[Freesurfer] Visualizing specific cortical parcels in Desikan Killiany atlas

External Email - Use Caution Dear experts, I have a basic visualization question. I would like to create a surface brain figure with specific cortical parcels colored. Similar to https://secure-web.cisco.com/1DryTPj2WrD-LULa8TF6HVh2xwKTLAaWDFvIpAUrs4z6O2VOFttAjezDQX2aR4Z5m6bFRIW

Re: [Freesurfer] mris_fix_topology taking ages

the volume). You can often see defects better on this surface (they look likes holes or handles; you should at least see some) On 6/1/2021 4:55 PM, Ellen Ji wrote: *External Email - Use Caution * Hi Doug, when you say it did not finish, could you clarify

Re: [Freesurfer] mris_fix_topology taking ages

, and the orig.nofix and see if you can find a big topo error On 5/31/2021 11:16 AM, Ellen Ji wrote: External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice fr

[Freesurfer] mris_fix_topology taking ages

External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E

Re: [Freesurfer] Abormally high foldind index

Have you looked at the surfaces for those subjects? > > Cheers > Bruce > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Ellen Ji > Sent: Tuesday, March 30, 2021 5:44 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [F

[Freesurfer] Abormally high foldind index

External Email - Use Caution Dear Experts, While the majority of our subjects have a folding index between 5-30, there are a couple of *extreme* outliers in the thousands or even negative. Could this hint that a particular part of recon-all failed and should be rerun? Thank yo

Re: [Freesurfer] left-right flip?

utputfile.nii.gz On 9/16/20 12:03 PM, Fischl, Bruce wrote: I think so, but I defer to Doug *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Ellen Ji *Sent:* Wednesday, September 16, 2020 11:05 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] left-right flip?

Re: [Freesurfer] left-right flip?

Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ellen Ji Sent: Wednesday, September 16, 2020 3:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] left-right flip? External Email - Use Caution Hi Douglas, I found the dicom

Re: [Freesurfer] left-right flip?

hanged sides relative > to the nifti. > That is a fiducial. And do you know what side the fiducial was placed > on? mri_info does not help. How did you convert from dicom? > > ps. Please make sure to post to the list and not to us personally > > > On 9/15/2020 12:58 PM, Ellen J

Re: [Freesurfer] left-right flip?

that I can't just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: > Hi Ellen > > Can you cc the list so that others can respond? What was your input data? Did > you not have dicoms? > > Cheers > Bruce > > -----Original

[Freesurfer] left-right flip?

erstanding what this means (how would bias occur during segmentation?) - https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal Many thanks for your input, Ellen --- Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen...@bli.uzh.ch homanlab

[Freesurfer] Permission denied mri_surf2surf

External Email - Use Caution Dear experts, I created a loop for mri_surf2surf so that it would run for 300+ subjects. For most of them, it ran successfully. However, it did not work for 30 subjects. I then went to investigate one by one and I am getting a Permission denied erro

[Freesurfer] mri_aparc2aseg: how to remove redundant output labels?

(:)); length(u) % total number of labels - I believe the extra labels are from the Freesurfer LUT. How can I make sure they are not added when running mri_aparc2aseg? (such that only my annotation labels are included in the output) Thank you very much, Ellen * Ellen Ji, PhD Postdoct

[Freesurfer] mri_aparc2aseg doesn't write output

External Email - Use Caution Dear experts, I am running mri_aparc2aseg and, based on the output, it seems to run through successfully until the very end where it does not actually write the file (I receive "error: niiWrite(): error opening file mri/aparc.500+2mm.nii.gz"). Howev

[Freesurfer] bbregister using freesurfer v7

input! Ellen Ji, PhD Postdoctoral researcher * Individual Differences in Psychosis (IDP) Lab Psychiatric University Hospital University of Zürich ellen...@bli.uzh.ch ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https