[Freesurfer] Best mesh generation from hippocampus aseg segmentation

External Email - Use Caution Hi: Which is the best library or software to create the hippocampus mesh from aseg segmentation? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] mri_surf2vol method one

External Email - Use Caution Hi Freesurfer experts, I'm trying to write the normals of the GM/WM meshes to the entire ribbon. We usually do it by: 1) Generate normal files from rh.white and lh.white mris_convert rh.white rh.white.gii mris_convert -n rh.white

Re: [Freesurfer] please help me

External Email - Use Caution hi Bruce thank you very very much On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce wrote: #yiv6786467954 #yiv6786467954 -- _filtered {} _filtered {} _filtered {}#yiv6786467954 #yiv6786467954 p.yiv6786467954MsoNormal,

[Freesurfer] mri_nu_correct error: flar --uchar not recignized

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to compute volumetric data from MPRAGE images by using recon-all as decribed athttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all I've got the following message: mri_nu_correct.mni --i orig.mgz --o nu.mgz

Re: [Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

Where did you get the ct from? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of 1248742467 Sent: Thursday, October 22, 2020 7:25 AM To: freesurfer Subject: [Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m) External Email - Use Caution

[Freesurfer] There is no view-label option after loading the .annot file

External Email - Use Caution Hello, Fs my freesurfer version is 6, I see others have the view button after load .annot file,But my version does not have this option. Do I need to update the version? And I have installed fs6, can I install fs 7.1 on the same machine? What's more,

[Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

External Email - Use Caution hello, fs when i use the write_annotation.m, the error message occurs: `The non-existent field'numEntries' is referenced. Error write_annotation (line 62) count = fwrite(fp, int32(ct.numEntries),'int'); Error test_1 (line 13)

Re: [Freesurfer] longitudinal study

Hi Ken, you should always look at the output from the …long.base directories, those are the final outputs. Looks to me that you are looking at the cross sectional produced surfaces from the first stage. Those will be - in different spaces (as the heads are in different positions in the

Re: [Freesurfer] starting longitudinal pipeline after mri_robust_template

Hi Marisa, That should be possible. You can run the long pipeline up to that step, replace the corresponding files with your version and continue from there. Best, Martin > On 1. Oct 2020, at 10:32, Marisa Johanna Nordt wrote: > > External Email - Use Caution > Hello, >

Re: [Freesurfer] lta files longitudinal pipeline

Hi Marisa, the -affine flag was only for some debugging and is currently not supported. It may also not do what you think it does. It will remove scaling difference between your time points. This makes sense if you have test-retest scans and want to remove scanner calibration scaling

Re: [Freesurfer] Question: Longitudinal Edits

Hi Suzan, (sending this also to the FS support list, where these questions fit best, but sometimes I miss emails there). If edits are necessary or not depends purely on the quality of your data. I.e. old scanners, low contrast, motion artefacts etc. It also depends on the number of

[Freesurfer] Issue with extracted thickness value from significant cluster or peak vertex

External Email - Use Caution Hi, I am using FS 7.1.0. After running the surface thickness GLM analysis I get one cluster after correction for multiple comparison showing a significant group difference. I want to make a plot illustrating this group difference. However, when using

[Freesurfer] unpacksdcmdir in version 7: issues with cfg files

External Email - Use Caution Hi! We are encountering some issues with unpacksdcmdir in version 7.1.1. In particular, it turns out that the handling of cfg files seems to have changed, which makes things somewhat impractical. Old (v5.3) cfg files cannot be used anymore, because