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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
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:
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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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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. < DGREVE@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 CautionHello, 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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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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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. < DGREVE@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 CautionThanks 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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:
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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. <DGREVE@mgh.harvard.edumailto:DGREVE@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 CautionThanks 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. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edumailto:DGREVE@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<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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. < DGREVE@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 CautionThanks 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. < DGREVE@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 CautionThanks 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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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:
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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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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. <DGREVE@mgh.harvard.edu <mailto:DGREVE@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. > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Greve, Douglas N.,Ph.D. -
Sam W