Try
mri_segstats --seg Cluster1_R.nii.gz --id 1 --sum sum.R.dat
That will give you the number of voxels that have a value=1 times the
size of the voxel (so the volume). It will not be in MNI space unless
the nifti files you sent are in MNI space.
On 12/21/2022 5:42 PM, Beatriz Cavendish
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Hello,
I would like to know the step by step to obtain volume (mm3) from a
volumetric mask in the MNI space (follow the attached nifti file). I
checked the forum but the tutorials are for surface extraction and cortical
thickness.
Yours sincerely,
Hi Rene,
I don’t see any errors in your recon-all log.
I’m wondering if ‘ln -sf’ works on Mac.
Can you try the following:
1. cd to ‘surf’ directory
2. ln -sf lh.pial.T1 testlink
3. ls -l testlink
4. ls -lt ?h.pial* ?h.white* ?h*.sphere.reg
Can you send the output from those commands?
Yujing
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Greetings,
I am writing regarding the request to grant the password to
unzip FS_7_2_0_ubuntu_18_04_06.ova file
Thanks and regards,
Ganeshkaran
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Hi Andrew,
Sorry for the late response. Copied below is the suggestions from Martin.
“
I looked at those images. A few points:
- bias fields seem to be very different, I think using --iscale helps a little
here, if very high accuracy of the registration is important, one should do a
bias
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I do not get the cingulate, for example...
On Wed, Dec 21, 2022 at 4:35 PM Rosalia Dacosta Aguayo
wrote:
> Hi Douglas,
>
> I am only getting the main volumes like putamen right and left, amygdala,
> right and left...just gross anatomy.
>
> Rosie
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Hi Douglas,
I am only getting the main volumes like putamen right and left, amygdala,
right and left...just gross anatomy.
Rosie
On Wed, Dec 21, 2022 at 4:32 PM Douglas N. Greve
wrote:
> what are you not getting?
>
> On 12/21/2022 10:11 AM,
what are you not getting?
On 12/21/2022 10:11 AM, Rosalia Dacosta Aguayo wrote:
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Maybe is -qcache ?
*
*
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
Dear Freesurfer group,
Could you tell me which is the flag I need to use
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Maybe is -qcache ?
On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo
wrote:
> Dear Freesurfer group,
>
> Could you tell me which is the flag I need to use to get all the brain
> parcellation when I run recon-all? It seems I am getting the
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Dear Freesurfer group,
Could you tell me which is the flag I need to use to get all the brain
parcellation when I run recon-all? It seems I am getting the tables with
few volumes and I guess there is something wrong.
Best wishes and Merry Christmas,
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Dear Dr Greve, thank you so much for answers to my questions.
Regarding question 2, yes I meant leaving only columns I need, for instance
I am interested in lobes. I ran these commands on my data
# mri_annotation2label --subject subject --hemi lh
Not sure what it will do then. It will put vertices in that region. When
you run samseg, add --save-mesh
On 12/21/2022 8:18 AM, Don Se wrote:
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Ah, I see. However, I would like to get it for brain scans with a
pathology (a tumour).
2022-12-21, tr, 05:39
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Ah, I see. However, I would like to get it for brain scans with a pathology
(a tumour).
2022-12-21, tr, 05:39 Douglas N. Greve rašė:
> Why not samseg?
>
> On 12/20/2022 12:50 PM, Donatas Sederevičius wrote:
>
> External Email - Use Caution
>
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