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Dear freesurfer experts
I am still unable to register RH area and volume files to the LH of a
symmetrical template for a number of longitudinally processed subs. This is
only the case when using the --jac flag (all run fine without).
There appears
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Version 6.0
Thanks,
Rachel
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Iglesias Gonzalez,
Eugenio
Sent: Monday, January 7, 2019 2:50:57 AM
To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
I'm not sure what you mean. If you are turning off PVC, why are you computing
RBV and MGX? What is your command line? What do you mean that these options
don't seem to work?
On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
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Hi Douglas,
Thanks for helping.
To
No. You can use mri_concat with --mtx option, where the argument to --mtx is an
asci matrix that is square and diagonal with the weighting factors on the
diagonal. You could also use mri_glmfix with the --X option, where X is an
ascii column matrix of weighting factors (make sure that the the su
Do you have a T2 or a FLAIR? Can you upload the subject so we can take a look?
On 1/6/19 6:20 PM, Rusche, Johann wrote:
Dear Freesurfers,
I have been processing my T1 dataset through the longitudinal pipeline with the
-3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large
a
For MGX, the field of view is reduced to reduce computation and space usage;
this requires a new registration matrix. For RBV, the voxel size is changed in
addition. In both cases, a new registration is computed from the input
registration
On 12/21/18 2:29 PM, Matthieu Vanhoutte wrote:
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Hi everybody,
after finishing my group analysis I am currently trying to run a ROI analysis.
However I have some problems/general questions.
I am trying to draw a ROI on fsaverage in order to use the mri_label2label
command afterwards.
I opened Freev
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I used the following command to obtain only rescaled voxel-wise PET image
(with no PVC):
*mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe
--seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o nopvc*
If I omitted
On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
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I used the following command to obtain only rescaled voxel-wise PET image (with
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg
gtmseg.mgz --default-seg-merge --auto-mas
Hi Larissa,
The latest development version of freeview supports drawing labels on
surface. You can take a look here on how to update freeview:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
In the latest version, you can draw paths on surface and use custom fill
to create/edit labels
What is $SUBJECTS_DIR/${template}/surf/lh.sphere.reg ? If template is not
fsaverage_sym, can you send this file to me too?
On 1/7/19 5:21 AM, James Michael Roe wrote:
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Dear freesurfer experts
I am still unable to register RH area and volume files to the LH
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Hi Ruopeng,
Thank you very much for your quick answer and advice. So I am going to update
freeview!
Thanks!
Larissa
Gesendet mit der WEB.DE Mail App
Am 07.01.19 um 17:35 schrieb Ruopeng Wang
> Hi Larissa,
>
> The latest development version of fr
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Hello,
I'm trying to calculate the volume using pial files. Is there a way to convert
?h.pial files into nii formats? Or is there a command to calculate the volume?
Thank you so much in advance for your help.
Best regards,
Da-Yea Song
-
Have you tried aparcstats2table?
This command does not convert, but it extracts all the stats which allows you
to play with the volume and any other stats.
https://surfer.nmr.mgh.harvard.edu/fswiki/aparcstats2table
Johann
From: freesurfer-boun...@nmr.mgh.harva
Hi Da-Yea
mris_volume can be used to compute the volume of any closed surface.
cheers
Bruce
On Mon,
7 Jan 2019, Song, Da-Yea wrote:
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Hello,
I’m trying to calculate the volume using pial files. Is there a way to
convert ?h.pial files into nii
Hi Douglas,
Thanks for your swift reply. I just shared a link to a Partners Dropbox folder
with you as our group (lazargp) does not have a folder in /cluster/outgoing.
No T2 or FLAIR unfortunately. Other than MPRAGE T1 we only have fMRI and DTI
scans.
Thanks,
Johann
__
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Thanks for the quick reply. Have sent the file to you now
- James
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: 07 January 2019 17:42
To: freesurfer@nmr.mgh.harvard.edu
S
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Dear Kersten,
I have a question about how to interpret cortical thickness difference between
groups.
I have three groups(A, B, and C) and five time points(t=0,0.5, 1,2,3).
To see the difference between group A and group B, I constructed the follow
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Hello,
Are the WM-hypointensities segmented in the same way as the rest of the
subcortical regions? i.e., using the probablistic atlas referenced in the 2002
Fischl et al paper?
Thanks,
- Eli
Houston Methodist. Leading Medicine. Houston Methodis
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Hello FreeSurfer Developers,
I'm attempting to run recon-all on schizophrenia patients and
controls. For some reason freesurfer is crashing.
I wanted to know the reason for frequent crashing.
I'm using Ubuntu 16.04 LTS and
freesurfer-Linux-centos6_x8
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