Dear All, I would like to ask you for some advice about segmenting MRI from infants data.
In particular, these are my questions:
1. if I have two different templates related to two different time points in the 1st year of life, and one of this two is clearly a bad quality MRI image (even visible from the T1 image), the other one is quite good. While with the good one I can reconstruct and segment the image perfectly, with the bad one the software is of course missing lots of part during the reconstruction. Is there the possibility to set up some lower threshold in the ‘recon-all' script to allow the segmentation to get more areas considered, even with this bad quality image?
2. I know that the program register the volume with the MNI305 atlas, that is supposed to work well with adults but not with infants: I am actually trying to avoid in my whole neuroimaging analyses (also with other softwares) to “stretch” the infants brain to an adult one. From the high quality MRI infants image that I was able to segmented, the output seems to be fine, but my concern was whether using as a reference an adult brain could affect the results in my case, although the segmentation seems to be well done.
I checked the FreeSurfer website but I couldn’t find this information! Any advice would be really appreciated!
Best Regards
Chiara
---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
Hello Chiara,
I believe there is some precedent for using Freesurfer for group analysis without warping: http://onlinelibrary.wiley.com/doi/10.1002/hbm.20158/abstract
Anthony
On 2/15/16 1:08 PM, Chiara Bulgarelli wrote:
Dear All, I would like to ask you for some advice about segmenting MRI from infants data.
In particular, these are my questions:
- if I have two different templates related to two different time
points in the 1st year of life, and one of this two is clearly a bad quality MRI image (even visible from the T1 image), the other one is quite good. While with the good one I can reconstruct and segment the image perfectly, with the bad one the software is of course missing lots of part during the reconstruction. Is there the possibility to set up some lower threshold in the ‘recon-all' script to allow the segmentation to get more areas considered, even with this bad quality image?
- I know that the program register the volume with the MNI305 atlas,
that is supposed to work well with adults but not with infants: I am actually trying to avoid in my whole neuroimaging analyses (also with other softwares) to “stretch” the infants brain to an adult one. From the high quality MRI infants image that I was able to segmented, the output seems to be fine, but my concern was whether using as a reference an adult brain could affect the results in my case, although the segmentation seems to be well done.
I checked the FreeSurfer website but I couldn’t find this information! Any advice would be really appreciated!
Best Regards
Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk mailto:cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com mailto:bulgarelli.chiara3@gmail.com
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.
Hi Chiara
1. If the image is bad then I doubt trying to make the code segment "more" will make it significantly more accurate, but if you upload a volume or post an image we can see. Note that Lilla and Eugenio have more recent tools specifically for newborns that might do significantly better.
2. While we do register to MNI space it is almost exclusively for coordinate reporting and shouldn't change the analysis (we don't "stretch" to fit the MNI template or anything)
cheers Bruce
On Mon, 15 Feb 2016, Anthony Dick wrote:
Hello Chiara,
I believe there is some precedent for using Freesurfer for group analysis without warping: http://onlinelibrary.wiley.com/doi/10.1002/hbm.20158/abstract
Anthony
On 2/15/16 1:08 PM, Chiara Bulgarelli wrote: Dear All, I would like to ask you for some advice about segmenting MRI from infants data.
In particular, these are my questions:
- if I have two different templates related to two different time
points in the 1st year of life, and one of this two is clearly a bad quality MRI image (even visible from the T1 image), the other one is quite good. While with the good one I can reconstruct and segment the image perfectly, with the bad one the software is of course missing lots of part during the reconstruction. Is there the possibility to set up some lower threshold in the ‘recon-all' script to allow the segmentation to get more areas considered, even with this bad quality image?
- I know that the program register the volume with the MNI305 atlas,
that is supposed to work well with adults but not with infants: I am actually trying to avoid in my whole neuroimaging analyses (also with other softwares) to “stretch” the infants brain to an adult one. From the high quality MRI infants image that I was able to segmented, the output seems to be fine, but my concern was whether using as a reference an adult brain could affect the results in my case, although the segmentation seems to be well done.
I checked the FreeSurfer website but I couldn’t find this information! Any advice would be really appreciated!
Best Regards
Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
Many thanks for your helpfulness, Dr. Fischl. Your information have been useful for me.
Moreover, I will follow your suggestion: browsing on your website, I understand that Dr. Lilla Zollei could be the right person I can ask for more details.
Best wishes
Chiara
---------------- Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London
cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com
On 15 Feb 2016, at 19:24, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Chiara
If the image is bad then I doubt trying to make the code segment "more" will make it significantly more accurate, but if you upload a volume or post an image we can see. Note that Lilla and Eugenio have more recent tools specifically for newborns that might do significantly better.
While we do register to MNI space it is almost exclusively for coordinate reporting and shouldn't change the analysis (we don't "stretch" to fit the MNI template or anything)
cheers Bruce
On Mon, 15 Feb 2016, Anthony Dick wrote:
Hello Chiara, I believe there is some precedent for using Freesurfer for group analysis without warping: http://onlinelibrary.wiley.com/doi/10.1002/hbm.20158/abstract Anthony On 2/15/16 1:08 PM, Chiara Bulgarelli wrote: Dear All, I would like to ask you for some advice about segmenting MRI from infants data. In particular, these are my questions:
- if I have two different templates related to two different time
points in the 1st year of life, and one of this two is clearly a bad quality MRI image (even visible from the T1 image), the other one is quite good. While with the good one I can reconstruct and segment the image perfectly, with the bad one the software is of course missing lots of part during the reconstruction. Is there the possibility to set up some lower threshold in the ‘recon-all' script to allow the segmentation to get more areas considered, even with this bad quality image? 2. I know that the program register the volume with the MNI305 atlas, that is supposed to work well with adults but not with infants: I am actually trying to avoid in my whole neuroimaging analyses (also with other softwares) to “stretch” the infants brain to an adult one. From the high quality MRI infants image that I was able to segmented, the output seems to be fine, but my concern was whether using as a reference an adult brain could affect the results in my case, although the segmentation seems to be well done. I checked the FreeSurfer website but I couldn’t find this information! Any advice would be really appreciated! Best Regards Chiara
Chiara Bulgarelli PhD Student, Centre for Brain and Cognitive Development Birkbeck College, University of London cbulga01@mail.bbk.ac.uk // bulgarelli.chiara3@gmail.com _______________________________________________ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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.
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Chiara Bulgarelli