[Freesurfer] mri_vol2vol

Hi Freesurfer experts I am always a little confused with the registration matrices from tracula output. If we need to have the DTI maps like dtifit_MD.nii.gz in the recon space, do we use the matrix anatorig2diff.bbr.dat? mri_vol2vol --mov //dmri/dtifit_MD.nii.gz --targ //mri/brainmask.mgz --reg /

[Freesurfer] Tracula - set echo spacing

Hi Anastasia and Tracula experts, We are running a new set of tracula analysis from Bay 6 and are wondering how do we define the number of echo spacing in the dmrirc file. Is it a number that we get from the header of the field map dicoms? set echospacing = ... Thanks a lot Celine -- Celine

Re: [Freesurfer] mri_cvs_register using high resolution images

ransform that you computed to align your lowres and high res volumes? > Lilla > > On Wed, 6 May 2015, Celine Louapre wrote: > >> Thank you Lilla for the suggestion. >> You mean that I should run mri_cvs_register on the high res volume, is >> that correct? In that case, h

Re: [Freesurfer] mri_cvs_register using high resolution images

> Could you compute the registration with the high res volumes, maybe with > an initialization from the low res volumes? > > Lilla > > On Wed, 6 May 2015, Celine Louapre wrote: > >> Hi Freesurfer experts >> I am planing to do a voxelwise group analysis

[Freesurfer] mri_cvs_register using high resolution images

Hi Freesurfer experts I am planing to do a voxelwise group analysis from images acquired at 7T, and I wanted to use the mri_cvs_register script, which gives very nice normalization outputs. I was wondering how to adapt the script to images that we have with 0.33mm isotropic resolution, and which ar

[Freesurfer] TRACULA: distance between tract sections in pathstats.byvoxel.txt

between 2 sections along one tract? Thank you Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list

Re: [Freesurfer] Problem with a recon edit

ection (wm_edit_3.png). Do this for a few slices around each location > that needs to be pushed out so that it has more effect, then save the wm > volume and rerun recon-all. > > Hope this helps, and let me know if you have any more questions. > > Best, > Lee > > On Wed,

Re: [Freesurfer] Problem with a recon edit

Hi everyone I don't know if someone had the chance to look at the data we uploaded for advice to edit the recons (see below). Thank you so much Celine On Fri, 2015-01-16 at 11:43 -0500, Celine Louapre wrote: > Thanks Bruce > The aseg is correct, no ventricule labeled there (I was u

Re: [Freesurfer] Problem with a recon edit

i Celine > > hard to tell from the slices. Are there voxels labeled ventricle there? > If so, you need to correct the aseg. If not, it's probably a topological > defect that is fixed incorrectly. If you upload the subject we'll take a > look > Bruce > On Fri, 16 Jan 2

[Freesurfer] Problem with a recon edit

ime I couldn't have it work correctly. Would you have a clue to help me on that? I can put the data in some folders if you want to take a look at the entire volumes. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radi

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

way to work around, or should I just try to do it only from non pvr glm analyses? Celine > > X and C have different numbers of columns. What was your mri_glmfit > command line? If you used a --pvr, then the pcc script will not work. > doug > > On 09/22/2014 01:21 PM, Ce

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

> should be something like cache.th13.abs.y.ocn.dat > also, you can look in mri_glmfit-sim --help to get info about each > output file > > On 09/19/2014 04:47 PM, Celine Louapre wrote: >> Indeed I ran mri_glmfit-sim. What file is the output of mri_segstat? >> The cache.th13.abs.

Re: [Freesurfer] Scatter plot from mri_glmfit analyses

create labels (ie, annotations) of > the clusters as well as run mri_segstats to get means in each cluster > for each subject. Try that link now > doug > > On 09/18/2014 12:15 PM, Celine Louapre wrote: >> Hi Doug and FS team >> >> I did glm analyses using m

[Freesurfer] Scatter plot from mri_glmfit analyses

Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the gl

Re: [Freesurfer] select_talairach_point function?

