Re: [Freesurfer] mri_average vs mri_concat

what is a labeled vertex? What file format? mgz? annot? On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote: > the source files are labelled vertices from 20 subjects: > > -T1s were labelled using an MNI software > -Surfaces were created in FreeSurfer and surface overlays of the > labels were

[Freesurfer] Postdoctoral Position at UCSF in California, USA on cognitive neuroscience of language processing

The Hoeft Lab (http://brainLENS.org PI: Fumiko Hoeft MD PhD) at the UCSF Dept of Psychiatry and Weill Institute for Neurosciences is looking for an exceptional postdoc in the field of neurolinguistics, with advanced neuroimaging, computational, programming and

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

I think the difference in voxel size (1mm vs 1.3mm) is problematic. You will get more smoothing with the 1.3mm (ie, partial volume effects), and that could easily show up in the thickness measurements On 10/05/2016 12:19 PM, Martin Juneja wrote: > Hi Dr. Greve, > > After I compare the two

Re: [Freesurfer] Quantifying volumes

Dear Douglas, I have a ".curv" file that contains the curvature information inside an automatically delineated ROI and 0 everywhere else. I would like to calculate the volume of this ROI, Can I extract statistics directly from the ".curv" file? Best regards, Josue

Re: [Freesurfer] Quantifying volumes

Hi Josue the *.curv won't help you with the volume. If it is a label file you should be able to give it to mris_anatomical_stats with -l to compute the volume cheers Bruce On Wed, 5 Oct 2016, Josue Luiz Dalboni Da Rocha wrote: > Dear Douglas, > > I have a ".curv" file that contains the

Re: [Freesurfer] Quantifying volumes

Dear Bruce, Thank you very much for your answer! Can I convert the data from '.curv' to '.label' in order to extract the volume? What I was trying to do was to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label). Is it

[Freesurfer] group analysis

Dear FreeSurfers, I would like to study the interaction between age and cortical thickness in patients and controls. My hypothesis is that there is an interaction and that cortical thickness is decreasing faster with age in patients than in controls. I have both Male and Female included in 6

[Freesurfer] [FreeSurfer] TRACULA Registration transform matrix

Hi experts, We're trying to convert an ROI in T1 MRI space to diffusion space in order to collect FA values from the ROI (using TRACULA output files). Is there a t1 to dwi transform matrix to use with TRACULA? Thanks, Lauren ___ Freesurfer mailing

[Freesurfer] ERROR: QdecGlmDesign::Create: bad factor!

Dear freesurfer team, I was trying to run QDEC with two discrete factors but I got this error and could not quite figure out what is wrong. Your suggestion would be highly appreciated. The table and the error is as shown below: Data table /Applications/freesurfer/subjects/qdec/qdec.table.dat

Re: [Freesurfer] MS lesion - white / pial surface issue

I believe this is fixed in V6, but if you upload a dataset we can try it out and confirm cheers Bruce On Wed, 5 Oct 2016, Fire Tech wrote: Dear freesurfer experts   working with MS patients I have several subjects with pial/white surface issues due to wm lesions. Following a suggestion I

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Hi Dr. Greve, After I compare the two protocols (after using mri_info in FSL on raw dicom file), I get following parameters used in both the protocols. After looking at both the protocols parameters below, could you please share your thoughts on whether parameters are in match enough to go ahead

Re: [Freesurfer] FreeView questions

Hi Anders, Try turn off/on color bar or change the overlay thresholds to see if it updates. I believe this is fixed in v6.0. As to rotate the 3D view by certain degrees, there is no GUI for that. You can do that in the command-line via "-cam" options. Run "freeview -h" for more info on how

Re: [Freesurfer] group analysis

there is a tutorial with similar variables available here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Oct 5, 2016 at 9:22 AM, charles laidi

Re: [Freesurfer] Input file in subcortical analysis using mri_glmfit

We don't have a program for it. You can do something in matlab, like a = MRIread('aseg.mgz'); ov = a; % create a new volume ov.vol = zeros(size(ov.vol)); % set all voxels to 0 ind = find(a.vol == 17); % left hippo from FreeSurferColorLUT.txt ov.vol(ind) = ValueForLeftHippo; % Do the same

Re: [Freesurfer] Functional Connectivity Follow-up question

I don't know that there will be a big difference. The surface-based fMRI time course originally comes from the volume of course, so you're not freeing yourself from the voxels. If you want to extract the time course from the surface, you can do it with something like cd session/bold/002

Re: [Freesurfer] Quantifying volumes

Hi Josue sorry, I'm confused. What does the curv file have to do with your ROI? Curv is a format for storing a scalar field over the surface and the ?h.curv file typically contains the spatially smoothed mean curvature cheers Bruce On Wed, 5 Oct 2016, Josue Luiz Dalboni Da Rocha wrote: >

Re: [Freesurfer] Input file in subcortical analysis using mri_glmfit

Thank you for your response. I ran the mri_glmfit with the aseg table rather than --y as you suggested. I am interested in visualizing the results of the mri_glmfit analysis in the form of "blobs" indicating the brain regions in which groups differ (as possible with freeview or tksurfer in

Re: [Freesurfer] Quantifying volumes

I would binarize the curv file with mri_binarize --i lh.yourcurvfile --abs --min .001 --o lh.yourcurvfilebin.mgh Then compute the volume with mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum On 10/05/2016 09:09 AM, Josue Luiz Dalboni

[Freesurfer] MS lesion - white / pial surface issue

Dear freesurfer experts   working with MS patients I have several subjects with pial/white surface issues due to wm lesions. Following a suggestion I found in the mailing list using aseg to classify these areas as right /left lesion I get much better results for white surface. However the pial

Re: [Freesurfer] group analysis

This is a straightforward extension to the FSGD examples. You have 3 discrete factors (2 diagnosis, 2 gender, 6 centers), this yields 2*2*6=24 classes. With one covariate, you would have 24 covariate regressors (one for each class) for a total of 48. You would then need to create a contrast

Re: [Freesurfer] mri_average vs mri_concat

what are the source files ("all files"). What data type, value range, where did they come from? On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote: > Hi Doug > > So, of course now it works without --keep-filetype... :p it looks > pretty much the same was when I use --keep-filetype. > >

Re: [Freesurfer] mri_average vs mri_concat

Depending upon the type of the data, the --keep-datatype may mess things up quite a bit. What happens if you don't include that? It will not create an annotation. maybe you mean some other file type? On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote: > > Hi Doug > > I spoke with you at the

Re: [Freesurfer] mri_average vs mri_concat

the source files are labelled vertices from 20 subjects: -T1s were labelled using an MNI software -Surfaces were created in FreeSurfer and surface overlays of the labels were created using mri_vol2surf -Surface overlays were registered to fsaverage using mri_surf2surf and then averaged to create