[Freesurfer] vertices are -1 when using vol2label

[Sam W]

External Email - Use Caution

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 with the command above?

Best regards,
Sam
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[Freesurfer] convert to fsaverage

[Sam W]

External Email - Use Caution

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?

Thanks!

Best regards,
Sam
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Re: [Freesurfer] midsagittal mask

[Sam W]

External Email - Use Caution

Hi Bruce,

Thank you for the response! Which freesurfer command do I need to run with
-t 0?

Best regards,
Sam


On Sat, Aug 27, 2022 at 3:44 AM Fischl, Bruce 
wrote:

> I don’t think we ever write out the mid-sagittal plane, but we do compute
> 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> *On Behalf Of *Sam W
> *Sent:* Friday, August 26, 2022 8:37 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] midsagittal mask
>
>
>
> *External Email - Use Caution*
>
> 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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>
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[Freesurfer] midsagittal mask

[Sam W]

External Email - Use Caution

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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Re: [Freesurfer] labels in anatomical space

[Sam W]

External Email - Use Caution

Hi Bruce,
I have my subject's T1 image that I use as input in my recon -all call. But
all the output from freesurfer  (eg, surfaces in surf directory, labels in
the label directory) are in freesurfer's space, aren't they?
When I load the label with T1.mgz it appears in the correct location, but
not when I load the native T1 image of the subject the label is not
correct. So I simply want to have the labels in the native T1w-space of my
subject.
The same way I can for example convert a volume in from freesurfer space
into native anatomical space (
https://secure-web.cisco.com/18dzfcomDtZKgTXJmODZL5YQnaa7EaSXDzc-sFiqm5_S_ti1SsYzb9jJcW91yyAIetFqdYWWqFTbZvpEq8BUY0_Jqq9s6yLMhtA1J2_MM06vmMim_16wjJfSILdm1MDzlX2B5KnvnnscKzhpRtYAYCS-MsKoPi2FCUavsTmrAqi0F--8HVzcU-S06NO3ZR_Z4S8UFw0eCJiTTo44QvMRfhR-t4ozX1ycpYpHV-h9MQl8KE0DV-OrqsV7uQU_gxbaLIl7SQeLo9fLKXARb5PZ9X-IHyfQhf_PIcOb6l4jJqZME_CByZqGbYbpvpD3tYyXIg3Q5SZyGvjmG_QnzD_xw6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat)
 can I do
the same with freesurfer labels?
Best regards,
Sam


On Fri, Jun 3, 2022 at 4:59 PM Fischl, Bruce 
wrote:

> The conformed space is an anatomical one, so I’m still not clear what
> “anatomical space” you want to map it to. What are you trying to do with
> it? And when you visualize the label in freeview in the volume does it
> appear in the correct location?
>
>
>
> *From:* freesurfer-boun...@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*
>
> Hi Bruce,
>
>
>
> Thanks for your help!
>
> I got the label after running mri_annotation2label using the
> label\lh.aparc.annot file on an individual subject. I always assumed (maybe
> wrongly) that labels correspond to surfaces and are defined in freesurfer's
> conformed space.
>
>
>
> Best regards,
>
> Sam
>
>
>
>
>
> On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce 
> wrote:
>
> Hi Sam
>
>
>
> We need more information. What do you mean by “freesurfer space”? Is it on
> an individual subject or fsaverage? Volume or surface? How did you create
> it?
>
>
>
> 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 anatomical space
>
>
>
> *External Email - Use Caution*
>
> 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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Re: [Freesurfer] labels in anatomical space

[Sam W]

External Email - Use Caution

Hi Bruce,

Thanks for your help!
I got the label after running mri_annotation2label using the
label\lh.aparc.annot file on an individual subject. I always assumed (maybe
wrongly) that labels correspond to surfaces and are defined in freesurfer's
conformed space.

