[Freesurfer] Run stats for both hemisphere?
Dear freesurfer experts, I am wring to ask a stupid question, which I did not find the answer in the mailing list. I am going to run stats on the thickness data as described in the tutorial, do I have to run separately for each hemisphere? If I am not wrong, we have to specify the hemi in the data assembling stage. Are we able to run once for both hemis in the glm and correction stage? If not, I am a little confused in the correction stage, which we specify the --2spaces in the simulation. As indicated in the tutorial, this is for adjusting p for both hemis. Another question is about subcortical areas. Do we have to run stats for the cortical and subcortical areas separately? Thanks *-* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia ___ 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] Run stats for both hemisphere?
Thanks Doug, After re-watching these tutorial videos, I think I've understood these questions. Really appreciated for your answer. Regards *-* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia On 4 September 2017 at 09:04, Douglas Greve wrote: > > > On 8/27/17 4:35 AM, Xianwei Che wrote: > > Dear freesurfer experts, > > I am wring to ask a stupid question, which I did not find the answer in > the mailing list. > > I am going to run stats on the thickness data as described in the > tutorial, do I have to run separately for each hemisphere? If I am not > wrong, we have to specify the hemi in the data assembling stage. Are we > able to run once for both hemis in the glm and correction stage? > > When you run recon-all, it will processes both hemis. After that, eg, > mris_preproc, you must specify the hemi > > > If not, I am a little confused in the correction stage, which we specify > the --2spaces in the simulation. As indicated in the tutorial, this is for > adjusting p for both hemis. > > Right, if you are eventually going to analyze both hemis, then you need to > correct for multiple comparisons across both hemispheres. > > > Another question is about subcortical areas. Do we have to run stats for > the cortical and subcortical areas separately? > > Do you mean an ROI volume or surface area analysis? Then, yes. > > > Thanks > > *-* > Mr Xianwei Che > PhD Candidate > Monash Alfred Psychiatry Research Centre (MAPrc) > Central Clinical School & the Alfred > Monash University > Level 4, 607 St Kilda Road, Melbourne 3004, Australia > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 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] group analysis on thickness/mask
Dear experts, I am going to run a group analysis on thickness but limit the results to certain regions, say prefrontal cortex. l did find this thread but failed to make it work on my data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). I know I could extract the signal of the ROI but also interested in this way. Here are my questions: 1. mri_binarize should be working on the average data or the single data in each participant. If it should be on individual data, what the loop should be (if I have a text file SUBJECTS listing the participants). 2. How the --match is used. I --helped the mri_binarize but did not get it. Is it for specifying the ROI by number, say the number of PFC? 3. If I could finish the mask creation and merge to label; do I have to undergo the data concatenating stage (i.e. preproc, surf2surf) or directly move to glm. I saw another thread skipping these stages but it's on volume data ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html). Thank you so much! *-* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia ___ 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] group analysis on thickness/mask
Dear Doug, Thank you for the answer. I will try it out. Regards *-* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia On 12 September 2017 at 01:44, Douglas N Greve wrote: > > > On 09/10/2017 04:02 AM, Xianwei Che wrote: > > Dear experts, > > > > I am going to run a group analysis on thickness but limit the results > > to certain regions, say prefrontal cortex. l did find this thread but > > failed to make it work on my data > > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard. > edu/msg48693.html). > > I know I could extract the signal of the ROI but also interested in > > this way. > > > > Here are my questions: > > 1. mri_binarize should be working on the average data or the single > > data in each participant. If it should be on individual data, what the > > loop should be (if I have a text file SUBJECTS listing the participants). > Actually, I don't know what [subjects] is supposed to mean. You should > include the index for the ROIs you want in the analysis > > 2. How the --match is used. I --helped the mri_binarize but did not > > get it. Is it for specifying the ROI by number, say the number of PFC? > There is no PFC ROI. You will have to piece it together from other ROIs. > You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. > Look in the section for aparc+aseg.mgz > > 3. If I could finish the mask creation and merge to label; do I have > > to undergo the data concatenating stage (i.e. preproc, surf2surf) or > > directly move to glm. I saw another thread skipping these stages but > > it's on volume data > > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard. > edu/msg32190.html). > Yu can move directly to the GLM > > > > Thank you so much! > > > > > > /-/ > > Mr Xianwei Che > > PhD Candidate > > Monash Alfred Psychiatry Research Centre (MAPrc) > > Central Clinical School & the Alfred > > Monash University > > Level 4, 607 St Kilda Road, Melbourne 3004, Australia > > > > > > ___ > > 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 > gr...@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/ > > ___ > 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 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] group analysis on thickness/mask
Dear Doug, After some trial and error I am still not able to run group analysis in ROI manner. Here is my understanding: I need to define a label (mri_binarize ?) in which my ROIs should be labeled as 1 with other regions being 0. Then I can take this label to glm with --lable and then run correction. If this is a right way can you tell me a little bit more of how to do this. I am working on cortical thickness data. Thanks huge *-* Mr Xianwei Che PhD Candidate Monash Alfred Psychiatry Research Centre (MAPrc) Central Clinical School & the Alfred Monash University Level 4, 607 St Kilda Road, Melbourne 3004, Australia On 12 September 2017 at 08:42, Xianwei Che wrote: > Dear Doug, > > Thank you for the answer. I will try it out. > > Regards > > *---------* > Mr Xianwei Che > PhD Candidate > Monash Alfred Psychiatry Research Centre (MAPrc) > Central Clinical School & the Alfred > Monash University > Level 4, 607 St Kilda Road, Melbourne 3004, Australia > > On 12 September 2017 at 01:44, Douglas N Greve > wrote: > >> >> >> On 09/10/2017 04:02 AM, Xianwei Che wrote: >> > Dear experts, >> > >> > I am going to run a group analysis on thickness but limit the results >> > to certain regions, say prefrontal cortex. l did find this thread but >> > failed to make it work on my data >> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu >> /msg48693.html). >> > I know I could extract the signal of the ROI but also interested in >> > this way. >> > >> > Here are my questions: >> > 1. mri_binarize should be working on the average data or the single >> > data in each participant. If it should be on individual data, what the >> > loop should be (if I have a text file SUBJECTS listing the >> participants). >> Actually, I don't know what [subjects] is supposed to mean. You should >> include the index for the ROIs you want in the analysis >> > 2. How the --match is used. I --helped the mri_binarize but did not >> > get it. Is it for specifying the ROI by number, say the number of PFC? >> There is no PFC ROI. You will have to piece it together from other ROIs. >> You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. >> Look in the section for aparc+aseg.mgz >> > 3. If I could finish the mask creation and merge to label; do I have >> > to undergo the data concatenating stage (i.e. preproc, surf2surf) or >> > directly move to glm. I saw another thread skipping these stages but >> > it's on volume data >> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu >> /msg32190.html). >> Yu can move directly to the GLM >> > >> > Thank you so much! >> > >> > >> > /-/ >> > Mr Xianwei Che >> > PhD Candidate >> > Monash Alfred Psychiatry Research Centre (MAPrc) >> > Central Clinical School & the Alfred >> > Monash University >> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia >> > >> > >> > ___ >> > 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 >> gr...@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/ >> >> ___ >> 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 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.
