Re: [Freesurfer] mz3 for freesurfer brain render

5, 2020, 1:09 PM Douglas N. Greve wrote: > I don't know what you are asking for. Can you elaboraet? > > On 6/5/2020 10:41 AM, Kate Marvel wrote: > > External Email - Use Caution > > Hi Freesurfer team, > > I would like to do a brain render using freesurfer

[Freesurfer] mz3 for freesurfer brain render

External Email - Use Caution Hi Freesurfer team, I would like to do a brain render using freesurfer ROIs. Is there .mz3 file for freesurfer brain atlas? Thanks, -- kate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] code for estimating volume

External Email - Use Caution Hi Iglesias, I would like to learn the two ways for estimating volumes mentioned in another post, see below. Please send me the codes in Freesurfer to do this. Thank you, Kate -- Forwarded message - From: Iglesias Gonzalez, Juan

Re: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans

eers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of Kate Marvel > > *Reply-To: *Freesurf

[Freesurfer] hippocampus subfield segmentation using Siemen and GE scans

External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different

Re: [Freesurfer] how to calculate the ROI volumes of grey matter using Desikan atlas

e Section 4.2 here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#IndividualStatsfiles). > > > Regards, > Thomas > > On Sun, Mar 15, 2020 at 7:22 PM Kate Marvel wrote: > >> External Email - Use Caution >> >> >> Hi Freesurf

[Freesurfer] how to calculate the ROI volumes of grey matter using Desikan atlas

External Email - Use Caution Hi Freesurfer community, I would like to know how to compute the ROI volumes of grey matter using Desikan atlas? Is there a threshold value set for this? is it 0.2? Thanks kate ___ Freesurfer mailing list

Re: [Freesurfer] Which FDG-PET file to use for PETSufer?

n info is correct. > Load one into freeview to assure that the cor view actually shows up as > cor, etc. One thing you will not be able to check is whether there is a > left-right flip > > On 2/24/2020 3:30 PM, Kate Marvel wrote: > > External Email - Use Caution > Hi

[Freesurfer] Which FDG-PET file to use for PETSufer?

External Email - Use Caution Hi FreeSurfer Users, I would like to perform PET analysis using PETSurfer and I have the following FDG-PET NIfTI files below: 1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 3.

Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

image (which will be stored in > .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the > registration and/or change the output format (if you specify file.nii or > file.nii.gz it will write in Nifti) > > cheers > Bruce > > > On Mon, 24 Feb 2020, Kate Marvel wrote:

Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

format for storing images. > > On 2/21/2020 7:52 AM, Kate Marvel wrote: > > External Email - Use Caution > Hi All, > > How do you convert the registered file (.lta) into NIfTI format in > PETsurfer. > > Thanks, > > > __

[Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer

External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] how to perform No Partial Volume Correction for PET using PETSURFER

External Email - Use Caution Sorry for that. psf is zero. Thank you very much Douglas. Kate On Thu, Feb 20, 2020 at 3:55 PM Douglas N. Greve wrote: > yes, they are, thought I don't know why you include "psf6" in the output > folder. > > On 2/20/2020 3:36

[Freesurfer] how to perform No Partial Volume Correction for PET using PETSURFER

External Email - Use Caution Dear All, I would like to perform no partial volume correction of PET using PETSURFER. The steps followed in doing this is shown below: gtmseg --s Patient_1 mri_concat Patient_1_pet.nii.gz --mean --o Patient_1_pet_tac_vol_mean.nii.gz mri_coreg --s

Re: [Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?

is set to 0. MaskThresh should be between 0 and 1 > > this is all kind of messy and unprincipled and the results are very > sensitive to the values you set above . which is why I avoid it. > > On 1/27/2020 9:23 PM, Kate Marvel wrote: > > External Email - Use Cautio

Re: [Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?

--help. Also look at the PETsurfer wiki page for typical usage > > On 1/27/2020 3:54 PM, Kate Marvel wrote: > > External Email - Use Caution > Hi Freesurfer community, > > I would like to know the arguments to use for symmetric Geometric Transfer > Matrix and t

[Freesurfer] what is the argument for arguments for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the PETsurfer ?

External Email - Use Caution Hi Freesurfer community, I would like to know the arguments to use for symmetric Geometric Transfer Matrix and two-compartment model (Meltzer Method) in the petsurfer command "mri_gtmpvc". Thank you, -- kate

Re: [Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics

parcellation/Schaefer2018_LocalGlobal/Parcellations/project_to_individual > > The gcs files will be incorporated into freesurfer at some point. > Aihuiping (cc-ed) will attach the gcs files in the next email. > > Thanks, > Thomas > > On Wed, Jan 15, 2020 at 7:40 AM Kate Marvel wrote: >

[Freesurfer] how to include Schaefer atlas into freesurfer and compute surface statistics

External Email - Use Caution Dear Freesurfer team, I would like to include Schaefer atlas into freesurfer. The Schaefer atlas can be found in the link below: