Re: [Freesurfer] Color LUT help

Hi Stephanie - The arcuate fasciculus is reconstructed when you run TRACULA on your diffusion data, but it is not an ROI. Please refer to the tutorial for how to run TRACULA and how to visualize the tracts: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula a.y __

Re: [Freesurfer] TRACULA exports white matter tract labels without DTI data

Hi Yong - If you do not have diffusion data, you won't be able to map your subjects' white matter tracts. In a T1 scan there is no contrast between white matter tracts that would allow you to segment them, as white matter looks uniform. All you could do is transform some generic labels from an a

Re: [Freesurfer] TRACULA tracts corrections

Hi Joelle - See my previous email, you should download the 6.0 version. In this version TRACULA will attempt to detect which tracts require reinitialization, so hopefully you'll see an improvement in this. a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [frees

Re: [Freesurfer] TRACULA tract reconstruction

Hi Joelle - From your trac-all.log file it looks like you're not running the official 6.0 release but a beta version: build-stamp.txt: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae This does not include the TRACULA updates that were included in the final 6.0 version. Please download 6.0

[Freesurfer] Volume comparison between groups and QDEC

Dear Dr Doug, I have two groups of subjects (80 patients and 40 controls). I analyzed the data using Freesurfer v6.0. I want to study the difference between the groups in "precentral gyrus volume". After "recon-all" I built Qdec table and I used Qdec to compute the comparison by including eTIV a

Re: [Freesurfer] recon-all freezes while CORRECTING DEFECT 60

Hi Daniel you can load the ?h.defect_labels as an overlay on either the inflated.nofix or orig.nofix surface and use it to find the location of that defect. Usually this means something big is wrong - it should be obvious looking at the inflated.nofix I would think. If you can't find it, uplo

Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS coordinate

when you specify -n it write out surface normals instead of surface locations. Or you can use Doug's method cheers Bruce On Tue, 9 May 2017, Jerry Jeyachandra wrote: Hi Bruce, Thanks for the response. I've run the operation and have examined the output. From my understanding the file conta

Re: [Freesurfer] Maps showing correlations between structural measures

Dear Dr. Greve, I created two stacks: one with volume and the other with LGI using mris commands as following: mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas volume --out Corr_CV_LGI/lh.vol.mgh mris_preproc --fsgd CV_LGI.fsgd --target fsaverage --hemi lh --meas pial_lgi --out

Re: [Freesurfer] mri_convert : pix vs no pix ?

When freesurfer reads in an img/hdr file, it makes assumptions about the how the data are oriented, so, implicitly, you are using orientation info. If you do not have a .mat file, then you can't change the header, so you have to change the pixels On 05/09/2017 01:45 PM, Shane Schofield wrote:

Re: [Freesurfer] mri_convert : pix vs no pix ?

Sorry, I don't quite understand yet.. Would the header be important as I am not using img / hdr ? Under what sort of circumstances would pix be favourable? I am using .nii after executing mri_convert to go from img/hdr to nii. I note that pix is used in other older threads too. On Tuesday,

Re: [Freesurfer] Obtaining surface normal vector from plial surfaceRAS coordinate

Hi Bruce, Thanks for the response. I've run the operation and have examined the output. From my understanding the file contains both a vertex list (XYZ) and a face list containing (V1,V2,V3...). Is the XYZ of the vertex list the actual surfaceRAS coordinates of the surface as viewed on FreeView

Re: [Freesurfer] mri_convert : pix vs no pix ?

When the pixel data are flipped, you are actually changing the way that the data are stored on disk (while keeping the direction info in the header constant). On 05/09/2017 12:52 PM, Shane Schofield wrote: > Dear Doug, > I am trying to flip some PET images so that they are in the same > orien

[Freesurfer] mri_convert : pix vs no pix ?

