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Hello,
I have registered example_func.nii.gz to the anatomical image using
bbregister and then I looked at the registered file with tkregister2.
$ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o
f-in-anat.nii.gz
$ tkregister2
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Hi,
In a Freesurfer help webpage it says that to convert an image (eg
brain.mgz) from freesurfer to anatomical native space (eg rawavg.mgz) we
should use mri_vol2vol, but for a segmentation (aseg.mgz) we should use
mri_label2vol. I converted the aseg.mg
:12 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Are they exactly the same? Try
> mri_diff file1.mgz file2.mgz
> I would not expect them to be all that different, just a few voxels here
> and there
>
> On 4/16/19 3:47 PM, Sam W. wrote:
> >
> >
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Hi,
I created a series of labels with mri_annotation2label (aparc.a2009s
labels) and then created a reg file with:
tkregister2 --mov mri/rawavg.mgz --noedit --s bert --regheader --reg
register.dat
and the volume:
mri_label2vol --label labels/lh.G_cingul
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Hi,
I just finished reconall and now I'd like to convert the aseg.mgz to native
functional space.
My first thought was to simply convert the aseg.mgz to native functional
space with mri_vol2vol:
mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func
ical space
> (mri_vol2vol) so that it is in registration with the anatomical;
> transferring it to anat space handles partial voluming better.
>
> On 4/16/19 8:21 PM, Sam W. wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > I just
t; The registration actually goes from anat to func. mri_label2vol knows
> this. In any case, it is just a matrix that can easily be inverted.
>
> On 4/18/19 11:58 AM, Sam W. wrote:
> >
> > External Email - Use Caution
> >
> > Hi Doug,
> > Thanks! After reg
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Hi,
After bbregister, I ran mri_label2vol to convert a segmentation file to
native functional space
mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
aseg-in-func.nii --temp example_func.nii
Now I would like to check how well the e
> you have to use the output of mri_label2vol in the freeview command
>
> On 5/13/2019 5:02 PM, Sam W. wrote:
>
> External Email - Use Caution
> Hi,
>
> After bbregister, I ran mri_label2vol to convert a segmentation file to
> native functional space
>
> mri_la
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Hi,
How can I check how many vertices an image of my subject has?
Best regards,
Sam
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Hello,
I'm trying to create label files of the aparc+aseg ROIs but cannot find the
aseg annotations. The ?h.aparc.annot does not contain subcortical regions
that exist in the aparc+aseg.mgz volume. Is there a way to apply
mri_annotation2label to aseg
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Hi,
I would like to create a registration matrix from orig.mgz to diffusion
space. I created a reg file with
bbregister --t2 --init-fsl --reg /data/FS/sub01/reg.dat --mov
/data/FS/sub01/B0.nii.gz --s sub001
but how can I invert this registration so th
re out the directionality.
>
> On 7/22/19 4:24 PM, Sam W. wrote:
> >
> > External Email - Use Caution
> >
> > Hi,
> > I would like to create a registration matrix from orig.mgz to
> > diffusion space. I created a reg file with
> >
> > b
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Hi,
Is it possible to convert a label file like rh.cuneus.label into asc? I
tried
mris_convert --label rh.cuneus.label ctx-rh-cuneus rh.white rh.cuneus.asc
but got an error:
ERROR: unknown file annot file type specified for output: rh.cuneus.asc
Tha
Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Use lta_convert with --invert. BTW, the registration matrix is already
> anat-to-diffusion
>
> On 7/22/2019 7:50 PM, Sam W. wrote:
>
> External Email - Use Caution
> Thanks Doug! I'll use lta then, but
> Bruce
> On Tue, 23 Jul 2019, Sam W. wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi,
> >
> > Is it possible to convert a label file like rh.cuneus.label into asc? I
> > tried
> > mris_convert --label rh.cuneus.label ctx-rh-c
ever vertex in the surface, and also contains no
> information about topology (e.g. which vertices are connected by an edge)
>
> cheers
> Bruce
>
>
> On Wed, 24 Jul 2019, Sam W. wrote:
>
> >
> > External Email - Use Caution
> >
> > Thanks Bruce. Can I
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Hello,
I have run recon-all on T1 scans of patients with WM lesions. I noticed
however that for some patients the lesion is excluded from
aparc.a2009s+aseg.mgz but for other patients it is included (and labelled
as non-lesion).
Ultimately I'd like to ex
um lesions.sum.dat --thmin 0.5
> --regheader subject
> This will output a list of lesions clusters in lesions.sum.dat and their
> coordinates. you can see which ones are left and with ones are right.
>
>
>
> On 9/3/2019 5:17 PM, Sam W wrote:
>
> External Email - Use
e voxels in the lesion in orig.mgz with voxels from
> orig.lrrev-in-orig.mgz and re-run
> Let me know how it goes
>
> On 9/18/19 6:52 PM, Sam W wrote:
> >
> > External Email - Use Caution
> >
> > Thanks Doug. The problem is that for some patients the lesion aff
sterfv command. Try running that
> to see if the registration is accurate. What is the nature of anat.nii?
