[Freesurfer] Problem of VolumeRoiCorticalThickness
Hi all, I want to extract cortical thickness for a ROI (dlpfc) which was defined in volume space. I search it in Freesurfer Wiki and find the description in website (http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness). But, in the second, it said it need an T1 volume (average of subjects) which was called TT_avg152T1.nii. How can I calculate it? What is the voxels of ROI and T1.nii, 1*1*1 mm2? Thank you Wang Kangcheng___ 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] problem of Label file
Dear Bruce, The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right? Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China ___ 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] problem of Label file
Dear Bruce, I creat the file of label according to the manual of free surfer. The website was http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File --> Save Label. Thank you very much. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl 写道： > hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a > detailed description of how you created the label? This seems like a bug. > > cheers > Bruce > > > On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: > >> I’m sorry. I am a new learner of freesurfer and don’t know whether the >> numbers are reasonable. The sig.mgh and file of label was in the attachment. >> Thank you. >> > > > 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] problem of Label file
Dear Bruce No, I used QDEC to create label. It should be fsaverage. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午10:00，Bruce Fischl 写道： > using tksurfer? On what fsaverage? > > On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: > >> Dear Bruce, >> I creat the file of label according to the manual of free surfer. The >> websitewas >> http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. >> >> (1) hold down shift then left click and drag to draw the ROI. >> (2) save the label by selecting File --> Save Label. >> Thank you very much. >> >> Wang Kangcheng >> Faculty of Psychology, Southwest University, China >> Email: kangchengwang0...@gmail.com / wangkangcheng@163.com >> Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China >> 在 2014年6月19日，下午9:45，Bruce Fischl 写道： >> >> hmmm, the sig.mgh looks fine. No outlier values in it. Can you >> give us a detailed description of how you created the label? >> This seems like a bug. >> >> cheers >> Bruce >> >> On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: >> >>I’m sorry. I am a new learner of freesurfer and >>don’t know whether the numbers are reasonable. The >>sig.mgh and file of label was in the attachment. >>Thank you. >> >> 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] problem of Label file
Dear Bruce No, I used QDEC to create label. It should be fsaverage. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午10:00，Bruce Fischl 写道： > using tksurfer? On what fsaverage? > > On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: > >> Dear Bruce, >> I creat the file of label according to the manual of free surfer. The >> websitewas >> http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. >> >> (1) hold down shift then left click and drag to draw the ROI. >> (2) save the label by selecting File --> Save Label. >> Thank you very much. >> >> Wang Kangcheng >> Faculty of Psychology, Southwest University, China >> Email: kangchengwang0...@gmail.com / wangkangcheng@163.com >> Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China >> 在 2014年6月19日，下午9:45，Bruce Fischl 写道： >> >> hmmm, the sig.mgh looks fine. No outlier values in it. Can you >> give us a detailed description of how you created the label? >> This seems like a bug. >> >> cheers >> Bruce >> >> On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: >> >>I’m sorry. I am a new learner of freesurfer and >>don’t know whether the numbers are reasonable. The >>sig.mgh and file of label was in the attachment. >>Thank you. >> >> 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] Why the result was not same for the same subject
Dear experts I used freesurfer (Version 5.3) to calculate one subject for ten times and extract the number of each index. However, I found that the number was different each time. Is this normal? Why the result was not same for the same subject? Thank you Wang Kangcheng ___ 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] Why the result was not same for the same subject
Dear Bruce Yes. The following is an example result for the subject (The id from Sub_1 to Sub_10 is the same subject) that I calculate ten times. rh.aparc.a2009s.volume rh_G_and_S_frontomargin_volume Sub_1 1713 Sub_2 1950 Sub_3 1789 Sub_4 1783 Sub_5 1879 Sub_6 1778 Sub_7 1892 Sub_8 1782 Sub_9 1799 Sub_10 1799 Thank you Wang Kangcheng ___ 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.