Dear Doug,I am trying to flip some PET images so that they are in the same orientation as the T1.I came across this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29281.htmlCan you explain what what it means to change the pixel data? Should I use pix or without pix? For cont

Re: [Freesurfer] illustration of a nifti volume on fsaverage

Hi James if it is registered to MNI space I guess you could do vol2surf directly on fsaverage, but it won't be very accurate and will for sure miss things cheers Bruce On Tue, 9 May 2017, james pardon wrote: Thank you Bruce. What if the nifti volume has not been processed at all in Freesur

Re: [Freesurfer] Multicenter studies

For the interaction it would be 0.5 -0.5 -0.5 0.5 On 5/9/17 8:32 AM, Laura Ferrero Montes wrote: > >Thank you for the information. I just want to be sure if I have > understood it properly. >If I had two groups and two sites, my design matrix would be like: > > GroupDescriptorFile 1 > Cl

Re: [Freesurfer] Mri_segstats on longitudinal data (NVoxels)

Sorry, I'm not sure what you are trying to do. Can you send command lines? On 5/9/17 6:42 AM, Ferdi van de Kamp wrote: Hi all, My question is twofold using an user specified ROI in MNI512-space I ask Freesurfer to create tables for both cross-sectionally& longitudinally processed data. M

Re: [Freesurfer] illustration of a nifti volume on fsaverage

You can use mri_coreg to register the volume to fsaverage, then use the registration when running freeview or tksurfer On 5/9/17 10:19 AM, james pardon wrote: Thank you Bruce. What if the nifti volume has not been processed at all in Freesurfer? My only aim is to illustrate an overlay on FSAV

Re: [Freesurfer] White matter volume of a costumized Gyrus

You will need to create an annotation with your label in it. This might be tricky to do depending on what you want. The easy way is to run mris_label2annot with only your label, then run mri_aparc2aseg to generate something like the wmparc.mgz (look in the recon-all.log file for the command lin

Re: [Freesurfer] illustration of a nifti volume on fsaverage

Thank you Bruce. What if the nifti volume has not been processed at all in Freesurfer? My only aim is to illustrate an overlay on FSAVERAGE, with the obvious caveat of skipping surface construction for this nifti. Thanks, James On Tue, May 9, 2017 at 2:42 PM, Bruce Fischl wrote: > if the nifti

Re: [Freesurfer] illustration of a nifti volume on fsaverage

if the nifti volume is from an individual subject that has been run through recon-all (e.g. an fmri map): 1. Use bbregister to register the fmri to the recon surfaces 2. Use mri_volsurf to sample the fmri data onto the surface 3. Use mri_surf2surf to map from the individual to fsaverage cheers

Re: [Freesurfer] White matter volume of a costumized Gyrus

Hi Josue how would you define the borders of the white matter of the gyrus? I guess you could use the wmparc stuff and just count voxels based on a distance constraint cheers Bruce On Tue, 9 May 2017, Josue Luiz Dalboni Da Rocha wrote: Dear Freesurfer team, I am working with calculat

Re: [Freesurfer] Multicenter studies

Thank you for the information. I just want to be sure if I have understood it properly. If I had two groups and two sites, my design matrix would be like: GroupDescriptorFile 1 Class PatientsGroup1 Class PatientsGroup2 Class ControlsGroup1 Class ControlsGroup2 If I want to test for the

[Freesurfer] illustration of a nifti volume on fsaverage

Dear All, Apologies in advance for the naive question. Could you please let me know what is the best way of transferring a nifti overlay volume to fsaverage, solely for illustration purposes? I think I should start by registering with fsaverage volume and then overlay with Freeview, but I'm not s

[Freesurfer] White matter volume of a costumized Gyrus

Dear Freesurfer team, I am working with calculated volumes of a gyrus (a costumized label). I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in label format). According to the freesurfer tutorial (as I understood), one of the stats outputted from mris_anatomical_sta

[Freesurfer] Mri_segstats on longitudinal data (NVoxels)

Hi all, My question is twofold using an user specified ROI in MNI512-space I ask Freesurfer to create tables for both cross-sectionally& longitudinally processed data. Mri_segstats performed over both cross-sectional data folders and longitudinal data folders However, when inspecting the data,

Re: [Freesurfer] REPOST: Two stage model question

Hi Martin, thanks for your reply. From your email I understand that looking at the rate of change between time points is more useful than spc if I want to look at only 2 time points at a time. I have a pre training scan, a post training scan (approximately 3 weeks apart with a training interv

[Freesurfer] Probabilistic atlas illustration

Dear all In the paper "A computational atlas of the hippocampal formation using *ex vivo*, ultra-high resolution MRI" (DOI:10.1016/j.neuroimage.2015.04.042 ;2015) y