9 Feb
2018
9 Feb
'18
1:07 p.m.
If you've already run qcache, then it will be in the subject/surf folder with a name like lh.thickness.fsaverage.fwhm10.mgz
On 2/6/18 11:22 PM, 박경일 wrote:
Thanks, Bruce. From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are different among subjects. As far as i understand, it is the subject space, not common space. is that right? If so, how can i get the thickness values in common space to compare the vertex data between subjects?
(I'd already run recon-all and qcache process.)
Kyung
2018-02-03 0:33 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:
Hi Kyung you should look at the mris_convert help. It has an example of how to convert a scalar overlay like a curv file to ascii: Convert a scalar overlay file to ascii: mris_convert -c lh.thickness lh.white lh.thickness.asc it needs the surface as an input to do the conversion properly. cheers Bruce On Fri, 2 Feb 2018, 박경일 wrote: Hi Bruce I found a directory having a file with ".curv", open terminal and run following command. [root@localhost surf]# mris_convert rh.curv rh.curv.asc nquads=4587523, nvertices=476 ERROR: MRISread: file 'rh.curv' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory what is wrong? Thanks as always. Kyung 2018-01-31 0:04 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Kyung the thickness values are stored as "curvature" file format that you can load into matlab with read_curv.m. Alternatively, you can convert them to ascii with mris_convert and do what you want with them. For each index, you can look up its location on the white or pial (or whatever surface). That is, for the 2nd thickness value (index 1), you would go find vertex #1 on the other surface and read its location that way cheers Bruce On Tue, 30 Jan 2018, 박경일 wrote: Hi Bruce, I am very new for FS, so did not understand you comments completely. sorry.. For cortical thickness from each vertex in one subject, which scripts should follow "mris_convert"? And another question is how to recognize the location of each vertex in brain finally. thank you so much Kyung 2017-11-13 10:06 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: p.s. if you want the vertices to correspond, first run recon-all -qcache for each subject. That will generate a set of thickness maps in fsaverage space at predefined smoothing levels (so that the vertex numbers correspond across subjects) On Mon, 13 Nov 2017, 박경일 wrote: Hi Bruce,What I want is the values of cortical thickness in each vertex in each subject. Is that possible? Thanks so much. Kyung 2017-11-13 0:43 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Kyung you can load them into matlab or convert them to ascii if you want Bruce On Sun, 12 Nov 2017, 박경일 wrote: Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung _______________________________________________ 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. -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kipark@snuh.org <mailto:kipark@snuh.org> / ideopki@gmail.com <mailto:ideopki@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> 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. -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kipark@snuh.org <mailto:kipark@snuh.org> / ideopki@gmail.com <mailto:ideopki@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> 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. -- Kyung-Il Park, MD, PhD. Professor, Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center. Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 Email: kipark@snuh.org <mailto:kipark@snuh.org> / ideopki@gmail.com <mailto:ideopki@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> 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.--
Kyung-Il Park, MD, PhD.
Professor,
Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center.
Office: 82-2-2112-5756 / Fax: 82-2-2112-5635
Email: kipark@snuh.org mailto:kipark@snuh.org / ideopki@gmail.com mailto:ideopki@gmail.com
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