Best regards,
Sam


On Fri, Jun 3, 2022 at 4:33 PM Fischl, Bruce 
wrote:

> Hi Sam
>
>
>
> We need more information. What do you mean by “freesurfer space”? Is it on
> an individual subject or fsaverage? Volume or surface? How did you create
> it?
>
>
>
> 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 anatomical space
>
>
>
> *External Email - Use Caution*
>
> Hello!
>
> I have a label in freesurfer space, and I would like it to be in
> anatomical space. Is this possible?
>
> Best regards,
>
> Sam
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] labels in anatomical space

[Sam W]

External Email - Use Caution

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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[Freesurfer] extracting BAs in freesurfer

[Sam W]

External Email - Use Caution

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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[Freesurfer] Fwd: label to surface

[Sam W]

External Email - Use Caution

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 to surface
To: Freesurfer support list 


Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However
probtrackx requires a file that contains both the whole surface file (eg,
lh.pial) as well as the overlay (the scalar values associated with the
vertices of the roi).
I can create such a file with FSL's label2surf command which creates a
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running
probtrackx with the overlay from mri_label2label --outmask does not work.
It also needs the associated 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 a follow up question please? I created the overlay with
> mri_label2label using --outmask as you suggested, but now I'd like to merge
> that overlay with the pial surface (lh.pial). Is there a tool I can 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 file into a surface/overlay? Thank you!
>> Best regards,
>> Sam
>>
>> ___
>> Freesurfer mailing 
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>>
>>
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Re: [Freesurfer] label to surface

[Sam W]

External Email - Use Caution

Hi Doug,
I'm using this command:
mri_label2label --srclabel lh.fusiform.label --trglabel output.label --s
sub01 --regmethod surface --hemi lh --outmask outmask.gii
Best regards,
Sam


On Fri, Jul 10, 2020 at 9:48 PM Douglas N. Greve 
wrote:

> 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 surface file (eg,
> lh.pial) as well as the overlay (the scalar values associated with the
> vertices of the roi).
> I can create such a file with FSL's label2surf command which creates a
> gifti file that encodes both the surface and the overlay.
> My question is whether I can do the same with freesurfer? Running
> probtrackx with the overlay from mri_label2label --outmask does not work.
> It also needs the associated 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 a follow up question please? I created the overlay with
>> mri_label2label using --outmask as you suggested, but now I'd like to merge
>> that overlay with the pial surface (lh.pial). Is there a tool I can 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 file into a surface/overlay? Thank you!
>>> Best regards,
>>> Sam
>>>
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>>
>>
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Re: [Freesurfer] label to surface

[Sam W]

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 surface file (eg,
lh.pial) as well as the overlay (the scalar values associated with the
vertices of the roi).
I can create such a file with FSL's label2surf command which creates a
gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running
probtrackx with the overlay from mri_label2label --outmask does not work.
It also needs the associated 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 a follow up question please? I created the overlay with
> mri_label2label using --outmask as you suggested, but now I'd like to merge
> that overlay with the pial surface (lh.pial). Is there a tool I can 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 file into a surface/overlay? Thank you!
>> Best regards,
>> Sam
>>
>> ___
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>>
>>
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Re: [Freesurfer] label to surface

[Sam W]

External Email - Use Caution

It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay with
mri_label2label using --outmask as you suggested, but now I'd like to merge
that overlay with the pial surface (lh.pial). Is there a tool I can 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 file into a surface/overlay? Thank you!
> Best regards,
> Sam
>
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[Freesurfer] label to surface

[Sam W]

External Email - Use Caution

Hi,
Is there a way to convert a label file into a surface/overlay? Thank you!
Best regards,
Sam
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[Freesurfer] white vs pial target surface

[Sam W]

External Email - Use Caution

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 which situation
should I use the white over the pial surface?
Best regards,
Sam
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Re: [Freesurfer] output of mri_surf2vol looks fragmented

[Sam W]

