Re: [Freesurfer] Segmentation question
HI Yusif you can read our 1999 paper (Anders Dale first author) for the basics, although it has evolved considerably since then cheers Bruce On Thu, 23 Feb 2017, yusif Al-kheder wrote: > Hello, > I was wondering how does Freesurfer segment the white matter from the grey > matter. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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] Segmentation question
Hello, I was wondering how does Freesurfer segment the white matter from the grey matter. ___ 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] segmentation question
There is no separate label for Wernike's (it is a functional, not anatomical, definition). Heschl's gyrus is separate from STG. Perhaps Christophe can weigh in on his labels. On 11/5/15 11:42 AM, Ahtam, Banu wrote: Dear All, I am new to freesurfer and would appreciate your help with the following questions. I tried to look through the previous posts but couldn’t find the answers to all my questions. Thank you in advance. Best, Banu My question: I wanted to look at certain language related regions in the brain such as Heschl’s gyrus, Wernicke’s area, and planum temporale. I am looking at the lh.aparc.stats file right now. I see that there is a label for superior temporal gyrus which would involve all these three regions. I was wondering if Heschl’s gyrus, Wernicke’s area, and planum temporale are also segmented and labelled separately. In the previous posts, I saw that anterior portion of transverse temporal corresponds to Heschl’s gyrus, and under lh.aparc.stats file it is labelled as transversetemporal. I am still not sure about planum temporale and Wernicke’s areas though. I saw planum temporale in the lh.aparc.a2009s.stats file (it is called G_temp_sup-Plan-tempo, if I am correct). However, I am not sure if it is a good idea getting values from two different stat files (planum temporale from this one, and the rest from the other). Also, could you tell me if Wernicke’s area is segmented, and if so how is it labelled? Banu Ahtam, DPhil Post-doctoral Research Fellow Boston Children's Hospital Fetal-Neonatal Neuroimaging & Developmental Science Center http://childrenshospital.org/FNNDSC ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] segmentation question
Dear All, I am new to freesurfer and would appreciate your help with the following questions. I tried to look through the previous posts but couldn’t find the answers to all my questions. Thank you in advance. Best, Banu My question: I wanted to look at certain language related regions in the brain such as Heschl’s gyrus, Wernicke’s area, and planum temporale. I am looking at the lh.aparc.stats file right now. I see that there is a label for superior temporal gyrus which would involve all these three regions. I was wondering if Heschl’s gyrus, Wernicke’s area, and planum temporale are also segmented and labelled separately. In the previous posts, I saw that anterior portion of transverse temporal corresponds to Heschl’s gyrus, and under lh.aparc.stats file it is labelled as transversetemporal. I am still not sure about planum temporale and Wernicke’s areas though. I saw planum temporale in the lh.aparc.a2009s.stats file (it is called G_temp_sup-Plan-tempo, if I am correct). However, I am not sure if it is a good idea getting values from two different stat files (planum temporale from this one, and the rest from the other). Also, could you tell me if Wernicke’s area is segmented, and if so how is it labelled? Banu Ahtam, DPhil Post-doctoral Research Fellow Boston Children's Hospital Fetal-Neonatal Neuroimaging & Developmental Science Center http://childrenshospital.org/FNNDSC ___ 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] Segmentation question
FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi ___ 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] Segmentation question
Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi ___ 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] Segmentation question
Hi Rashmi, Several of the morphometry stats were changed between 5.1 and 5.3. I don't remember the specifics, but Doug or someone else on the list may know. Alternatively, you could use the mri_segstats from 5.3 to calculate the morphometry stats for your 5.1 data. -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: I am using version V5.1.0 is it different for that or the information is the same irrespective of the version I use. Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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
Re: [Freesurfer] Segmentation question
Here is the recon-all table for 5.1, see the segstats step. You can also search for that flag in the recon-all script and see what input/flags are passed to mri_segstats. https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.1 On Thu, 7 Nov 2013, Rashmi Singh wrote: Can you tell me what is the input file that free surfer used to calculate STV. I am not sure the webpage below gives that information. Thanks, Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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
Re: [Freesurfer] Segmentation question
Can you tell me what is the input file that free surfer used to calculate STV. I am not sure the webpage below gives that information. Thanks, Rashmi On 11/7/13 1:57 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Rashmi, This page has the definition you are looking for (FS v5.3). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi 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
[Freesurfer] segmentation question
Happy soon-to-be Independence Day FreeSurfers, I am in the process of trying to fix the segmentation of my surface and I had a few general questions: Is editing the voxels the only way one can change what is counted as white vs. grey matter? Is there any way to indicate with control points what is grey vs. white vs. CSF? It has been particularly trying with monkey data considering how much extra tissue they have surrounding their brain :) that doesn't always get clipped using the strip skull step. Thanks! Andy Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0921 mobile: (202) 679-1279 [EMAIL PROTECTED]___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