Hi I just find out how to launch the command, it is in the terminal where tksurfer is running, after the % sign. (I didn't understand what the tcl window was meaning) Best Celine > Hi > I am sorry if my question is really basic, but I am choosing the seeds for > fsfast resting state connectivity a

[Freesurfer] select_talairach_point function?

Hi I am sorry if my question is really basic, but I am choosing the seeds for fsfast resting state connectivity analysis, and I am looking at the different options in the litterature. Seeds are often presented with the talairach coordinates, and I was looking for a way to find the corresponding ver

[Freesurfer] Extract seed from resting state networks mask (Yeo and Buckner maps)

Best Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

line - This command assumes that --intrc is a tracula output > directory, containing all the files that tracula saves in such a > directory. What are you trying to get stats from? > > a.y > > On Mon, 3 Mar 2014, Celine Louapre wrote: > >> Hi Anastasia >> I have fi

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

> This will regenerate all the pathstats.* files, but now the parts of the > tract that go through the lesions will have zero values (or very low, if > they're mixed in with some neighboring voxels). > > Let us know if this worked! If not I may be able to implement something.

Re: [Freesurfer] Pb with a registration of diffusion images processed with tracula and anat images

TI data in the same session. For this subject, were they acquired in >> different sessions or was the subject removed and replaced back in the >> scanner? When you sample the data onto the surfaces, you should always >> use a registration file. >> >> doug >> >> On 02

[Freesurfer] Pb with a registration of diffusion images processed with tracula and anat images

e DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Departme

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]

't it? > > > > doug > > > > > > On 2/17/14 10:41 PM, Celine Louapre wrote: >> The lesion_vol2vol volume is still not correctly overlapping the DTI. >> >> The only command that didn't give me registration issue is mri_convert >> wh

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]

olate and then binarize the mask was one possible option). I can show you the results tomorrow if you prefer Celine > > what does it look like if you run > > tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1 > > > > On 2/17/14 10:00 PM, Celine Louapre wrote

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]

rong? > doug > > > > > On 2/17/14 9:30 PM, Celine Louapre wrote: >> Hi Doug >> I don't know if you had the chance to read my email below to resample a >> lesion mask on diffusion images. Anastasia gave me the registration file >> to use (anatorig2diff.bbr

[Freesurfer] Resample a mask on diffusion images using bbregister registration matrix

threshold parameter but it does not solve the problem of the registration file? also mri_convert And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension as the diffusion space? Thanks a lot Best Celine -- Celine Louapre, MD-PhD Research

Re: [Freesurfer] resample lesion mask on diffusion images processed with tracula

n pass to mri_vol2vol the dmri/xfms/anatorig2diff.bbr.dat > transform. That's the one generated by bbregister for the > anatomical-diffusion registration. > > Hope this helps, > a.y > > On Thu, 13 Feb 2014, Celine Louapre wrote: > >> Hello freesurfer team >> I have

[Freesurfer] resample lesion mask on diffusion images processed with tracula

Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found sev

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

ould be applied to DTI maps that were > masked by the lesions?) > I would like to keep the advantage of having the DTI weighted metrics in > particular. > Thanks a lot for your help! > Celine > > -- > Celine Louapre, MD-PhD, > Research Fellow at Massachusetts General Hospita

[Freesurfer] Compute DTI metrics in NAWM in Tracula

exclusion of the lesion? (I guess the last step of trac-all -path could be applied to DTI maps that were masked by the lesions?) I would like to keep the advantage of having the DTI weighted metrics in particular. Thanks a lot for your help! Celine -- Celine Louapre, MD-PhD, Research Fellow at

Re: [Freesurfer] GLM p value display

eline > Hi Celine, you should report the clusterwise p-value (which is neither > of those). > doug > > On 12/17/2013 12:11 PM, Celine Louapre wrote: >> Hi all >> I am wondering what is the best to present GLM results in a table on top >> of the visual display.

[Freesurfer] GLM p value display

? Thanks for advices Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https