Re: [Freesurfer] Hippocampal subfields total volume differences

[Mojmír Vinkler]

Wow, longitudinal segmentation is absolutely awesome! It reduced our
measurement error by more than 30%. I can't wait when the hippocampal
longitudinal segmentation is ready.

By the way, I want to run (cross-sectional) hippocampal subfields on
longitudinal data using additional T2 with lower resolution and I was
wondering if I should use multispectral segmentation

recon-all -s  -hippocampal-subfields-T1T2  

or just additional scan

recon-all -s  -hippocampal-subfields-T2   

Since my T1 and T2 scans are quite well aligned, I wanted to use
-hippocampal-subfields-T2,
but I saw you recommending T1T2 in mailing list. Thanks!

(I'm also blocked by a bug with .ctf files
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48412.html,
but I'm fine with waiting for fix)

Thanks!
Mojmir

On Fri, Jul 15, 2016 at 12:33 PM Iglesias, Eugenio 
wrote:

> Dear Mojmir,
> using ~400 subjects, we found that the subfield module was a bit better
> than the ASEG volumes at discriminating Alzheimer’s patients from controls
> (see the Neuorimage paper). But, in any case, the difference is small.
> Regarding longitudinal segmentation: we just got a paper about this
> accepted, see
>
> http://www.nmr.mgh.harvard.edu/~iglesias/pdf/Neuroimage_2016_longitudinal.pdf
> I still need to find time to clean up the code and put it up on
> FreeSurfer. For the time being, you can run the subfield module on the
> longitudinally analyzed recons (method “L-INIT” in the paper).
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 15 Jul 2016, at 09:00, Mojmír Vinkler  wrote:
>
> Hi Juan,
>
> Thanks! You're right, they really are tightly correlated (although their
> absolute values differ by 30%). We tried it on couple of subjects, but
> didn't find subfields to be significantly better than aseg stats though. By
> the way, is Freesurfer capable of using multiple scans from the same
> subject (longitudinal study, same modality) to make more precise
> measurements? For example by using T1 from the same subject / different
> time instead of T2 in subfields?
>
> Thanks!
> Mojmir
>
> On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio 
> wrote:
>
>> Hi Mojmir,
>> ASEG typically gives a larger estimate of the volume, though highly
>> correlated with that from the subfield package. We have found the
>> measurements from the subfield package to be a bit more reliable, though.
>> Cheers,
>> Eugenio
>>
>> Juan Eugenio Iglesias
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 13 Jul 2016, at 16:07, Mojmír Vinkler 
>> wrote:
>>
>> Hi experts,
>>
>> I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal
>> subfields segmentation. I only need to measure total hippocampus volume,
>> but measurements from basic `recon-all` were too volatile and I was hoping
>> that using subfields with T2 modality would reduce variance. However,
>> volume measured by hippocampal subfields is significantly different from
>> volume in aseg.stats.
>>
>> Here are volumes for right hippocampus from various methods:
>> aseg.stats - 3312.8
>> rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8
>> rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) -
>> 2503.97
>> rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation)
>> - 2596.09
>>
>> I checked labeling visually and there were no obvious problems. Is such
>> a large difference common? Am I missing something? What number should be
>> most trusted?
>>
>> Thanks for any hints!
>> Mojmir
>>
>> ___
>> Freesurfer mailing list
>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> 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.
>>
> 

Re: [Freesurfer] Hippocampal subfields total volume differences

[Iglesias, Eugenio]

Dear Mojmir,
using ~400 subjects, we found that the subfield module was a bit better than 
the ASEG volumes at discriminating Alzheimer’s patients from controls (see the 
Neuorimage paper). But, in any case, the difference is small.
Regarding longitudinal segmentation: we just got a paper about this accepted, 
see
http://www.nmr.mgh.harvard.edu/~iglesias/pdf/Neuroimage_2016_longitudinal.pdf
I still need to find time to clean up the code and put it up on FreeSurfer. For 
the time being, you can run the subfield module on the longitudinally analyzed 
recons (method “L-INIT” in the paper).
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 15 Jul 2016, at 09:00, Mojmír Vinkler 
mailto:mojmir.vink...@gmail.com>> wrote:

Hi Juan,

Thanks! You're right, they really are tightly correlated (although their 
absolute values differ by 30%). We tried it on couple of subjects, but didn't 
find subfields to be significantly better than aseg stats though. By the way, 
is Freesurfer capable of using multiple scans from the same subject 
(longitudinal study, same modality) to make more precise measurements? For 
example by using T1 from the same subject / different time instead of T2 in 
subfields?

