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

External Email - Use Caution Hi Bruce, I am coming back to this request as I was wondering: would it be possible to load freesurfer surface atlases in surfstat in order to label my surfaces? Is their format compatible? I saw surfstat only accepts a limited array of formats... Tha

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

External Email - Use Caution Hi Loïc, you can load the atlases using `read_annotation` in Matlab, then of course use them for whatever purpose you like (including in surfstat). This code should get you started: subjects_dir = '/data/mystudy'; subject_id = 'subject1'; hemi = 'l

Re: [Freesurfer] recon-all exited ERRORS

External Email - Use Caution Dear Jennifer, I think I have found the solution in the the archives of Freesurfer's mailing list by searching the keyword 'nu_correct'. With pre v6.0 versions of freesurfer, the Talairach transform step will fail at the mri_nu_correct.mni command on

Re: [Freesurfer] recon-all exited ERRORS

External Email - Use Caution Dear Bruce, Thank you for replying. I think I have found the solution in the the archives of Freesurfer's mailing list by searching the keyword 'nu_correct'. I uninstalled version 5.3.0, and installed 6.0.0, it worked. I finished the whole recon-all st

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

Hi Loic sorry, can you ask whoever maintains surfstat? Or maybe someone else on the list knows? I don't. You can label surfaces manually with the dev version of freeview if you want. cheers Bruce On Thu, 23 May 2019, Loïc Daumail wrote: External Email - Use Caution Hi

Re: [Freesurfer] recon-all exited ERRORS

glad to hear it worked out Bruce On Thu, 23 May 2019, Qiannan Z wrote: External Email - Use Caution Dear Bruce, Thank you for replying. I think I have found the solution in the the archives of Freesurfer's mailing list by searching the keyword 'nu_correct'. I uninstalled vers

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

External Email - Use Caution Afaik SurfStat is not maintained anymore and I think it's been this way for quite a while now. Maybe someone else knows better? The website is at http://www.math.mcgill.ca/keith/surfstat/ and it says 'Updated 26 September 2008'. I'm not sure whether

[Freesurfer] Hind's V1 Error for Freesurfer 6

Dear Freesurfer group, We are interested in processing the Hind's V1 areas in addition to the Broadman areas. I am using a developmental verison of Freesurfer 6 from 1/18/2019 on Centos 6. I copied the V1_average into my $SUBJECTS_DIR folder and ran the following command on one subject (JS45

[Freesurfer] XL defect in recon-all

Dear Freesurfers, I tried to launch "recon-all -all" for an high-resolution 7T 0.75 isotropic MEMPRAGE, but the process got stuck on a XL defect in rh, numbered 54, measuring over 20,000 voxels!! How do I check, and eventually fix, this defect? Thank you, Vale _

Re: [Freesurfer] XL defect in recon-all

You can look at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview But if you are using high res, I would run high res stream I put together for the HCP: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 5/23/19 2:59 PM, Barletta,

[Freesurfer] Postdoctoral fellowships available in Toronto

External Email - Use Caution The Rotman Research Institute at Baycrest (RRI) is seeking 9 outstanding postdoctoral fellows. A sub-set of the prospective fellows will be selected to be sponsored as the institutional candidates for a Banting Post-Doctoral Fellowship, and will work t

Re: [Freesurfer] TrackVis question

You need to use the gradients extracted from the data by FSL (or freesurfer). Ruopeng > On May 23, 2019, at 5:02 PM, Alan Francis wrote: > > External Email - Use Caution > > > Hi Ruopeng - > > I used Diffusion Toolkit to recon DTI data that was preprocessed using FSL. > This

[Freesurfer] Error with mri_glmfit command

External Email - Use Caution Hi FS experts, I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates). My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Ag