[Freesurfer] mri_glmfit

External Email - Use Caution Dear FS experts, I am working on a surface based analysis using FS 7.1.1 and I would like to run mri_glmfit between two groups using the flag "--label" to restrict analysis within lobes. I ran these commands on fsaverage mri_annotation2label

Re: [Freesurfer] questions about mri_glmfit

12:22 PM, James Brown wrote: Dear Freesurfer experts, I have 2 questions about the command mri_glmfit and I appreciate your help. 1- Are there any settings or flags that can be used in mri_glmfit to restrict statistical comparison of surface based analysis to specific ROIs rather than whole brain

[Freesurfer] questions about mri_glmfit

External Email - Use Caution Dear Freesurfer experts, I have 2 questions about the command mri_glmfit and I appreciate your help. 1- Are there any settings or flags that can be used in mri_glmfit to restrict statistical comparison of surface based analysis to specific ROIs rather

[Freesurfer] cortical thickness in frontal lobe

External Email - Use Caution Dear Freesurfer experts, We are new to Freesurfer. We appreciate your help & apologize if the question is simple. We need cortical thickness in lobes instead of parcellates. Is it correct to take the average of the parcelates from the aparc+aseg.stats

[Freesurfer] Fwd: average lobar cortical thickness

External Email - Use Caution Dear Freesurfer experts, I would like to know if this procedure is correct. I have cortical thickness data from aparc+aseg for every ROI in DTK atlas (i.e. output of recon-all). I need average cortical thickness in frontal, parietal, temporal,

[Freesurfer] average lobar cortical thickness

External Email - Use Caution Dear Freesurfer experts, I would like to know if this procedure is correct. I have cortical thickness data from aparc+aseg for every ROI in DTK atlas (i.e. output of recon-all). I need average cortical thickness in frontal, parietal, temporal,

Re: [Freesurfer] mri_segment

takes two steps! Thank you for pointing this out. I would check your results to see if it is doing the right thing. I also think that the input to mri_segment is not the norm.mgz, but rather the brain.mgz, which is more aggressively normalized On Mon, Oct 24, 2022 at 2:01 PM James Brown wrote:

Re: [Freesurfer] mri_segment

is it correct procedure to increase the high limit of WM up to 125 or 140? On Mon, Oct 24, 2022 at 1:46 PM James Brown wrote: > Dear Dr Bruce, Fischl, > > Thank you very much for the detailed explanation. I would like to ask two > additional questions and I highly appreciat

Re: [Freesurfer] mri_segment

set the gm peak, just scale the white to 110-ish, then gray lands wherever the intrinsic contrast of the image puts it Cheers Bruce On Sat, Oct 22, 2022 at 10:18 PM James Brown wrote: > Dear Freesurfer experts, > I would like to inquire about the flags "-whi" and "

[Freesurfer] mri_segment

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flags "-whi" and "-ghi" in the command "mri_segement". According to FS wiki, the command "mri_normalize" sets white matter voxels around ~110 and gray matter around ~70. - The default white

[Freesurfer] Creating a lobar atlas

External Email - Use Caution Dear colleagues Freesurfer experts, I would like to create an atlas (my atlas) for the white matter like "wmparc.mgz" so I can generate statistics. I would like this atlas to be limited to the following structures (frontal lobe, parietal lobe,

Re: [Freesurfer] White matter normalization of FLAIR images

artifacts in e.g. interlaced acquisitions 4. We estimate the bias field from the white matter, then apply it to the whole brain. I don’t think nonmax_suppress will do anything without surfaces though Cheers Bruce On Tue, Sep 27, 2022 at 7:20 AM James Brown wrote: > Dear Dr Gre

Re: [Freesurfer] White matter normalization of FLAIR images

like -FLAIRpial or -T2pial so it uses it (in which case it will first normalize it), but hopefully someone else can confirm cheers Bruce On Fri, Sep 23, 2022 at 2:40 PM James Brown wrote: > Dear Dr Bruce, > Thank you very much for your guidance. > I ran recon-all on a subject &quo

Re: [Freesurfer] White matter normalization of FLAIR images

to normalize FLAIR Sincerely, Hi JamesB there is T2/FLAIR normalization in recon-all if you process it through there. You can look for "nonmax_suppress" if you want to find the command line cheers Bruce On Fri, Sep 23, 2022 at 2:06 PM James Brown wrote: > Dear Freesurfer expe

Re: [Freesurfer] White matter normalization of FLAIR images

back about the proper way to correct FLAIR images for bias fields and normalize white matter intensity in FLAIR images. Thank you JamesB On Wed, Sep 21, 2022 at 10:18 AM James Brown wrote: > Dear Freesurfer experts, > In order to normalize white matter intensity of T1 images and correct

[Freesurfer] White matter normalization of FLAIR images

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. We do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1

Re: [Freesurfer] White matter normalization

your conversation with Doug can continue. Liam Sennott On Fri, Sep 16, 2022 at 10:25 AM James Brown wrote: > Hi Dr Greeve, > I greatly apologize if I missed in the log file (attached) how freesurfer > normalizes flair. but I couldn't figure it out. Thanks for guidance > > James

Re: [Freesurfer] White matter normalization

-qC1h6XYGUYypkmYk5aJ4XGxrWAwEwV97nVfN9eNbnOSLJ0hXT6mMz9W3_sbOiTe2A3fOoRCRTelL2kBwzKt_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Fconfirm%2Ffreesurfer%2Fc325cabc74fbe917245a011d762c75fc2f62c6ca On Fri, Sep 16, 2022 at 10:25 AM James Brown wrote: > Hi Dr Greeve, > I greatly apologize if I missed in the log file (at

Re: [Freesurfer] White matter normalization

e the same normalization that is applied to the t1)  On Mon, Sep 12, 2022 at 4:01 PM James Brown wrote: > Dear Freesurfer experts, > In order to normalize white matter intensity of T1 images and correct for > bias field. I do the following steps: > mri_convert T1.nii.gz T1.mgz > mri_

[Freesurfer] White matter normalization

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. I do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1

[Freesurfer] Freeview heat map

External Email - Use Caution Dear Freesurfer developers, I analyzed some data in Freesurfer. At the end, I used "mri_segstats" to measure a parameter of interest for every ROI in DKT atlas. I would like to load the mean values of this parameter to Freeview (every ROI in DKT has

Re: [Freesurfer] SNR for PET images

al Message ‐‐‐ On August 14, 2018 5:07 PM, James Brown wrote: > Hi Freesurfer team, > I would like to use "mri_segstat" to compute SNR for regions of interest. My > question is, if I use PET images as input does this mean that SNR will be > computed for the PET signal in t

[Freesurfer] SNR for PET images

External Email - Use Caution Hi Freesurfer team, I would like to use "mri_segstat" to compute SNR for regions of interest. My question is, if I use PET images as input does this mean that SNR will be computed for the PET signal in the ROIs? Thanks for any help

[Freesurfer] Q & A Forum in neuroimaging techniques

External Email - Use Caution > Dear Colleagues, > We would like to create Q & A forum about issues in neuroimaging techniques. > Experts from the Martinos Center and Oxford FMRIB will be invited to build > this forum and to answer questions and provide plans for critical

[Freesurfer] Q & A Forum in neuroimaging techniques

External Email - Use Caution Dear Colleagues, We would like to create Q & A forum about issues in neuroimaging techniques. Experts from the Martinos Center and Oxford FMRIB will be invited to build this forum and to answer questions and provide plans for critical technical