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 greve@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 greve@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.