External Email - Use Caution

Thanks Doug.
I added --ribbon ribbon.gz to the mri_vol2surf command but the output was
exactly the same as omitting it. I think mri_vol2surf automatically loads
ribbon.mgz when I include the --subject sub01.
Just for my understanding, why shouldn't they look exactly the same if all
I'm doing is going from vol2surf and back (surf2vol) using the same ROI?
I guess when I convert a volumetric ROI to a surface with mri_vol2surf I
will lose volumetric information which I cannot recover with mri_surf2vol,
is that right?
Best regards,
Sam


On 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 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
> sub01 --o lh_fusiform.gii --hemi lh
> mri_surf2vol --o lh_fusiform_post.nii.gz --subject sub01 --so
> surf/lh.white lh_fusiform.gii
>
> shouldn't lh_fusiform_pre and lh_fusiform_post look the same?
> lh_fusiform_post looks fragmented.
>
> Best regards,
> Sam
>
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[Freesurfer] output of mri_surf2vol looks fragmented

[Sam W]

External Email - Use Caution

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
sub01 --o lh_fusiform.gii --hemi lh
mri_surf2vol --o lh_fusiform_post.nii.gz --subject sub01 --so surf/lh.white
lh_fusiform.gii

shouldn't lh_fusiform_pre and lh_fusiform_post look the same?
lh_fusiform_post looks fragmented.

Best regards,
Sam
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[Freesurfer] concatenate transformations

[Sam W]

External Email - Use Caution

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 regards,
Sam
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[Freesurfer] orig2rawavg transformation matrix

[Sam W]

External Email - Use Caution

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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[Freesurfer] dwi to native transformation

[Sam W]

External Email - Use Caution

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 --reg nodif2orig.dat --dti
--init-fsl --fslmat nodif2orig.mat

2. then I aligned my dwi images to orig.mgz using the reg file from step 1
mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o
dwi-in-freesurfer.nii

3. finally I mapped dwi-in-freesurfer image to native anatomical space
mri_vol2vol --target mri/rawavg.mgz --regheader --mov dwi-in-freesurfer.nii
--o dwi-in-rawavg.nii

However I only get the registration file nodif2orig.mat, which only maps
the nodif to freesurfer space? How can I get an fsl.mat for the
transformation from freesurfer to native space? mri_vol2vol has no flag to
output an fsl-type registration file.

Best regards,
Sam
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[Freesurfer] different target image for registration

[Sam W]

External Email - Use Caution

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 nodif.nii.gz --reg nodif2orig.dat --dti
--init-fsl

mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o
dwialigned.nii

mri_label2vol --regheader dwialigned.nii.g --temp mri/rawavg.mgz
--aparc+ageg  --o labels.nii

I'm not sure if the last command is valid, because I think bbregister and
mri_vol2vol use the orig.mgz, whereas mri_label2vol uses rawavg.

Best regards,
Sam
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[Freesurfer] registration of dwi images

[Sam W]

External Email - Use Caution

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 dataset?

After eddy correction I extracted the first b0 image (nodif.nii.gz) and run
the bbregister command:
bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg
/home/samm/nodiffb2orig.dat --dti --init-fsl --o
/home/samm/registered_b0.nii.gz

Thanks!
Sam
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Re: [Freesurfer] issue with lesions

[Sam W]

External Email - Use Caution

Hi Doug,
anat is a T1w image and is well aligned with orig when I run the
tkregisterfv command.
But I suspect I know what the problem might be. When I run

mri_vol2vol --mov /data/sub01/anat.nii --fstarg --reg /data/sub01/reg.lta
--o anat-in-fs.mgz --s sub01

(the lta file was generated with mri_coreg), the orientation of
anat-in-fs.mgz turns out incorrect. In freeview the superior label is at
the back of the brain and the inferior label at the front of the brain (ie,
the face is facing down). I don't understand this as the anat is in RAS,
and the anat and orig appeared well aligned when I ran the tkregisterfv
command above.
Do you have an idea what I might be doing wrong?

