Re: [Freesurfer] issue with lesions

[Greve, Douglas N.,Ph.D.]

If they are aligned in tkregisterfv, then you can use use --regheader 
instead of --reg something.lta

On 9/24/19 7:10 PM, Sam W wrote:
>
> 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. 
> mailto: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.
>> mailto: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
>> >>

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 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
>> >>

Re: [Freesurfer] issue with lesions

[Greve, Douglas N.,Ph.D.]

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. 
mailto: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
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu  
>> >
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

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
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] issue with lesions

[Greve, Douglas N.,Ph.D.]

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
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu  
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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Re: [Freesurfer] issue with lesions

[Greve, Douglas N.,Ph.D.]

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]

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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