Re: [Freesurfer] Masking cortical thickness

I think you could just load the cortex.label map onto the surface and edit those regions out. Then they will not contribute to smoothed maps, etc... Doug: any reason this wouldn't work? Bruce On Tue, 13 Feb 2018, James Hobart wrote: > Hi all, > I am looking to mask out a small region of the G

[Freesurfer] Masking cortical thickness

Hi all, I am looking to mask out a small region of the GM when calculating the cortical thickness of ROIs across the brain. Essentially I have a couple of cases with small GM lesions where the cortical thickness is less likely to be meaningful for my analysis. I have binary lesion masks and also

Re: [Freesurfer] map values to vertices {Disarmed}

Thank you, Bruce. I did reconstruct the surfaces from that subject. These are the steps that I've taken: recon-all -s -i -all mris_register /surf/.sphere fsaverag5/.?reg.template.tif /surf/.fsaverage5.sphere.reg mri_surf2surf -s -h --sval-xyz .pial --trgsubject fsaverage5 --tval m

Re: [Freesurfer] map values to vertices {Disarmed}

Hi Fred we usually use mri_vol2surf for this kind of thing. Did you reconstruct surfaces from that subject? cheers Bruce On Tue, 13 Feb 2018, Frederick Barrett wrote: Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuo

Re: [Freesurfer] Problems running LGI {Disarmed}

Dear Andrew, thank you very much! Yes, you were right! Now it works fine. best regards Dusan From: Hoopes, Andrew Sent: Tuesday, February 13, 2018 12:23 PM To: Freesurfer support list; Dusan Hirjak Subject: Re: [Freesurfer] Problems running LGI Hi Dusan, I

[Freesurfer] map values to vertices {Disarmed}

Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuous variable (non-integer) to each vertex on a surface so that I can visualize these values on the surface (or an inflated brain), but I can't figure out how to do this. I

Re: [Freesurfer] Problems running LGI

Hi Dusan, I just remembered that this is probably due to SIP being enabled on your mac, which blocks libraries stored in /usr. I would suggest disabling SIP and rerunning to see if that fixes things: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best, And

[Freesurfer] inter-hemisphere registration on customised template

Dear Freesurfer experts, I am writing to ask how to do the surface-based inter-hemispheric registration based on the customised template, instead of fsaverage. I am planning to calculate the lateralisation index for each vertex, which means I should to use the symmetry template, for example, f

Re: [Freesurfer] IndexError: list index out of range

*I also got this error when I ran w/ python 2: python2 $FREESURFER_HOME/bin/asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i aparc.a2009s+aseg.lst -m max Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 5

Re: [Freesurfer] IndexError: list index out of range

Hi Doug, I am also getting the error "IndexError: list index out of range" - I got the same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table: asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i aparc.a2009s+aseg.lst -m max Parsing the .stats files Traceba

[Freesurfer] quantifyHAsubregions.sh , HBT/FS60/CA

Hi Eugenio, Is it possible to use *quantifyHAsubregions.sh* to write out the three different hippocampal subfield outputs ? - HBT: the hippocampus is subdivided into head, body and tail. - FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e., no head/body subdivision for the hippocampal