[Freesurfer] Multiple and equidistant circular ROIs on the surface

Hi FS expert, I was wondering if it is possible to create multiple "circular" ROIs on a surface with equidistant distance. Since the distance between vertex is not constant, it works if the number of vertices between ROIs it is the same. Any suggestion will be very appreciated! Thank you in advan

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Hi Doug, We conducted a cortical thickness analysis in patients versus controls and generated a group atrophy map. We additionally conducted a resting state functional connectivity study in volume space using healthy controls. Ideally we would like to create a series of circular ROIs evenly distr

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Thanks Bruce and Doug, this works. Currently, I am trying to do a similar thing, but delimiting the parcellation in one concrete region instead the whole cortex.To do that i tried: 1) Convert the label (concrete brain region) into an annot file [ mris_label2annot ]. 2) Use mris_divide_parcellatio

Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

Thank you for your fast reply, Bruce. (1) *** mris_label2annot: [ejones:test] (nmr-stable53-env) mris_label2annot --s fsaverage/ --h lh --ctab ColorTest.txt --a test --l mask_region_ROIS.label Reading ctab ColorTest.txt Number of ctab entries 2 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:3

[Freesurfer] volume DTI metrics to sruface

FS experts, I have seen several posts regarding volume-to-surface projections, but I am not 100% confident about which parameter should I use with mri_vol2surf that better fit my needs. Currently, my data are several DTI-metric volumes per subject already normalized to MNI152 space (both 1mm and

[Freesurfer] glmfit flag --frame-mask

Dear FS Experts, I have seen few posts about this mri_glmfit flag, and I would like to know how it works. In an older post, ( https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32412.html), Doug suggested to use this flag when only some subjects should be exclude for each vertex (i,

[Freesurfer] mri_glmfit version

Dear FS experts We have been playing around with different mri_glmfit versions. I processed all my data with FS v5.1, and then I run the mri_glmfit with both the 5.1 and 5.3 versions, using exactly the same X, same contrasts matrix and obviously the same images. Our concern is that the results dif

[Freesurfer] Qdec/Tksurfer keyboard input error

Dear Freesurfer experts: Recently, I have update my OS to Ubutnu 16.04. Afterwards, I tried to re-run some analysis using Qdec 1.4 (stable 5.1) and Qdec 1.5 (stable 6.0). However, I am not able to input any threshold via my keyboard (neither the Subjects or Display tab). This issue also happens wh

Re: [Freesurfer] PVC on DTI

Dear Doug, We are trying to compute partial volume correction in DWI images, using your PEtsurf approach, to correct CSF contamination. Afterwards, we will compute whatever DTI metric from the corrected data and project it to surface. As you suggested in your previous post (https://www.mail-archi

[Freesurfer] PETsurf non linear registration

Dear Freesurfer experts, I have been working with the PETsurf pipeline. I was wondering if there is any chance to use a non-linear registration (i.e ANTS) in order to compute the %tissue per voxel in native space. Currently, I am using your pipeline to process DWI data. Due to some EPI artifacts

[Freesurfer] PETsurf and mri_compute_volume_fractions

Dear FreeSurfer experts, I am trying to obtain partial volume fractions of a DTI volume. When using the PETsurf framework (mri_gtmpvc), I obtain a pvf.nii.gz volume with GM, WM, subcortical, CSF and Skull tissue % values. However, when running the mri_compute_volume_fraction, the output diffears.

[Freesurfer] LME Matlab toolbox

Greetings, The aim of this mail is about some problems that I am facing using the standalone copy (that is becouse I am using v5.1) of the LNE Matlab Tool provided on the FreeSurfer Wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels). Currently, I am carrying out a longitud

[Freesurfer] asegstats2table Longitudinal data.

FS experts, The aim of this mail is about some errors I had encountered when I try to generate a table from some *.stats files obtained after a longitudinal analysis. After running the command : *long_stats_slopes --qdec ./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas v

Re: [Freesurfer] asegstats2table Longitudinal data.

Thanks Martin, The provided command works! Best, Victor Hospital de Sant Pau, Barcelona ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended

[Freesurfer] Surface-based kernel operations

Dear Freesurfer experts, I would like to preform several operations in surface files using spatial kernels (i.e mean value in a 3x3 grid, nearest neighbour value, etc). In summary, perform operations in the surface such as a 2D matrix/image. Is it possible to do it with Freesurfer? I tried to ope

Re: [Freesurfer] Surface-based kernel operations

Thanks Bruce and Doug! Bruce, I think the option of the sphere is the one that better fits my needs, since I need to perform conv operations + derivatives. How should address this issue? I am not very familiar with sphere files (nor metric tensors) and do not know how to open/where to find those f

[Freesurfer] Version Beta 7.0

External Email - Use Caution Freesurfer developers, I have seen from the download webpage, that there is already a v7.0 beta version. Since we were planing to re-run a lot of individuals 1000+ with Freesurfer6, I was wondering if you could provide timings regarding the release of s

[Freesurfer] Deface DICOM

External Email - Use Caution Dear FS experts, I am using mri_deface to annon our data. Nevertheless, for a recent project, we were requested to share our DICOM original files, instad of .nii or .mgz. Thus, I was wondering if you know a simple way to deface T1 data inputing a DICOM

[Freesurfer] version upgrade/migration

External Email - Use Caution Dear Fs experts, We have multiple subjects with strong/focal atrophy processed with Freesurfer5.1 We want to re-process them to the newest version in order to have all the capabilities/segmentations/outputs from the newest recon-all, but we do NOT want