Best regards,
Sam

On Mon, Sep 23, 2019 at 8:18 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> mri_coreg should have printed out tkregisterfv 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 anatomical space) to orig.mgz? I thought this would work:
> mri_coreg --mov /data/sub01/anat.nii.gz --targ orig.mgz --reg
> /data/sub01/reg.lta
> mri_vol2vol --mov /data/sub01/lesion.nii --fstarg --reg
> /data/sub01/reg.lta --o lesion-in-fs.mgz --s sub01
>
> but the resulting lesion-in-fs.mgz does not align well with orig.mgz...
> Best regards,
> Sam
>
>
>
> On Thu, Sep 19, 2019 at 4:54 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> There is  not an easy way to do this. FS expects an intact whole brain,
>> and it tries to fit such into every brain, ie, it is trying to force a
>> whole cerebellum where there is none. What some people do is to fill the
>> lesion with "reasonable" intensities, eg, from the contralateral side.
>> Eg, you could left-right reverse the subject:
>> mri_convert orig.mgz --left-right-reverse-pix orig.lrrev.mgz
>> mri_coreg --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta
>> mri_vol2vol --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta --o
>> orig.lrrev-in-orig.mgz
>> Then replace the 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 affects
>> > the segmentation dramatically. For example I have one patient with a
>> > large lesion in the right cerebellum which is partly in GM and partly
>> > in WM. If I load the aseg file I see that a portion of the right
>> > cerebellar hemisphere is assigned to the left cerebellar hemisphere
>> > (the right white matter is also being assigned to the left hemisphere)
>> > and the whole cerebellum looks distorted. I suppose there is no way to
>> > inform freesurfer about the lesion during recon-all?
>> > I followed the steps in the FsTutorials for the cerebral cortex, but
>> > how can I do the same for the cerebellum patient? What is the
>> > recommended way to fix a bad segmentation due to cerebellum lesions?
>> > Control points, white matter edits, or something else?
>> > Sam
>> >
>> > On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > You can get the volume from the aseg.stats file. Unfortunately, we
>> > do not separate the lesions into left and right. You could do
>> > something like
>> > mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
>> > mri_volcluster --i wmlesions.mgz --sum 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 Caution
>> >>
>> >> 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 extract a) volume information in WM and b)
>> >> volume information of the

Re: [Freesurfer] issue with lesions

[Sam W]

External Email - Use Caution

Thanks Doug, I'll try that. How would you register the lesion image (which
is anatomical space) to orig.mgz? I thought this would work:
mri_coreg --mov /data/sub01/anat.nii.gz --targ orig.mgz --reg
/data/sub01/reg.lta
mri_vol2vol --mov /data/sub01/lesion.nii --fstarg --reg /data/sub01/reg.lta
--o lesion-in-fs.mgz --s sub01

but the resulting lesion-in-fs.mgz does not align well with orig.mgz...
Best regards,
Sam



On Thu, Sep 19, 2019 at 4:54 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> There is  not an easy way to do this. FS expects an intact whole brain,
> and it tries to fit such into every brain, ie, it is trying to force a
> whole cerebellum where there is none. What some people do is to fill the
> lesion with "reasonable" intensities, eg, from the contralateral side.
> Eg, you could left-right reverse the subject:
> mri_convert orig.mgz --left-right-reverse-pix orig.lrrev.mgz
> mri_coreg --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta
> mri_vol2vol --mov orig.lrrev.mgz --targ orig.mgz --reg lrrev.lta --o
> orig.lrrev-in-orig.mgz
> Then replace the 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 affects
> > the segmentation dramatically. For example I have one patient with a
> > large lesion in the right cerebellum which is partly in GM and partly
> > in WM. If I load the aseg file I see that a portion of the right
> > cerebellar hemisphere is assigned to the left cerebellar hemisphere
> > (the right white matter is also being assigned to the left hemisphere)
> > and the whole cerebellum looks distorted. I suppose there is no way to
> > inform freesurfer about the lesion during recon-all?
> > I followed the steps in the FsTutorials for the cerebral cortex, but
> > how can I do the same for the cerebellum patient? What is the
> > recommended way to fix a bad segmentation due to cerebellum lesions?
> > Control points, white matter edits, or something else?
> > Sam
> >
> > On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > You can get the volume from the aseg.stats file. Unfortunately, we
> > do not separate the lesions into left and right. You could do
> > something like
> > mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
> > mri_volcluster --i wmlesions.mgz --sum 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 Caution
> >>
> >> 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 extract a) volume information in WM and b)
> >> volume information of the WM lesion. I think I can get the the WM
> >> volume from the wmparc.stats file. For the lesion volume I think
> >> I can take the WM-hypointensities from the aseg file right?
> >> However I noticed that if a lesion is on the right hemisphere,
> >> the Right-WM-hypointensities shows 0s in all columns, which
> >> cannot be right.
> >> I have a mask of the lesion (1s where lesion occurs, 0s
> >> elsewhere) in anatomical space, can I use this mask somehow in FS
> >> to inform recon-all where the lesion occurs?
> >> Thanks in advance!
> >> Sam
> >>
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Re: [Freesurfer] issue with lesions

