Dear FreeSurfer expert
I wonder that whether I can use the command aparc2statstable to get the cortical thickness or is it better to get the cortical thickness of a volume defined ROI or is there the easy way to get the most accurate cortical thickness from ROI
I am following the pipeline "VolumeRoiCorticalThickness" but I do not understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii.
Sorry if this question is too obvious for me to overlook something. Any help is appreciated since I am newbie on FreeSurfer. Best regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
You can use aparcstats2table to report the thickness, surface area, and volume as a table from a group of subjects. Is that what you want?
On 03/13/2017 02:01 AM, Duy Nguyen wrote:
Dear FreeSurfer expert
I wonder that whether I can use the command aparc2statstable to get the cortical thickness or is it better to get the cortical thickness of a volume defined ROI or is there the easy way to get the most accurate cortical thickness from ROI
I am following the pipeline "VolumeRoiCorticalThickness" but I do not understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii.
Sorry if this question is too obvious for me to overlook something. Any help is appreciated since I am newbie on FreeSurfer. Best regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doughlas
Thank you for your quick response. I am studying the group analysis from the tutorial. I would like to ask if I could change to the cortical thickness data from the specific ROI I am interested in to analyze. If it can, please show me how.
Thank you again and Best regards Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com duy.nguyenbme@gmail.com*
On Tue, Mar 14, 2017 at 3:01 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You can use aparcstats2table to report the thickness, surface area, and volume as a table from a group of subjects. Is that what you want?
On 03/13/2017 02:01 AM, Duy Nguyen wrote:
Dear FreeSurfer expert
I wonder that whether I can use the command aparc2statstable to get the cortical thickness or is it better to get the cortical thickness of a volume defined ROI or is there the easy way to get the most accurate cortical thickness from ROI
I am following the pipeline "VolumeRoiCorticalThickness" but I do not understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii.
Sorry if this question is too obvious for me to overlook something. Any help is appreciated since I am newbie on FreeSurfer. Best regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
If you run aparcstats2table with the -h option, it will give you documentation and examples. You can also find examples on the tutorial. aparcstats2table will extract all ROIs, but you can choose which one you want after that. Sorry, I'm not sure this has answered your question, but I'm not entirely sure what more you are asking.
On 03/16/2017 08:45 AM, Duy Nguyen wrote:
Dear Doughlas
Thank you for your quick response. I am studying the group analysis from the tutorial. I would like to ask if I could change to the cortical thickness data from the specific ROI I am interested in to analyze. If it can, please show me how.
Thank you again and Best regards Duy Nguyen
*--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme@gmail.com mailto:duy.nguyenbme@gmail.com*
On Tue, Mar 14, 2017 at 3:01 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You can use aparcstats2table to report the thickness, surface area, and volume as a table from a group of subjects. Is that what you want? On 03/13/2017 02:01 AM, Duy Nguyen wrote: > Dear FreeSurfer expert > > I wonder that whether I can use the command aparc2statstable to get > the cortical thickness or is it better to get the cortical thickness > of a volume defined ROI or is there the easy way to get the most > accurate cortical thickness from ROI > > I am following the pipeline "VolumeRoiCorticalThickness" but I do not > understand how I can get ROI mask called ROI5.nii and TT_avg152T1.nii. > > Sorry if this question is too obvious for me to overlook something. > Any help is appreciated since I am newbie on FreeSurfer. > Best regards, > *--v-- Peace --v--* > *Duy Nguyễn * > *Biomedical Engineering Department- IU HCMC* > *Cell: (+84)909999056* > *Email: duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com> <mailto:duy.nguyenbme@gmail.com <mailto:duy.nguyenbme@gmail.com>>* > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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Duy Nguyen