[Freesurfer] Using T2 or FLAIR data to improve pial surfaces

External Email - Use Caution Dear all I want to use T2 or FLAIR data to improve pial surfaces. I wonder, which one is better? using T2pial or FLAIRpial? Is there any difference in output? Thank you so much in advance for your time and help! Hengameh _

[Freesurfer] Group analysis

External Email - Use Caution Hi Freesurfers, I want to do group analysis on four groups and use the volume values in aseg,stats. 1- Is it correct that each subcortical segmentation is based on a "volumetric segmentation atlas" created by Freesurfer? 2- Are the volume values expres

[Freesurfer] Question about de-meaning the covariates and variables

External Email - Use Caution Hi Freesurfers, I'm stuck with the centering (de-meaning) issue. I have two discrete variables,gender and patient-control, and 2 continuous variables which are memory and age.I want to look for group differences as well as differences in relation to t

[Freesurfer] Group analysis

External Email - Use Caution Hello Freesurfer developers, 1- I want to extract the uncorrected clusters from the uncorrected significance maps obtained from mri_glmfit for structural data (to illustrate cluster, size, location, and significance) like abs.sig.cluster.summary (summ

Re: [Freesurfer] Group analysis

o use them? Thank you so much. Hengameh On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve wrote: > > > On 3/9/20 5:53 PM, Hengameh Marzbani wrote: > > > > External Email - Use Caution > > > > Hello Freesurfer developers, > > 1- I want to extract t

Re: [Freesurfer] Group analysis

wrote: > > > On 3/11/2020 4:21 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Thank you for the quick response. > > question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I > can see the clusters by tksurfer. But, Can I

Re: [Freesurfer] Group analysis

cal analysis or are you asking how to > account for subcortical analysis during correction for multiple > corrections? For the latter, use --3spaces > > On 3/12/2020 2:03 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > thank you for your detailed and helpful e

[Freesurfer] The input for FreeSurfer

External Email - Use Caution Hello Freesurfer developers, I have T1 weighted MRI images which are* not MPRAGE*. They are 2 dimensional sagittal or axial images with 3mm thickness (1.5 Tesla). Can I analyze these images by FreeSurfer? If yes, what tips should I consider? Thank

[Freesurfer] The input for Petsurfer

External Email - Use Caution Hello Freesurfer developers, I have PET images for brain and I want to analyze them with Petsurfer. But I don't have T1-weighted MRI of each subject. What should I do? Is it possible? Thank you in advance, Best regards, Hengameh ___

Re: [Freesurfer] The input for Petsurfer

, 2020 at 11:38 PM Douglas N. Greve wrote: > It is not really possible. It is designed assuming you have MRIs. > > On 7/24/2020 10:06 AM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Hello Freesurfer developers, > > I have PET images for brain

[Freesurfer] bad interpreter: No such file or directory error

External Email - Use Caution Hello Freesurfer developers, I have installed FreeSurfer v7 on 2 machines running Ubuntu and made sure that the setting are fine. Also, freeview works by simply typing the freeview command. However,I have tried to run recon-all. but, I have got the

Re: [Freesurfer] bad interpreter: No such file or directory error

External Email - Use Caution I appreciate your answer! On Thu, Jul 30, 2020 at 8:18 PM fsbuild wrote: > Hello Hengameh, > > You probably need to install tcsh (and or csh). > > I would try, > > $ sudo apt-get install csh tcsh > > - R. > > On

Re: [Freesurfer] The input for Petsurfer

External Email - Use Caution Thank you for your response. On Mon, Jul 27, 2020 at 7:19 PM Douglas N. Greve wrote: > Sorry, no, not with PETsurfer > > On 7/26/2020 1:05 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Thank you f

[Freesurfer] MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs

External Email - Use Caution Hello Freesurfer developers, For the purpose of reporting ROIs in my article, I need a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps: Step 1: mri_annotation2l

Re: [Freesurfer] MNI Coordinates from the Destrieux Atlas and aseg.stats ROIs

External Email - Use Caution Hello Freesurfer developers, I have deadline time to report these coordinates. I greatly appreciate your help and I'm looking forward to your kind response. Best regards, Hengameh On Fri, Nov 20, 2020 at 11:20 AM Hengameh Marzbani