Thanks!
Mojmir

On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Hi Mojmir,
ASEG typically gives a larger estimate of the volume, though highly correlated 
with that from the subfield package. We have found the measurements from the 
subfield package to be a bit more reliable, though.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 13 Jul 2016, at 16:07, Mojmír Vinkler 
mailto:mojmir.vink...@gmail.com>> wrote:

Hi experts,

I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields 
segmentation. I only need to measure total hippocampus volume, but measurements 
from basic `recon-all` were too volatile and I was hoping that using subfields 
with T2 modality would reduce variance. However, volume measured by hippocampal 
subfields is significantly different from volume in aseg.stats.

Here are volumes for right hippocampus from various methods:
aseg.stats - 3312.8
rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8
rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) - 2503.97
rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation) - 
2596.09

I checked labeling visually and there were no obvious problems. Is such a large 
difference common? Am I missing something? What number should be most trusted?

Thanks for any hints!
Mojmir
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Re: [Freesurfer] Hippocampal subfields total volume differences

[Mojmír Vinkler]

Hi Juan,

Thanks! You're right, they really are tightly correlated (although their
absolute values differ by 30%). We tried it on couple of subjects, but
didn't find subfields to be significantly better than aseg stats though. By
the way, is Freesurfer capable of using multiple scans from the same
subject (longitudinal study, same modality) to make more precise
measurements? For example by using T1 from the same subject / different
time instead of T2 in subfields?

Thanks!
Mojmir

On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio 
wrote:

> Hi Mojmir,
> ASEG typically gives a larger estimate of the volume, though highly
> correlated with that from the subfield package. We have found the
> measurements from the subfield package to be a bit more reliable, though.
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 13 Jul 2016, at 16:07, Mojmír Vinkler  wrote:
>
> Hi experts,
>
> I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal
> subfields segmentation. I only need to measure total hippocampus volume,
> but measurements from basic `recon-all` were too volatile and I was hoping
> that using subfields with T2 modality would reduce variance. However,
> volume measured by hippocampal subfields is significantly different from
> volume in aseg.stats.
>
> Here are volumes for right hippocampus from various methods:
> aseg.stats - 3312.8
> rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8
> rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) -
> 2503.97
> rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation)
> - 2596.09
>
> I checked labeling visually and there were no obvious problems. Is such a
> large difference common? Am I missing something? What number should be most
> trusted?
>
> Thanks for any hints!
> Mojmir
>
> ___
> Freesurfer mailing list
> 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.
>
>
> ___
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>
>
> 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] Hippocampal subfields total volume differences

[Iglesias, Eugenio]

Hi Mojmir,
ASEG typically gives a larger estimate of the volume, though highly correlated 
with that from the subfield package. We have found the measurements from the 
subfield package to be a bit more reliable, though.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 13 Jul 2016, at 16:07, Mojmír Vinkler 
mailto:mojmir.vink...@gmail.com>> wrote:

Hi experts,

I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields 
segmentation. I only need to measure total hippocampus volume, but measurements 
from basic `recon-all` were too volatile and I was hoping that using subfields 
with T2 modality would reduce variance. However, volume measured by hippocampal 
subfields is significantly different from volume in aseg.stats.

Here are volumes for right hippocampus from various methods:
aseg.stats - 3312.8
rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8
rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) - 2503.97
rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation) - 
2596.09

I checked labeling visually and there were no obvious problems. Is such a large 
difference common? Am I missing something? What number should be most trusted?

Thanks for any hints!
Mojmir
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[Freesurfer] Hippocampal subfields total volume differences

[Mojmír Vinkler]

Hi experts,

I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields
segmentation. I only need to measure total hippocampus volume, but
measurements from basic `recon-all` were too volatile and I was hoping that
using subfields with T2 modality would reduce variance. However, volume
measured by hippocampal subfields is significantly different from volume in
aseg.stats.

Here are volumes for right hippocampus from various methods:
aseg.stats - 3312.8
rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8
rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) - 2503.97
rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation)
- 2596.09

I checked labeling visually and there were no obvious problems. Is such a
large difference common? Am I missing something? What number should be most
trusted?

Thanks for any hints!
Mojmir
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