Hi Dorian you can load the aparc.annot for each subject and use it to chek if the spherical registration worked ok. It's easy enough to write a script to load these for each subject, then write a tif file with a medial view, and zip through them all with nmovie
cheers Bruce On Thu, 9 Mar 2017, Dorian P. wrote: > Thank you Bruce, Douglas. > Yes, I think thicknesses were obtained with v 5.3.0. There might be errors > as Bruce pointed out, I am going now through all maps to check them. This > makes me think of a question. Volumetric template registrations sometimes go > wrong. Does this happen also to surface registrations in FS sometimes ??? > > I am using other statistics, not glm, but thanks for suggesting it. Data are > imported and exported in R using some R functions I built myself, nothing > fancy, just using intermediate text files to get what I want and put it back > for visualization. > > Thank you > > On Thu, Mar 9, 2017 at 11:23 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > > On 03/08/2017 09:27 PM, Dorian P. wrote: > > Hi Freesurfers, > > > > I am using R to perform thickness analyses. All subjects are > > transformed in fsaverage space and all values are placed in a > matrix > > with 327684 columns (163842 for each hemisphere). I put the > results > > back in a surface file (.asc format) and then convert it to a > binary > > Freesurfer format. I then open the files in Freesurfer to view > them. > > > > Overall the results make sense and fall in the right places. > But I am > > concerned that some results fall into the corpus callosum, > which, if I > > remember correctly should not have any thickness value, and > therefore > > no results. > > > > Here is a screenshot: > > Inline image 1 > > > > Can someone help my understand what might be wrong? Or, if > this is > > normal, why I am finding thickness results where there is no > thickness? > Is this 5.3? The thickness may not be 0 in the medial wall, but > non-zero > values are meaningless and should be masked out or ignored. > > > > Is there a way to find label numbers for each vertex in > fsaverage > > space (i.e. list of parcel number for each vertex). This might > be > > useful to exclude certain vertices or compute summery > statistics of > > the results directly in R. > You can load the annotation into matlab with read_annotation.m > > > > Third question, is it possible to threshold the above map > based on > > minimal cluster area (i.e., in mri_surfcluster). If yes, do I > need to > > prepare a binary file with p-values for thresholding (0-1), or > can I > > use mri_surfcluster with t-score maps (0-Inf)? > You can use any map you want, you just have to specify the > threshold > correctly. Also, you will need to have a FWHM. To get this I > would run > an analysis in mri_glmfit using a design similar to what you > used in R > (small differences probably won't affect the FWHM measure). > > > > Thank you for your help. > > Dorian > > > > > > > > _______________________________________________ > > 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
