeSurfer experts,
>> I have 2 questions:
>> 1- I try to measure average convexity for temporal lobe by FreeSurfer, I
>> can see the values for each
>>
Dear FreeSurfer experts,
I have 2 questions:
1- I try to measure average convexity for temporal lobe by FreeSurfer, I
can see the values for each vertex when I overlay the e.g. lh.sulc in
lh.inflated, but I wonder if I can find these values somewhere else like in
stats files?
2- Is FreeSurfer
Dear FreeSurfer experts,
I have two questions please.
1- I cannot understand the concept of "existing labels". Why few labels
(such as #19) do exist in the LUT, but they cannot be overlaid on the
brain? What should I do if I need to map one of those labels on the brain
that disappear when I
t; On Feb 21, 2017, at 10:59 AM, N Saf <nali...@gmail.com> wrote:
>
> Dear Ruopeng,
>
> Thank you for the fast response ,where can I learn how to create my custom
> lookup table step by step ? and what the format of this file is?any help
> will be very appreciated.
>
>
gt; Ruopeng
>
> > On Feb 21, 2017, at 5:20 AM, N Saf <nali...@gmail.com> wrote:
> >
> > Dear Experts,
> >
> > I load the T1 and aseg file in freeveiw and select the lookup table ,and
> show as isosurface in 3D view for a label .Is it possible to change the
>
Dear Experts,
I load the T1 and aseg file in freeveiw and select the lookup table ,and
show as isosurface in 3D view for a label .Is it possible to change the
color(for example label 13 is blue but I want to show it as
yellow!).another question is that if I want to show multiple labels which
are
d I use another command myself to do the
Atlas Renormalization that the article proposed? (sorry if the question is
basic)
Best,
Nazanin
On Fri, Jan 20, 2017 at 9:16 AM, N Saf <nali...@gmail.com> wrote:
> Dear Bruce,
>
> thank you for your comprehensive explanation.
>
> Be
tions, but we have found that the partial
> volume correction improves e.g. test/retest reliability and probably
> accuracy, although that is harder to prove.
>
> cheers
> Bruce
>
>
>
> On Thu, 19 Jan 2017, N Saf wrote:
>
> Dear Bruce
>>
>> is the
, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Nazanin
>
> the volumes reported in the aseg.stats file have been corrected for
> partial volume effects.
>
> cheers
> Bruce
>
> On Wed, 18 Jan 2017, N Saf wrote:
>
> Dear FreeSurfers,
>> I have a q
Dear FreeSurfers,
I have a question about aseg file. I load the aseg file of bert subject in
itk-snap and read the volume for 17 and 53 label but it is a bit larger of
the volume in bert stats file. I do the same for some of my subjects too
and I see the same result .I don't know why it is like
suming the rawavg.mgz has the 208x176x176 dimensions (which it should)
>
> cheers
> Bruce
> On Mon, 9 Jan 2017, N Saf wrote:
>
> Dear Bruce,
>>
>> thank you for your fast reply ,I think I could not explain the problem
>> correctly . I want the number of slice
it
possible?
Best Regards,
Nazanin
On Mon, Jan 9, 2017 at 5:51 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
> Hi Nazanin
>
> all our segmentations are in subject space, so it should be pretty
> straightforward
>
> cheers
> Bruce
>
> On Mon, 9 Jan 2017,
Dear freesurfers,
I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have
manual segmentation for hippocampus in my subject space(208x176x176)as
well. I want to compute the dice coefficient with one simple Matlab code.
how can I do it correctly ?if I want to bring the aseg to
Dear Freesurfers,
I try to register my subject with cvs atlas in mni space I use this command
mri_cvs_register --mov subject.nii --mni
I got this error:
Using m3z type morph files.
amir : at least one mean and/or Gaussian curvature file is missing (.H, .K)
ore specific. Are you finding
> some inaccuracies that you want to correct?
>
> cheers
> Bruce
>
>
>
> On Sun, 19 Jun 2016, N Saf wrote:
>
> Dear Freesurfer,
>>
>> I wonder if it is possible to segment just one sub-cortical structures
>> like
>> h
Dear Freesurfer,
I wonder if it is possible to segment just one sub-cortical structures like
hippocampus by changing the algorithm (e.g. according to spatial prior
knowledge divided the image to some sub-images and do analysis just on that
sub-image which we sure the hippocampus located)and by
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