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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
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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
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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
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
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
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.
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
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
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
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
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,
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
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
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
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
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
Thanks Martin,
The provided command works!
Best,
Victor
Hospital de Sant Pau, Barcelona
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The information in this e-mail is intended
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
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
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