Re: [Freesurfer] mri_glmfit will not use mask or label

Try running it without --cortex On 6/26/19 4:57 PM, Jennifer Legault wrote: > > External Email - Use Caution > > Hi Freesurfer experts, > > I'm trying to constrain my sMRI analysis to only search for brain > regions (GMV) that are correlated with a behavioral measure within a > mask (mad

[Freesurfer] mri_glmfit will not use mask or label

External Email - Use Caution Hi Freesurfer experts, I'm trying to constrain my sMRI analysis to only search for brain regions (GMV) that are correlated with a behavioral measure within a mask (made from a functional contrast of interest, so that I'm only searching for regions that

[Freesurfer] Help for smoothing the pial surface

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI ) without having to run the entire recon-all process. Additionally, I want to ma

Re: [Freesurfer] recon-all error: Correcting defect

External Email - Use Caution Hello Bruce, Ok, I have sent to you the subject via FileDrop if you want to take a look. Thanks. Best regards, El mié., 26 jun. 2019 a las 17:04, Bruce Fischl () escribió: > Hi Miguel > > depending on the lesions it may not be fixable (since they ma

Re: [Freesurfer] recon-all error: Correcting defect

Hi Miguel depending on the lesions it may not be fixable (since they may change the topology of the cortex). If you upload the subject we will take a look, or you can try manually filling in the lesion in the wm.mgz (or marking it as lesion in the aseg.mgz) and seeing if that helps cheers Br

[Freesurfer] Viewing clusters regardless of significance

External Email - Use Caution Hi Freesurfer developers, I’m using the glmfit tutorial to see clusters for my data. I’m trying to view the uncorrected clusters on tksuefer using the command line tksurfer fsaverage lh inflated -overlay /path to data/cache.th13.abs.sig.ocn.annot but

Re: [Freesurfer] Freesurfer linear mixed models - viewing results

External Email - Use Caution Yes, that's possible due to the vertex correspondence between e.g. 'lh.shere' and 'lh.inflated'. You could import the 'lh.inflated' file from the fsaverage directory in a similar manner as the 'lh.sphere' file. A caveat may be that, if I am underst

[Freesurfer] Applying transformation to surface (e.g. pial) files

External Email - Use Caution Hello, first of all, please forgive me a trivial question, but digging through archives neither provided me with a simple answer, nor gave me an idea how to solve the problem in an elegant way. What I need to do is to apply transformation matrix (ac

Re: [Freesurfer] Interpretation question during LME steps

External Email - Use Caution Hi Daliah, sorry for the late response. In case it's still relevant, I have a few remarks: a) The results can be viewed on an inflated surface both in Matlab and in Freeview, whatever you prefer. There is a correspondence between the vertices of the

Re: [Freesurfer] Labelling SurfStat p-value surface map

External Email - Use Caution Just a short note regarding these errors: > > Le lun. 24 juin 2019 à 16:50, Loïc Daumail a > > écrit : > > > >> However, using mri_convert, I still get the same message with tclsh. > >> " > >> mri_convert lh.thickness template.mgh > >> /usr/share/modu

Re: [Freesurfer] Labelling SurfStat p-value surface map

External Email - Use Caution I found it hard to read the quoted mails and to follow along, but if I'm not mistaken you are trying to overlay a self-created mgh file with dimension 10242x1x1 onto the pial surface of sub-002 at sub-002/surf/lh.pial. How many vertices does sub-002/

Re: [Freesurfer] Labelling SurfStat p-value surface map

External Email - Use Caution Hi Freesurfer, Getting back the former request, I am still trying to load an overlay of my data onto a surface.. but it still doesn't work well. Here is the info of my overlay: " mri_info lh_emb_comp_sub-002.mgz Volume information for lh_emb_comp_sub-00

Re: [Freesurfer] Problem for LGI

External Email - Use Caution Hi, can you open those surface files (both lh.pial and rh.pial of the subject for which it fails) in freeview to check whether they are OK? Does it fail only for a single subject or for all subjects you tried? Best, Tim > On June 26, 2019 at 12:31