[Sam W]

External Email - Use Caution

Thanks Doug. The problem is that for some patients the lesion affects the
segmentation dramatically. For example I have one patient with a large
lesion in the right cerebellum which is partly in GM and partly in WM. If I
load the aseg file I see that a portion of the right cerebellar hemisphere
is assigned to the left cerebellar hemisphere (the right white matter is
also being assigned to the left hemisphere) and the whole cerebellum looks
distorted. I suppose there is no way to inform freesurfer about the lesion
during recon-all?
I followed the steps in the FsTutorials for the cerebral cortex, but how
can I do the same for the cerebellum patient? What is the recommended way
to fix a bad segmentation due to cerebellum lesions? Control points, white
matter edits, or something else?
Sam

On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You can get the volume from the aseg.stats file. Unfortunately, we do not
> separate the lesions into left and right. You could do something like
> mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
> mri_volcluster --i wmlesions.mgz --sum 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 Caution
> 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 extract a) volume information in WM and b) volume
> information of the WM lesion. I think I can get the the WM volume from the
> wmparc.stats file. For the lesion volume I think I can take the
> WM-hypointensities from the aseg file right? However I noticed that if a
> lesion is on the right hemisphere, the Right-WM-hypointensities shows 0s in
> all columns, which cannot be right.
> I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in
> anatomical space, can I use this mask somehow in FS to inform recon-all
> where the lesion occurs?
> Thanks in advance!
> Sam
>
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[Freesurfer] issue with lesions

[Sam W]

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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 extract a) volume information in WM and b) volume
information of the WM lesion. I think I can get the the WM volume from the
wmparc.stats file. For the lesion volume I think I can take the
WM-hypointensities from the aseg file right? However I noticed that if a
lesion is on the right hemisphere, the Right-WM-hypointensities shows 0s in
all columns, which cannot be right.
I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in
anatomical space, can I use this mask somehow in FS to inform recon-all
where the lesion occurs?
Thanks in advance!
Sam
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Re: [Freesurfer] label to asc

[Sam W.]

External Email - Use Caution

Thanks Bruce, that's helpful! I take it that it's not possible to create a
surface file simply using the information in the label file then?
The reason I'm confused is that "mris_convert lh.white lh.white.asc" will
convert a surface file to asc. The contents of lh.white.asc look similar to
what a label file contains, so I thought you could easily convert a label
into a surface and vice versa.
Also, if the label does not contain information about topology, how are we
able to convert a label to a volume with mri_label2vol?
Thanks in advance!
Sam

On Wed, Jul 24, 2019 at 10:42 PM Bruce Fischl 
wrote:

