Re: [Freesurfer] Cortical Thickness Zero Values

gt; though - I am more concerned about your subject with only 53 vertices in > it. You can visualize it by loading the ?h.cortex.label onto the inflated > surface. Everything not in the label should be set to 0 > > cheers > Bruce > > > > On Tue, 18 Oct 2016, Taha Abdullah

Re: [Freesurfer] Cortical Thickness Zero Values

The entire medial wall has thickness values of 0 because there is no > cortex there. There needs to be a surface in that area because we need a > closed surface. > > On 10/12/16 8:10 PM, Taha Abdullah wrote: > > Hello All, > > Quick question, I ran recon-all with the qcache op

[Freesurfer] Cortical Thickness Zero Values

9,000 vertices. Is there a method I can use to have a thickness value for each of the 163000+ vertices? I am not sure if this is a possible registration issue to mni305. Thanks in advance, Taha -- *Taha Abdullah* *Department of Physiology,* *Northwestern University Feinberg School of Medicine

Re: [Freesurfer] Projecting FA map onto fsaverge surface

surface, and also to get > thickness statistics (thickness is just the distance between corresponding > points on the white and pial surface). You don't need to do anything to map > from white to inflated within an individual. > > Best, > a.y > > > On Fri, 19 Aug 201

Re: [Freesurfer] Projecting FA map onto fsaverge surface

wrote: > > Hi Taha - Trying getting a .dat registration file from bbregister and > using that as the input to mri_vol2surf. There's a multimodal tutorial on > the freesurfer wiki that might be of help. > > Best, > a.y > > On Thu, 18 Aug 2016, Taha Abdullah wrot

[Freesurfer] Seed based volume output to surface

all zeros. I am not entirely sure what I am doing wrong here, it is probably somewhere in the last two commands. Possibly using mri_segstats or mri_read.m? Any help would be greatly appreciated. Apologize in advance for the long email. -- Taha Abdullah Department of Physiology Northwestern

Re: [Freesurfer] Extracting BOLD from a flattened surface

ach vertex? We don't have > anything to do that, but you can do it in matlab, eg, > M = fast_vol2mat(MRIread('lh.yourdata.mgh')); > M will be a 240x127000 matrix > > > On 5/4/16 8:36 PM, Taha Abdullah wrote: > > Hello Doug, > > Sorry for the confusing a

Re: [Freesurfer] Extracting BOLD from a flattened surface

gt; that for you. Flattening is irrelevant for this as it only changes the > xyz coordinate of the vertex and not the vertex identity. > doug > > > On 04/29/2016 11:24 AM, Taha Abdullah wrote: > > Hello Freesurfer Experts, > > > > Long story short--I would like to ex

Re: [Freesurfer] Recon-all -subcortseg finished with error

t the aseg). You can run the individual >> steps through the end of mri_ca_label if you want to stop there >> >> cheers >> Bruce >> >> On Fri, 29 Apr 2016, Taha Abdullah wrote: >> >> Hello All, >>

Re: [Freesurfer] Recon-all -subcortseg finished with error

e the surfaces give better > estimates of cortex and such (and we use them to automatically correct the > aseg). You can run the individual steps through the end of mri_ca_label if > you want to stop there > > cheers > Bruce > > > On Fri, 29 Apr 2016, Taha Abdullah wrote: &

[Freesurfer] Recon-all -subcortseg finished with error

such file or dir, specifically the /surf/lh.white. Is there a better way to run this type of analysis to save disk space and time? Possibly using -autorecon2'; would love any input. Thank you in advance! -- Taha Abdullah Department of Physiology Northwestern University Masters of Sc

[Freesurfer] Extracting BOLD from a flattened surface

ion or advice would be great! I put the commands just to give an idea of my workflow (most of the command lines are from the email server or the FS Wiki) and if there are any issues with my steps please let me know so I can correct them before starting the group analysis. Best, Taha -- Taha Ab