[Freesurfer] treatment effect compare to controls

Hi FreeSurfer, What would be the best way to compare the patient group before and after treatment with a control group? Should one use the tp1 and tp2 registered to the template from longitudinal analysis and compare those with the control group? Best regards, Amirhossein Manzouri

Re: [Freesurfer] Register.dof

Yes, if you've run the T1 through recon-all, then you can use bbregister to create a registration between the two. It will also resample to the T1 space, but you can also use mri_vol2vol to do so too. doug On 2/18/15 5:43 PM, Xiaomin Yue wrote: Hi, I like to transfer a epi file to a T1

Re: [Freesurfer] cluster colors

Yes - sorry this is probably easier with images. The files I'm visualizing are the sig.mgh (uncorrected) and cache.th13.abs.sig.ocn. mgh (cluster corrected) respectively, overlayed on an fsaverage brain. I am visualizing using tksurfer. When I run mri_glmfit, I get the example_sig output (see

Re: [Freesurfer] FSFAST

On 2/18/15 4:38 PM, sabin khadka wrote: Hi FS Users- After using FSFAST's preproc-sess command (I get the output files: fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz, fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell how well the EPIs are mapping onto

Re: [Freesurfer] Freesurfer with whole brain T1 and partial coverage FLAIR

Hi Ajay if it covers the whoe brain you might be ok, try it and see how it goes Bruce On Wed, 18 Feb 2015, Ajay Kurani wrote: Hello Freesurfer experts,    I have a question regarding the use of the -T2 and -FLAIR flags in freesurfer.  I have 2 scans: 1 whole brain MPRAGE and 1 partial brain

Re: [Freesurfer] Thin Surface

can you check mri_segmet and mris_make_surfaces and see if the auto-detected intensity parameters are reasonable? Things like max gray at csf border and such. If not, you can set them explicitly using the expert opts - this usually works Bruce On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote:

[Freesurfer] cluster colors

Hi FS experts, I had a quick question I was hoping someone could help me with; I used the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) to analyse two groups of subjects. I ran the mri_glmfit command, as well as the clusterwise correction

Re: [Freesurfer] Using TRACULA ROI for image in diffusionspace

Thank you very much Anastasia, May I please check with you if what I am thinking of doing sounds correct? I would use fslstats in FSL with the flag -R which gives me the maximum value. For Forceps major I get a value of 200, 20% of this value would be 40, so then in the path.pd.nii.gz image I

[Freesurfer] Fwd: treatment effect compare to controls

Hi FreeSurfer, I want to study the treatment effect on group pf 20 patients in 2 time points ( 6 month to 2 years) , I have also 2 time points from controls ( 2 to 3 years) . I ran longitudinal pile line and looked at the rate using qdec and the results shows positive significance from zero ,

Re: [Freesurfer] Using TRACULA ROI for image in diffusionspace

Merci bien :). On Wed, Feb 18, 2015 at 2:54 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats, because that will give you a robust maximum (i.e., if there are a couple of voxels that are outliers with a very

Re: [Freesurfer] Using TRACULA ROI for image in diffusionspace

Hi Barbara Anne - Actually it's fine if you use the -r flag in fslstats, because that will give you a robust maximum (i.e., if there are a couple of voxels that are outliers with a very high value it won't take them into account, which is probably a good idea here). Then use 20% of that

[Freesurfer] Freesurfer with whole brain T1 and partial coverage FLAIR

Hello Freesurfer experts, I have a question regarding the use of the -T2 and -FLAIR flags in freesurfer. I have 2 scans: 1 whole brain MPRAGE and 1 partial brain FLAIR (bottom of cerebellum/brainstem gets cut off on some subjects). I wanted to see if freesurfer would still be able to run

[Freesurfer] Register.dof

Hi, I like to transfer a epi file to a T1 space. Is it possible? Thanks, Xiaomin On Tue, Feb 17, 2015 at 1:13 PM -0800, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: We don't have anything to do this directly. However, we do have this tool: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

Re: [Freesurfer] Thin Surface

Thanks, Bruce. I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs. Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable? Do they depend on scanning characteristics or do you have a sort of standard parameters for the software? Regards, Pedro

Re: [Freesurfer] Thin Surface

Hi Pedro I can't tell - you need to click around in the images and see what you think Bruce On Wed, 18 Feb 2015, Pedro Rosa - Gmail wrote: Thanks, Bruce. I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs. Expert opts would be -seg-wlo and -seg-ghi? Which values

Re: [Freesurfer] Register.dof

Hi Doug, Thanks for your response. I did run bbregister to register the EPI to T1, but it did not resample the EPI to T1 space, just generated a register.dof6.dat file, which is expected according to the help document. Also, the help document of bbregister doesn’t indicate resampling or