> Hi Sam
>
> they are not the same. A label is just a list of vertices in the surface
> (with some possibly voxel coordinates and also with a single
> value/vertex).
> It doesn't have to be 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 ask you a very basic question? What exactly is the
> > difference between a surface and a label file? I thought the difference
> was
> > that the label file is just a normal text file containing the vertices
> that
> > are used to construct a surface. If so, is there a tool that allows me to
> > create a surface from a label file? mri_label2surf would be my first
> guess,
> > but that doesn't seem to exist.
> > Best regards,
> > Sam
> >
> >
> > On Wed, Jul 24, 2019 at 4:18 PM Bruce Fischl  >
> > wrote:
> >   Hi Sam
> >
> >   the labels are already ascii
> >
> >   cheers
> >   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-cuneus rh.white
> >   rh.cuneus.asc
> >   >
> >   > but got an error:
> >   >
> >   > ERROR: unknown file annot file type specified for output:
> >   rh.cuneus.asc
> >   >
> >   > Thanks!
> >   > Sam
> >   >
> >   >
> >   >___
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> >
> >
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Re: [Freesurfer] label to asc

[Sam W.]

External Email - Use Caution

Thanks Bruce. Can I ask you a very basic question? What exactly is the
difference between a surface and a label file? I thought the difference was
that the label file is just a normal text file containing the vertices that
are used to construct a surface. If so, is there a tool that allows me to
create a surface from a label file? mri_label2surf would be my first guess,
but that doesn't seem to exist.
Best regards,
Sam


On Wed, Jul 24, 2019 at 4:18 PM Bruce Fischl 
wrote:

> Hi Sam
>
> the labels are already ascii
>
> cheers
> 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-cuneus rh.white rh.cuneus.asc
> >
> > but got an error:
> >
> > ERROR: unknown file annot file type specified for output: rh.cuneus.asc
> >
> > Thanks!
> > Sam
> >
> >
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Re: [Freesurfer] transformation question

[Sam W.]

External Email - Use Caution

Thanks Doug! Could you clarify what you mean by the registration already
being in anat-to diffusion?  The only thing I did was to run bbregister
using B0 as the -mov image and saving the reg.lta. If I understood
correctly the registration matrix should be diffusion-to-freesurfer,
shouldn't it?
Now I ran lta_convert --inlta reg.lta --invert --outfsl
freesurfer-to-diff.mat. I believe freesurfer-to-diff encodes the
transformation from freesurfer space to diffusion space, is that correct?
Best regards,
Sam

On Tue, Jul 23, 2019 at 3:15 AM 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 which tool do you recommend I use for
> inverting the matrix in order to have a freesurfer-to-diffusion
> registration matrix? bbregister does not seem to offer the option to invert
> matrices. Is tkregister2 the preferable tool to use here? I realize there
> is an --lta-inv ltafile option. Would this be correct?:
>
> tkregister2 --mov B0.nii.gz --fstarg --fslregout fsl.mat --s sub01
> --lta-inv reg.lta
>
> I'd like to output an FSL-style registration matrix because I intend to
> use some of FSL tools.
>
> Thanks for your help!
> Sam
>
> On Mon, Jul 22, 2019 at 10:35 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> In most of the tools there is an option to invert the matrix before you
>> apply it. If you save the registration matrix as an LTA instead of DAT,
>> then most of the tools will figure 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
>> >
>> > 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 that the transformation goes
>> > from freesurfer to diffusion space?
>> > Thanks!
>> > Sam
>> >
>> > ___
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>>
>>
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>
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[Freesurfer] label to asc

[Sam W.]

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-cuneus rh.white rh.cuneus.asc

but got an error:

ERROR: unknown file annot file type specified for output: rh.cuneus.asc

Thanks!
Sam
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Re: [Freesurfer] transformation question

[Sam W.]

External Email - Use Caution

Thanks Doug! I'll use lta then, but which tool do you recommend I use for
inverting the matrix in order to have a freesurfer-to-diffusion
registration matrix? bbregister does not seem to offer the option to invert
matrices. Is tkregister2 the preferable tool to use here? I realize there
is an --lta-inv ltafile option. Would this be correct?:

tkregister2 --mov B0.nii.gz --fstarg --fslregout fsl.mat --s sub01
--lta-inv reg.lta

I'd like to output an FSL-style registration matrix because I intend to use
some of FSL tools.

