[Freesurfer] comparison between two hemisphere in single
Thank you doug for you answer. So now I have two other question. 1- how can I check the inter hemisphere registration quality? e.g. can I check if the parcellation for the two hemisphere are matched well? or there is other ways? 2- how can I correct for multiple correction for single subject? calculate the p vale for each vertex (to find significant difference between the two hemisphere) and correct these for multiple correction. Regards, Ashkan > What is your mris_preproc command line? If you run mris_preproc with > --xhemi, it should give you two frames (left hemi and right hemi). If > you want to compute left-right, then add --paired-diff to the command > line. The output will be on the lh of fsaverage_sym. This can be > displayed on the white, pial, or inflated of fsaverage_sym. You can use > mris_apply_reg to map this back to the subject's native surface if you > want to display it there. > doug > > On 2/19/16 9:18 AM, Ashkan Faghiri wrote: > > Hello, > > > > sorry for asking this again > > > > I want to calculate the difference between the thickness of one > > subjects different hemispheres and show this on pial (left or right or > > even fsaverage_sys). so I have ran : > > > > surfreg --s $subject --t fsaverage_sym --lh > > surfreg --s $subject --t fsaverage_sym --lh --xhemi > > > > for my one subject. now I have two .reg files: > > shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg > > shahi/surf/lh.fsaverage_sym.sphere.reg > > > > If I am understanding this right, these two are the transform matrix > > for both hemisphere of my one subject to fsaverage_sym (*right?*) > > > > if I run mris_preproc with xhemi option I will get a vector which have > > the length equal to number of vertexes. it's values are left-right > > (*or right-left?*). how can I convert this vector to pial or inflated > > surface? and how can I use lh.fsaverage_sym.sphere.reg to register my > > pial directly to fsaverage_sym? > > > > Regards, > > Ashkan > > -- > > -- > > Ashkan Faghiri > > MSc student of Bioelectrical Engineering > > Department of Electrical Engineering > > Sharif University of Technology > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ 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] comparison between two hemisphere in single
Hello, sorry for asking this again I want to calculate the difference between the thickness of one subjects different hemispheres and show this on pial (left or right or even fsaverage_sys). so I have ran : surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi for my one subject. now I have two .reg files: shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg shahi/surf/lh.fsaverage_sym.sphere.reg If I am understanding this right, these two are the transform matrix for both hemisphere of my one subject to fsaverage_sym (*right?*) if I run mris_preproc with xhemi option I will get a vector which have the length equal to number of vertexes. it's values are left-right (*or right-left?*). how can I convert this vector to pial or inflated surface? and how can I use lh.fsaverage_sym.sphere.reg to register my pial directly to fsaverage_sym? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ 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] curved Surface projection
Hello I know it is not the best place to ask this kind of question. But I don't know any place to ask a question like this. I am looking to display "curved Surface projection" for brain mri (like explained in http://www.ajnr.org/content/24/6/1045.full). Can any one suggest me a tool to do this. Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ 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] comparison between two hemisphere in single
Thank you Douglas for your reply. I have perforemed surfreg --s subj1 --t fsaverage_sym --lh surfreg --s subj1--t fsaverage_sym --lh --xhemi mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s subj1 for my *one* subject. as I understand "lh.lh-rh.thickness.sm00.mgh" file is the difference between the two hemisphere of my one subject (it's dimension is 163842 x 1 x 1). so I should check if these values are significantly different than zero, right? but DOF of this vector is 0 so mri_glmfit returns "ERROR: DOF = 0". which is correct I think. I believe I can't do this procedure for single subject. I want to check if there is thickening or thinning between two hemisphere for one subject. what should I do exactly? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ 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] comparison between two hemisphere in single subject
Hello, I want to compare the two hemisphere in one subject (thickness for example). should I use? surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi then what? how can I compare the two hemisphere of one subject? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology ___ 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] fsaverage problem
Hello Bruce, thank you for your reply, and sorry that i couldn't reply on your mail (i don't know how). What do you mean by mapping an image to fsaverage space? do you mean we get a matrix of transformation? and if yes do we have access to this matrix? or do mean that when a subject is added the fsaverage is changed slightly? if the latter is correct, what I am worried are outliers not normal subjects. because they can change the average so much. Regards ___ 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] (no subject)
Hello again, I forgot to ask one of my main questions: averaging subjects to fsaverage. if i run recon-all with -qcache all my subjects will be averaged to fsaverage subject, right? then will the fsaverage change after i do this, and if it change doesn't it affect my future projects? WRG A.Faghiri ___ 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] (no subject)
Hello all, I have two question. 1- I am unable to read a surface to matlab, can you please give me an example. how should i load a surface with overlay to matlab and display it (e.g. do it for bert) 2- another question, can we use another test in place of t-test? how? WRG A.Faghiri ___ 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] (no subject)
hello, I have two question: 1- I use GNU-parallel to run recon-all on my computer. i have 50 or so subject but after processing around 10 subject i get this error: "rm no match found", and the process won't continue. it only give me this error one after another.do you know what is my problem? 2- When i use -qcache and fsaverage folder is present previously from other projects, is this folder average of my new subjects or all the subjects that i have run on this computer? WRG A.Faghiri ___ 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] quality check of T1 scans
hello. we have some T1 scans from a previous experiment. before starting to analyse them i wanted to know if there is any way to check if the quality of the images are good enough for a morphometric analysis. WRG A.Faghiri ___ 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.
