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Dear expert，
I saw a paper mentioned this ：
By using the *deformation field* from nonlinear registration, we can
> build the correspondence between voxels in the template and each
> linearly-aligned image. For instance, for each voxel (x, y, z) in t
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Could you explain what you are trying to achieve and which transformation you
are referring to? I don't get:
1) what are the input and output files of the registration for which you want
the deformation field?
2) What command did you use to perform th
Hi Ping
the displacement fields are stored in m3z format in the file
talairach.m3z. They are a vector field over the atlas that maps points in
the atlas to points in the original (not linearly aligned) space.
cheers
Bruce
On Wed, 28 Aug 2019, ping
cao wrote:
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Thank you very much.
On Wed, 28 Aug 2019 at 00:01, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> correct
>
> On 8/27/2019 11:28 AM, Zhi Li wrote:
>
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> I see. Hence I cannot set the contrast of interac
It is showing
b = g2 - g1
so negative means that g1 > g2
On 8/28/19 1:59 PM, Barletta, Valeria wrote:
>
> Forgot to report my contrast matrix:
>
> -1 1 0 0
>
>
> Thanks,
> Valeria
>
> *From:* Barletta, Valeria
> *Sent:* Wedn
recon-all does not do so well with data at 0.5mm. I created a high-res
patch for version 6.0 as part of my support fo r the HCP. You can get it
here https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp
this shold work much better.
On 8/27/19 10:15 AM, Giovana dos Santos Cover w
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In addition,
a) to convert the time series data into the conformed space and viceversa, I
have run the command line listed below:
SUBJECTS_DIR=/media/DATA_NAS/ADNI_USB/Dati/
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o
f-in-an
Is that all the output it prints to the terminal? It might be exceeding
your available memory (it will need at least 10G). What does the limit
command return?
On 8/28/19 6:27 PM, std...@virgilio.it wrote:
>
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>
> In addition,
>
> a) to convert the time series
You can download dev from here
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
On 8/26/19 1:01 PM, Westeneng, H.J. wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> It has previously been reported that vertex 40969 is the same as
> vertex 0, which creat
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Hi Marco,
Just added to the recon-all script on dev branch the read of T2 min/max
inside/outside and nsigma_below/above parameters, which are now being
passed to mris_make_surfaces.
As I mentioned on the github bug you created, I would be careful playin
You can use mri_vol2label. Run it with --help and make sure to use the
--surf option
On 8/27/19 8:32 AM, Nillo, Ryan Michael R wrote:
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>
> Hello FreeSurfer users/developers.
>
> I manually created a binary overlay file on the pial surface. I am interested
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Yes, that's it. The memory should be ok, but I will do a check.
Anyway, is there a way to register the ThalamicNuclei.v10.T1 into EPI space? I
would like to work in functional space.
> Il 29 agosto 2019 alle 0.34 "Greve, Douglas N.,Ph.D."
> ha sc
I'm not sure what the problem is. That recon-all.log file is for
fsaverage and it says that it finished without error. Can you be more
specific about the problem?
On 8/21/19 10:43 PM, liuxingze1993 wrote:
>
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>
> Hello，Dear FreeSurfer Developers,
>
> I’m a do
It looks like there is something wrong with your dicom file because it
does not have an image orientation tag (a very basic piece of
information). Are you sure it is the right dicom? You can also try
converting it to nifti with dcm2niix then feeding the nifti into recon-all
On 8/20/19 9:59 AM,
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Yes, that's it. The memory should be ok, but I will do a check.
Anyway, is there a way to register the ThalamicNuclei.v10.T1 into EPI space? I
would like to work in functional space.
> Il 29 agosto 2019 alle 0.32 "Greve, Douglas N.,Ph.D."
> ha scr
Freeview does not update in the viewer window to the correct slice position
when calling on viewport. This means instead of taking snapshots of N
slices of the brain from N specified slice coordinates, it takes the same
snapshot over and over again.
Originally, we found a workaround by disabling qt
correction:
the output of uname -a should be
Linux ncfood02.rc.fas.harvard.edu 3.10.0-957.12.1.el7.x86_64 #1 SMP Mon Apr
29 14:59:59 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
Sorry for the confusion.
On Wed, Aug 28, 2019 at 7:18 PM Hoke, Harris wrote:
> Freeview does not update in the viewer wind
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