Thanks for your help!
Sam

On Mon, Jul 22, 2019 at 10:35 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> In most of the tools there is an option to invert the matrix before you
> apply it. If you save the registration matrix as an LTA instead of DAT,
> then most of the tools will figure 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
> >
> > 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 that the transformation goes
> > from freesurfer to diffusion space?
> > Thanks!
> > Sam
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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[Freesurfer] transformation question

[Sam W.]

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

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 that the transformation goes from
freesurfer to diffusion space?
Thanks!
Sam
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[Freesurfer] aseg annotation2label

[Sam W.]

External Email - Use Caution

 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 labels?
Thanks!

Best regards,
Sam
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[Freesurfer] number of vertices

[Sam W.]

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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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Re: [Freesurfer] check FS to native registration in freeview

[Sam W.]

External Email - Use Caution

Thank you Douglas for your response. That's what I thought but wasn't sure.
I have another question if you don't mind. I would like to load the wm
surfaces as well, and overlay them on top of the mean functional scan.
However they are in conformed space whereas my mean functional scan is in
functional space. Also there is no :reg sub-option with the -f flag in
freeview. So how can I convert the wm surfaces to functional space?
Sam

On Tue, May 14, 2019 at 4:11 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> 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_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 example_func and aseg file align.
>
> I tried this
> freeview -v s01/example_func.nii s01/aseg.mgz:colormap=lut:reg=reg.dat
> but it does not result in a good alignment
>
> Best regards,
> Sam
>
>
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[Freesurfer] check FS to native registration in freeview

[Sam W.]

External Email - Use Caution

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 example_func and aseg file align.

I tried this
freeview -v s01/example_func.nii s01/aseg.mgz:colormap=lut:reg=reg.dat
but it does not result in a good alignment

Best regards,
Sam
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Re: [Freesurfer] convert aseg to functional space

[Sam W.]

External Email - Use Caution

Thanks again Doug, that makes sense. I was aware that the matrix could be
inverted but I thought we would need --inv for that. Does mri_label2vol
also convert label-to-temp when --label is used, or is this specific to
seg-to-temp conversion?
I'm asking because I also created labels with mri_annotation2label and
tried to convert them to functional space with this command:
mri_label2vol --label labels/lh.precuneus.label --reg reg.dat --subject s01
--o label-in-func.nii --temp example_func.nii --fill-ribbon --hemi lh#
reg.dat comes from bbregister -mov example_func.nii
but this did not work. The label-in-func.nii kept the voxel size and
orientation of the orig.mgz.
Do you have any idea what I'm doing wrong?
Best regards,
Sam

On Thu, Apr 18, 2019 at 6:13 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> 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 registering with bbregister -mov example_func.nii (to
> > get reg.dat), I tried
> > mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
> > aseg-in-func.nii --temp example_func.nii
> > the result looks good, but I'm wondering why it worked. The reg.dat
> > specifies the conversion from func to orig doesn't it? And the
> > mri_label2vol command above does the registration from seg to
> > example_func, which is the opposite direction to what reg.dat encodes.
> > Could you clarify that to me please?
> > Best regards,
> > Sam
> >
> >
> > On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > If you want to transfer a segmentation, then it is better to use
> > mri_label2vol with the --seg option. Run it with --help to get
> > examples.
> > Probably even better is to transfer your functional to anatomical
> > 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 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.nii.gz
> > --o
> > > aseg-in-rawavg.nii --regheader
> > > Is this a valid procedure to convert the aseg to functional space?
> > > I think the recommended way is to register the example_func to
> > > anatomical first:
> > > bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat
> > > and then use mri_vol2vol with the --inv flag
> > > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz
> > --o
> > > aseg-in-rawavg.nii --regheader --inv
> > > But I'm not sure... Could someone confirm which of the above  (or
> > > maybe none of them) is correct?
> > >
> > > Best regards,
> > > Sam
> > >
> > >
> > > ___
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> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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Re: [Freesurfer] convert aseg to functional space

[Sam W.]

