Re: [Freesurfer] : cortical thickness ceiling (using an ROI mask)
Hi Kari
what do you mean when you say "when I look at them in freeviewer the voxels
are definitely not in the correct spot". Do you mean the spectroscopy
voxels?
cheers
Bruce
On Fri, 22 Jul 2016, Kari Parsons wrote:
> Hi Bruce,
>
> Yes, I agree it doesn't seem right. They're LAG and ACG (I'm using
> spectroscopy voxels as my ROIs). The surfaces look reasonable when I'm
> running through the suggested steps on the freesurfer website for getting
> the surface thickness when using an roi as a mask, but when I look at
> them in freeviewer the voxels are definitely not in the correct spot
> (they're pretty far off).
>
> The acquisition parameters for the scan were pretty standard (BRAVO
> sequence with 1 mm^3 isotropic voxels). The steps that I ran through
> with the spectroscopy voxel were:
>
> tkmedit -f ${subj_T1} -overlay ${spectroscopy_voxel_mask} -fthresh 0.5
>
> mri_vol2surf --mov ${spectroscopy_voxel_mask} --hemi lh --out
> lh.${subj_number}.ACG.mgh
>
> cd ${subj_number}/surf
>
> tksurfer ${subj_number} lh inflated -overlay lh.${subj_number}.ACG.mgh
> -fthresh 0.5
>
> mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval
> lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
>
> mri_segstats --seg lh.${subj_number}.ACG.mgh --in
> ${subj_number}/surf/lh.thickness.fsaverage.mgh --sum
> segstats-${subj_number}.txt
>
> Thanks very much,
> Kari
>
> On 2016-06-02, at 6:53 PM, Bruce Fischl wrote:
>
>> Hi Kari
>>
>> the average thickness in some ROIs is 5mm??? Like which ones? That
>> certainly seems like something is wrong. Do the surfaces look accurate?
>> What were the parameters/resolution/sequence of the data you gave to
>> recon-all?
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 3 Jun 2016, Kari Parsons wrote:
>>
>>> Hi,
>>>
>>>I'm using ROI masks (spectroscopy voxels) to get cortical thickness
>>> values. I'm pretty much following the tutorial online
>>> ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks
>>> like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and
>>> I'm getting that as the maximum cortical thickness for a fair number of
>>> subject's ROI. I'd really like to hear thoughts on this: if it might be
>>> indicative of some error happening and if my mean or range cortical
>>> thickness is going to be thrown off by it?
>>>
>>> Thanks for your help,
>>> Kari
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
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>>
>>
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>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
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>> dispose of the e-mail.
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>
>
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>
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Re: [Freesurfer] : cortical thickness ceiling (using an ROI mask)
Hi Bruce,
Yes, I agree it doesn't seem right. They're LAG and ACG (I'm using
spectroscopy voxels as my ROIs). The surfaces look reasonable when I'm running
through the suggested steps on the freesurfer website for getting the surface
thickness when using an roi as a mask, but when I look at them in freeviewer
the voxels are definitely not in the correct spot (they're pretty far off).
The acquisition parameters for the scan were pretty standard (BRAVO
sequence with 1 mm^3 isotropic voxels). The steps that I ran through with the
spectroscopy voxel were:
tkmedit -f ${subj_T1} -overlay ${spectroscopy_voxel_mask} -fthresh 0.5
mri_vol2surf --mov ${spectroscopy_voxel_mask} --hemi lh --out
lh.${subj_number}.ACG.mgh
cd ${subj_number}/surf
tksurfer ${subj_number} lh inflated -overlay lh.${subj_number}.ACG.mgh -fthresh
0.5
mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval
lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
mri_segstats --seg lh.${subj_number}.ACG.mgh --in
${subj_number}/surf/lh.thickness.fsaverage.mgh --sum segstats-${subj_number}.txt
Thanks very much,
Kari
On 2016-06-02, at 6:53 PM, Bruce Fischl wrote:
> Hi Kari
>
> the average thickness in some ROIs is 5mm??? Like which ones? That
> certainly seems like something is wrong. Do the surfaces look accurate?
> What were the parameters/resolution/sequence of the data you gave to
> recon-all?
>
> cheers
> Bruce
>
>
> On Fri, 3 Jun 2016, Kari Parsons wrote:
>
>> Hi,
>>
>>I'm using ROI masks (spectroscopy voxels) to get cortical thickness
>> values. I'm pretty much following the tutorial online
>> ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks
>> like Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm
>> getting that as the maximum cortical thickness for a fair number of
>> subject's ROI. I'd really like to hear thoughts on this: if it might be
>> indicative of some error happening and if my mean or range cortical
>> thickness is going to be thrown off by it?
>>
>> Thanks for your help,
>> Kari
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] : cortical thickness ceiling (using an ROI mask)
Hi Kari
the average thickness in some ROIs is 5mm??? Like which ones? That
certainly seems like something is wrong. Do the surfaces look accurate?
What were the parameters/resolution/sequence of the data you gave to
recon-all?
cheers
Bruce
On Fri, 3 Jun 2016, Kari Parsons wrote:
> Hi,
>
> I'm using ROI masks (spectroscopy voxels) to get cortical thickness
> values. I'm pretty much following the tutorial online
> ('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like
> Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm
> getting that as the maximum cortical thickness for a fair number of subject's
> ROI. I'd really like to hear thoughts on this: if it might be indicative of
> some error happening and if my mean or range cortical thickness is going to
> be thrown off by it?
>
> Thanks for your help,
> Kari
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] : cortical thickness ceiling (using an ROI mask)
Hi,
I'm using ROI masks (spectroscopy voxels) to get cortical thickness
values. I'm pretty much following the tutorial online
('VolumeRoiCorticalThickness') as I'm quite new to Freesurfer. It looks like
Freesurfer has a maximum of cortical thickness ceiling at 5 mm, and I'm getting
that as the maximum cortical thickness for a fair number of subject's ROI. I'd
really like to hear thoughts on this: if it might be indicative of some error
happening and if my mean or range cortical thickness is going to be thrown off
by it?
Thanks for your help,
Kari
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
