[Freesurfer] modify intensity normalization pipeline

External Email - Use Caution Hello, Is there a way to modify intensity normalization pipeline in recon-all script? The temporal lobe is being very poorly segmented because white matter is being segmented as gray matter and therefore gray matter does not reach outer boundary of

[Freesurfer] poor inferior cerebellum segmentation

External Email - Use Caution Hello, Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar

[Freesurfer] recon-all error

External Email - Use Caution Hi, For some of my subjects I get the following error at the beginning of recon-all: mri_convert /path/to/inputt1.nii /path/to/mri/orig/001.mgz mri_convert /path/to/anat_t1.nii /path/to/mri/orig/001.mgz reading from /path/to/anat_t1.nii... NaN

Re: [Freesurfer] Calculate cortical thickness of a volumetric ROI

t; > > > > Best, > > > > Yujing > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer > *Sent:* Thursday, June 15, 2023 11:36 AM > *To:* Freesurfer support list > *Subject:* [Frees

Re: [Freesurfer] Asymmetry analysis

Use Caution > > That map is whatever you are studying. Eg, lh.thickness > > On 5/25/2023 1:30 PM, Carlos Alcocer wrote: > > External Email - Use Caution > Hello, > > I am trying to do an asymmetry analysis using steps detailed in *MailScanner > has detected a po

[Freesurfer] Calculate cortical thickness of a volumetric ROI

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using

[Freesurfer] Calculate cortical thickness of a volumetric ROI

External Email - Use Caution Hello, I am trying to calculate the cortical thickness of a volumetric ROI that I created that I have in subject space for every subject in my dataset. I was using

[Freesurfer] Asymmetry analysis

External Email - Use Caution Hello, I am trying to do an asymmetry analysis using steps detailed in

[Freesurfer] Volume transformation issue

External Email - Use Caution Hi, I am trying to transform a volumetric ROI from MNI152 space to native space. I am doing this in 2 steps. First (1) I am creating a registration file using bb register to create a registration file and then (2) I am using mri_vol2vol to transform

[Freesurfer] register to mni space

External Email - Use Caution I registered a subject to mni space using the mri_cvs_register command with the --mni flag. However, the output files do not include a new aparc.a2009s+aseg.mgz. I wanted this atlas overlayed on the mni registered subject so I could extract one of the

Re: [Freesurfer] creating average labels

ot sure that is what you are looking for. > > > > Best, > > > > Yujing > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Carlos Alcocer > *Sent:* Wednesday, April 19, 2023 1:02 PM

[Freesurfer] creating average labels

External Email - Use Caution Good afternoon, I would like to verify that the subcallosal cingulate cortex (SCC) segmentation of my subjects are correct. I want to do this by creating an average label of the left SCC and an average label of the right SCC which I can then map onto

[Freesurfer] T1 with contrast

External Email - Use Caution Can you use T1 with contrast in freesurfer or does it have to be non-contrast images? Tks, Carlos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Subcallosal cingulate cortex segmentation/parcellation

External Email - Use Caution Hi, I am interested in the aparc+aseg stats for the subcallosal cinuglate cortex (SCC). When learning freesurfer, the lectures/tutorials mention not to make manual edits to medial structures which I believe would include the SCC. Will the stat output

[Freesurfer] Autrecon-pial command

External Email - Use Caution Hello all, Does -autorecon-pial flag also recreate the statistics tables with the new surfaces? or do you have to run autorecon3 after to recalculate stats files? Tks, Carlos ___ Freesurfer mailing list

Re: [Freesurfer] Freeview Edit options restricted

External Email - Use Caution Also is it possible to not archive or not include email signature on that reply email. didn't mean to have my email signature on there On Tue, Mar 7, 2023 at 12:30 PM Carlos Alcocer wrote: > Thank you for your prompt response. Yes, while it d

Re: [Freesurfer] Freeview Edit options restricted

just switch to Navigate mode. > > Ruopeng > > On Mar 7, 2023, at 11:34 AM, Carlos Alcocer wrote: > > External Email - Use Caution > > Hello, > > When I try to do recon-edit, it does not let me click on certain options > ie. changin the brush size. It additionally

[Freesurfer] Freeview Edit options restricted

External Email - Use Caution Hello, When I try to do recon-edit, it does not let me click on certain options ie. changin the brush size. It additionally doesnt let me exit out of or minimize it. I am running the most recent version of freesurfer (7.3.2) on linux (wsl). I

[Freesurfer] Freeview Installation Error

External Email - Use Caution Hi, I have been trying to install FreeSurfer and I went to test out the freeview command but received the following error. freeview: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory I am