External Email - Use Caution

Hi Doug,
Thanks! After registering with bbregister -mov example_func.nii (to get
reg.dat), I tried
mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o
aseg-in-func.nii --temp example_func.nii
the result looks good, but I'm wondering why it worked. The reg.dat
specifies the conversion from func to orig doesn't it? And the
mri_label2vol command above does the registration from seg to example_func,
which is the opposite direction to what reg.dat encodes. Could you clarify
that to me please?
Best regards,
Sam


On Wed, Apr 17, 2019 at 11:27 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> If you want to transfer a segmentation, then it is better to use
> mri_label2vol with the --seg option. Run it with --help to get examples.
> Probably even better is to transfer your functional to anatomical 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 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.nii.gz --o
> > aseg-in-rawavg.nii --regheader
> > Is this a valid procedure to convert the aseg to functional space?
> > I think the recommended way is to register the example_func to
> > anatomical first:
> > bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat
> > and then use mri_vol2vol with the --inv flag
> > mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o
> > aseg-in-rawavg.nii --regheader --inv
> > But I'm not sure... Could someone confirm which of the above  (or
> > maybe none of them) is correct?
> >
> > Best regards,
> > Sam
> >
> >
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[Freesurfer] convert aseg to functional space

[Sam W.]

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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.nii.gz --o
aseg-in-rawavg.nii --regheader
Is this a valid procedure to convert the aseg to functional space?
I think the recommended way is to register the example_func to anatomical
first:
bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat
and then use mri_vol2vol with the --inv flag
mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o
aseg-in-rawavg.nii --regheader --inv
But I'm not sure... Could someone confirm which of the above  (or maybe
none of them) is correct?

Best regards,
Sam
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[Freesurfer] same aparc ROI with mri_label2vol?

[Sam W.]

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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-Post-dorsal.label --temp
mri/rawavg.mgz --subject bert --hemi lh --o roi-in-rawavg.nii.gz --proj
frac 0 1 .1 --fillthresh .3 --reg register.dat
When I load the roi-in-rawavg.nii.gz and the aparc.a2009+aseg.mgz volume in
freeview there are parts of the Cingulum in the aparc.a2009+aseg that are
not included in the roi-in-rawavg. Probably this is related to the
-fillthresh and -proj thresholds. Is there a way to get exactly the same
ROI with mri_label2vol as shown in the aparc.a2008+aseg volume?
Best regards,
Sam
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Re: [Freesurfer] same output with vol2vol and label2vol

[Sam W.]

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Thank you Douglas. So that means I can basically use either one for
freesurfer to native space conversion, is that right? Is there any case in
which label2vol should definitely be used instead of vol2vol?
Best regards,
Sam


On Tue, Apr 16, 2019 at 10:12 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:
> >
> > External Email - Use Caution
> >
> > 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.mgz of bert using both vol2vol
> > and label2vol and found no difference - The resulting output images
> > look exactly the same. Is there really an advantage of using label2vol
> > instead of vol2vol?
> > Thanks!
> > Sam
> >
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[Freesurfer] same output with vol2vol and label2vol

[Sam W.]

External Email - Use Caution

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.mgz of bert using both vol2vol and
label2vol and found no difference - The resulting output images look
exactly the same. Is there really an advantage of using label2vol instead
of vol2vol?
Thanks!
Sam
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[Freesurfer] problems with bbregister's output image

[Sam W.]

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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 --s sub001 --mov f-in-anat.nii.gz --reg reg.lta --surf

However if I click "coronal" tkregister2 shows the coronal surface as
expected, whereas it shows the horizontal volume. If I click "horizontal"
it shows the horizontal surface, whereas it shows the coronal volume. When
I click "sagittal" the sagittal surface and volume are loaded, but the
orientations are different. When I use the example_func as the mov image in
tkregister2 I don't get this issue.
I don't understand why the registered image "f-in-anat.nii.gz" is not
aligned with the anatomical image with the tkregister2 command, because
"f-in-anat.nii.gz" is exactly the output image of the bbregister
transformation from functional to anatomical space, isn't it?
Could someone please help me understand this?

Thanks
Sam
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