>
> On 9/20/2019 4:41 PM, Sam W wrote:
>
> External Email - Use Caution
> Thanks Doug, I'll try that. How would you register the lesion image (which
> is anato
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Hello!
I have run eddy on all my dwi images and then run bbregister using the
first b0 image as the source image.
The b0 image is now well aligned with the anatomical image but how can I
apply the same transformation to all other dwi images in my datase
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Hello!
I would like to register my dwidata to the anatomical image (rawavg.mgz). I
have run bbregister, but how can I specify a different target image?
bbregister uses the orig.mgz right?
These are the commands I used:
bbregister --s sub001 --mov nodi
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Hello!
I'm trying to create an fsl reg file that maps a dwi image to native
anatomical space.
1. I used bbregister to create a reg file that maps the transformation from
nodif to freesurfer's conformed space:
bbregister --s sub001 --mov nodif.nii.gz -
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Hello!
How can I get a transformation matrix that maps orig.mgz to rawavg.mgz? I
only see examples
bringing freesurfer results into original anatomical space with
mri_vol2vol, but I really just want the transformation matrix.
Thanks!
Best regards,
Sam
_
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Hello!
I performed two registrations: diffusion-to-orig.dat and
orig-to-rawavg.dat. Now I would like to concatenate the two transformation
matrices into a diffusion-to-rawavg.dat. Is there a command in freesurfer
that allows me to do that?
Best regard
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Hi,
I'm trying to understand mri_surf2vol and mri_vol2surf but I'm not able to
get the expected output when converting a surface back to volume.
These are the commands I'm using:
mri_vol2surf --mov lh_fusiform_pre.nii.gz --ref mri/orig.mgz --regheader
Wed, Jul 8, 2020 at 4:59 PM Douglas N. Greve
wrote:
> They will not look exactly the same. Try adding --ribbon ribbon.mgz
>
> On 7/6/2020 10:47 PM, Sam W wrote:
>
> External Email - Use Caution
> Hi,
> I'm trying to understand mri_surf2vol and mri_vol2surf bu
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Hello,
mri_vol2surf has the option to add a target surface (--surf) which can be
the white (default) or pial surface.
I get slightly different results depending on whether I use the white or
pial surface as the target surface, so I was wondering in whic
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Hi,
Is there a way to convert a label file into a surface/overlay? Thank you!
Best regards,
Sam
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n use to
achieve that result?
Best regards,
Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve
wrote:
> Use mri_label2label with the --outmask option
>
> On 7/8/2020 10:14 PM, Sam W wrote:
>
> External Email - Use Caution
> Hi,
> Is there a way to convert a label f
iated pial or white surface.
Best regards,
Sam
On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve
wrote:
> what do you mean merge with the pial?
>
> On 7/9/2020 8:07 PM, Sam W wrote:
>
> External Email - Use Caution
> It works great Doug, thanks a lot!
> Can I ask you
; what's your mri_label2label command?
>
> On 7/10/2020 3:05 PM, Sam W wrote:
>
> External Email - Use Caution
> Hi Doug and Tim,
> I'm running probtrackx with freesurfer surfaces as seeds. However
> probtrackx requires a file that contains both the whole surf
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Hi!
Just pinging. Is there a way to get the surface+overlay file as mentioned
above using freesurfer? Thank you!
Best regards,
Sam
-- Forwarded message -
From: Sam W
Date: Fri, Jul 10, 2020 at 9:05 PM
Subject: Re: [Freesurfer] label
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Hello!
Is it possible to extract brodmann areas not included in the aparc? For
example, BA9, BA10 and BA32?
Thanks!
Best regards,
Sam
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Hello!
I have a label in freesurfer space, and I would like it to be in anatomical
space. Is this possible?
Best regards,
Sam
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t;
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sam W
> *Sent:* Friday, June 3, 2022 9:12 AM
> *To:* Freesurfer support list
> *Subject:* [Freesurfer] labels in anatomi
nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sam W
> *Sent:* Friday, June 3, 2022 10:46 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] labels in anatomical space
>
>
>
> *External Email - Use Caution*
>
>
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Hello!
I have a volumetric mask of the cuneus and I would like to convert it to a
label and then convert that label to fsaverage space.
So far I did mri_vol2label --i cuneus.nii.gz --l cuneus.label
But how can I now convert cuneus.label to fsaverage?
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Hello!
I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into a
label so I tried:
mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label
but the resulting output file only has -1 as vertices. Is there anything
wrong w
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Hello!
I ran recon-all on my subject, is it possible to create a mask of the
midsagittal plane using freesurfer?
Best regards,
Sam
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gt; it when we segment the callosum. You could set the lateral distance to
> extend the callosum to 0 with -t 0 and then it will only label cc voxels in
> the mid-sagittal plane
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu
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