External Email - Use Caution
Great, that worked. I tried it and everything else stayed the same except
for the ICV. Thanks
:)
On Tue, Nov 13, 2018 at 12:22 PM Gamaliz wrote:
> Once I manually fix the registration how do I save it? I know there is
> SAVE REG. Wil
recon-all -s subject -segstats
> and the new ICV should appear in the aseg.stats file
>
> On 11/13/2018 12:08 PM, Gamaliz wrote:
> >
> > External Email - Use Caution
> >
> >
> > I have a fewT1 scans that have obvious incorrect registration
> > to
External Email - Use Caution
I have a few T1 scans that have obvious incorrect registration
to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I
am able to fix the registration, but I wonder how to use the ew
registration to recalculate the new ICV. I am intere
here is very little
> anatomical SNR left to build models with.
>
> good luck
> Bruce
> On Sun, 18 Mar 2018, Gamaliz wrote:
>
> [IMAGE]
>>
>>
>> On Sun, Mar 18, 2018 at 2:28 AM, Gamaliz wrote:
>>
>> Dear Freesurfer Team,
>>
>> I have about
Dear Freesurfer Team,
I have about 200 T1 coronal scans that were obtained with some shading in
the frontal and occipital regions. Not sure if it can be seen from the
attached picture, but the image fades toward the top and bottom (on the
axial view). The segmentation left out a large section of t
ill print out examples. Did you try that?
>
> On 5/16/17 9:26 AM, Bruce Fischl wrote:
>
> Hi gAbE
>
> you could try using mris_fill, or even mris_compute_volume_fractions
>
> cheers
> Bruce
> On Mon, 15 May 2017, Gamaliz wrote:
>
>
> My idea is to convert the reg
ill print out examples. Did you try that?
>
> On 5/16/17 9:26 AM, Bruce Fischl wrote:
>
> Hi gAbE
>
> you could try using mris_fill, or even mris_compute_volume_fractions
>
> cheers
> Bruce
> On Mon, 15 May 2017, Gamaliz wrote:
>
>
> My idea is to convert the reg
te:
> what was your mri_surf2vol cmd line? And what was the terminal output?
>
> On 5/15/17 9:59 PM, Gamaliz wrote:
>
> I looked at the ribbon.mgz, but it is a pial surface, not really
> delineated white matter the way I need it. There is a command called
> mri_sur2vol, I have tri
:
> not sure what you mean. Have you looked at the ribbon.mgz file?
>
> On 5/15/17 5:20 PM, Gamaliz wrote:
>
> I need to create an image which overlaps the T1/mgz and the outer surface
> of the white matter. How do I convert the surface into a mgz volum
I need to create an image which overlaps the T1/mgz and the outer surface
of the white matter. How do I convert the surface into a mgz volume?
--
gAbE
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Regions 2 and 41 are labeled as
Left-Cerebral-White-Matter
Right-Cerebral-White-Matter
respectively. However, there is no label in the aseg.stats,
wmparc.stats or xh.aparc.stats files.
The only label that seems to match it is the: CorticalWhiteMatterVol
in aseg.stats.
Where is the white matter
:
> more exact than what?
>
> On 4/25/17 2:07 PM, Gamaliz wrote:
>
> Is there any way to generate a file which is more exact? Or perhaps, is
> that file already there?
>
> On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve
> wrote:
>
>> The aseg.stats is generated wit
Is there any way to generate a file which is more exact? Or perhaps, is
that file already there?
On Tue, Apr 25, 2017 at 2:04 PM, Douglas Greve
wrote:
> The aseg.stats is generated with partial volume estimation
>
> On 4/25/17 12:40 PM, Gamaliz wrote:
>
> I wrote an algorithm
I wrote an algorithm which uses the number of pixels per region in the
aseg+aparc.mgz file. As this file has 1x1x1mm3 I was expecting the number
of pixels to match very closely the value of the volume; as each pixel
represents a 1 mm3 cube.(I did the same for cortical volume and got a
similar resul
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