Re: [Freesurfer] White matter surface don't change after editing

> Hi Dear Bruce > Thanks very much for your reply, I improved min_border_white to 100, > the lh.white line shrinks but still is far out in some area, and I notice > many topological defect appears as a result. > I failed to upload subject through ftp, it's always appear an error >

[Freesurfer] Projecting processed 4D functional data to individual surfaces

Hi All, I'm trying to project some processed resting-state data onto the surface to run some surface based parcellations, and I'm running into a bit of difficulty. Basically I'm using bbregister to register my functional to the T1, then mri_vol2surf to project to the surface with the

Re: [Freesurfer] mris_calc cluster infos

'mris_calc' is designed to perform be a simple "calculator" that performs a set of operations between two operands of the same type. These operands are either 3D structures (like volumes) or 1D arrays (like curvature files). You can add/subtract/multiply/divide/etc two operands. How would

Re: [Freesurfer] Gaussian curvature or Mean curvature

Dear Bruce Fischl, Thank you for your help. Best Regards, Han Byul Cho On Fri, Sep 16, 2016 at 8:27 PM, Bruce Fischl wrote: > Hi Han > > the ?h.curv files are the mean curvature of the white matter surface with > a Gaussian smoothing kernel applied to it over

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Anderson, My full design contrasts are below: /ContrastName1 HC > Grp1 /ContrastName2 HC < Grp1 /ContrastName3 HC > Grp2 /ContrastName4 HC < Grp2 /ContrastName5 Grp1 > Grp2 /ContrastName6 Grp1 < Grp2 /ContrastName7 M > F /ContrastName8 M < F /ContrastName9 HC/Grp1 M/F Interaction

[Freesurfer] Anatomy File Orientation Question

Hi all, I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz brainmask.nii.gz (then used

Re: [Freesurfer] FoV in additional scan

It does perform a registration, but this requires a decent initial alignment. Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 19 Sep 2016, at 14:43, pierre deman

Re: [Freesurfer] FoV in additional scan

Okay, thanks! Best, Renata On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Hi Renate, > as long as the additional scan is more or less aligned with the T1 in > physical coordinates (i.e., they appear decently aligned when you open them > in

Re: [Freesurfer] FoV in additional scan

Hi Renate, as long as the additional scan is more or less aligned with the T1 in physical coordinates (i.e., they appear decently aligned when you open them in Freeview), you should be fine and not need to do anything. Cheers, /E Juan Eugenio Iglesias Senior Research Fellow Translational

Re: [Freesurfer] FoV in additional scan

Does it perform a coregistration automatically when specified two images or is it better to perform it before running the recon-all ? On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Hi Renate, > as long as the additional scan is more or less aligned

[Freesurfer] FoV in additional scan

Dear Eugenio, We have another question about the Hippo Sf Segmentation with an additional scan. Some of our additional scans (FLAIRs or T2s) have a bigger field of view as compared to the T1 (ex.: they cover more of the neck almost up to the shoulders of the subjects, while the T1 has the

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

ok thanks. Cheers, Pierre On Mon, Sep 19, 2016 at 3:17 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Yes, you have so specify it separately. > Cheers, > /Eugenio > > > Juan Eugenio Iglesias > Senior Research Fellow > Translational Imaging Group > University College London >

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

Yes, you have so specify it separately. Cheers, /Eugenio Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 19 Sep 2016, at 14:13, pierre deman

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

Hi, I have a short question about the additional T2 scan as well. If I perform the full recon-all; recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all -hippocampal-subfields-T1T2 do I still have to precise myT2scan.nii.gz T2 for using the t2 for the hippocampal subfields as well ? or it

[Freesurfer] make_average_volume problems

Hi all, I'm trying making average volume from a set of subjects after making average-subject, but I get this error line: mghWrite(/home/Admin/Scrivania/SUBJ/average/tmp/make_average_vol-tmp-7513/orig-subj1/.mgh, -1): could not open file And then: Applying LTAtransformInterp (resample_type 1)

[Freesurfer] Course in Advanced Neuroimaging (Barcelona)

Dear colleagues, I am pleased to announce our upcoming Course in Advanced Neuroimaging held annually in Barcelona. It takes a practical approach and does not require qualifications or previous experience in neuroimaging. It will be taught in Spanish. The multidisciplinary programme provides

[Freesurfer] Antwort: Re: Dev builds not found

Hi Freesurfer users, I have the same problem as Leila - I am in need of the latest dev build and would really appreciate if someone could put it on another site where we could download it as long as the server is down. Hope that is possible! Best wishes Jessica

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Ajay, The mask is a file of the "curvature" type, that is, it contains vertexwise data, and should mask out the "unknown" region (that region in the medial aspect that is not cortex and is there to ensure the topology is the same as that of a sphere). The mask can alternatively be a .mgz file