Re: [Freesurfer] adding insula voxels

Hi Ani, I actually did end up fixing the insula mis-segmentation using either control points or WM edits for many subjects (I think the one I sent you too, not sure). However, I did notice that in some subjects, the edits will push the wm line out a little too much such that minor part of the

Re: [Freesurfer] adding insula voxels

I believe it's in the surfaces. It is apparent when I load the lh.pial and lh.white over the brainmask. thanks, Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] adding insula voxels

I uploaded one when I sent the first email, did you receive it? Uploaded to: ftp.nmr.mgh.harvard.edu ; cd transfer/incoming The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS folder for one subject. Should I go ahead and resend it?

[Freesurfer] adding insula voxels

Hi Bruce and FS group, Thanks again for the speedy replies and help with everything. Quick question about editing voxels (specifically those in the lh/rh insula). Should I simply add specific voxels to the aparc+aseg for this step? It was a little unclear on the wiki. Also, is there a specific

Re: [Freesurfer] adding insula voxels

Hi Bruce, Sorry for not clarifying. A number of subjects in our set have underestimated insula (usually anatomical right insula but sometimes both). I just uploaded an example to the ftp. I don’t think control points or wm edits can help with some of these so I wanted to see how we could go

[Freesurfer] freesurfer trouble with FTLD subjects

underestimations in most frontal gyri and insula. Thanks a lot, Adam Adam Mezher USC Imaging Genetics Center Marina Del Rey, CA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] question regarding control point edits

On Wed, 23 Jul 2014, Adam Mezher wrote: Hi Bruce, Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually? Thanks for clarifying

Re: [Freesurfer] question regarding control point edits

Hi Bruce, Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually? Thanks for clarifying! Adam Mezher Hi Adam I don't think so

[Freesurfer] question regarding control point edits

on numerous cases rather than doing control point edits on each case individually. Thank you, Adam Mezher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

[Freesurfer] hippocampus misestimation

Hi all, I was curious to know if anyone has been able to use edits to correct hippocampal under- or over-estimation. I've experienced a number of cases in which about half of the left hippocampus is labeled as ctx-lh-unknown or Left-Cerebral-White-Matter (for reference, I'm using FreeSurfer

[Freesurfer] empty norm.mgz file {Disarmed}

, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created? Thanks, Adam *Adam Mezher* Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San

Re: [Freesurfer] empty norm.mgz file {Disarmed}

loop. This bug is fixed in 5.3, but it won't generate anything reasonable with an empty input volume. Do you know why it is blank? Is the brainmask.mgz ok? The talariach.lta and .xfm? cheers Bruce On Fri, 6 Dec 2013, Adam Mezher wrote: Hi all, I'm having a similar issue to the one

[Freesurfer] -autorecon 3 error: error reading surf/lh.sphere

Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sphere and immediately exits afterward. Thank you, Adam *Adam Mezher* Staff Research Associate II Center

Re: [Freesurfer] -autorecon 3 error: error reading surf/lh.sphere

On Fri, 8 Nov 2013, Adam Mezher wrote: Hi Bruce, Yes I checked and the partition is not full, there should be ample space available. Do you have any other ideas? I've never come across this error before. Thanks, -Adam FilesystemSize Used Avail Use% Mounted on cosf:/cind

[Freesurfer] -autorecon2 -cp vs -autorecon2 without -cp

Hi all, Just curious to know what would happen to the image if, after making control point edits, I do not include the -cp flag to the run command? Conversely, what would happen if I include the -cp flag without having made edits? Thanks, Adam *Adam Mezher* Staff Research Associate Center