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Hello FSL and Freesurfer Experts,
We are trying to find the paths between 5 fMRI ROIs (seeds).
We are using the --network option.
How do we go about thresholding the fdt_path.nii.gz?
Thanks so much,
Joe
probtrackx2 --network -x ${dtidir}/seeds.txt -
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Hello Vittal,
Your output resembles the error from a previous post about running the old
Freesurfer 5.3 release on Ubuntu 16,
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-May/045393.html
You can try running that command listed at t
Hi Vittal
how much RAM do you have in your machine? Looking at the top of the
recon-all.log it seems like you have less than 1G. In general we
recommend a minimum of 2, which I suspect is the issue
cheers
Bruce
On Tue, 8 Jan 2019,
vittal korann wrote:
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Dear Freesurfer experts,
We installed today (8 jan 2019) the last version of Freesurfer dev and the
corresponding Runtime Matlab R2014b .
We tried segmentHA_T1.sh with bert to check if it worked.
We had a couple of errors related to an Invalid Mex-file
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Hello Alba,
As of Mac OS 10.11, El Capitan, DYLD_LIBRARY_PATH and
DYLD_FALLBACK_LIBRARY_PATH are ignored as environment variables at run time.
Same for all subsequent releases: Sierra = 10.12; High Sierra = 10.13;
Mojave = 10.14.
You could try sett
Dear FreeSurfers,
I am trying to update an mris_pmake command line that works with the pub v5.3.0
version with a new command line that works with pub v6.0.0 version. The purpose
is to compute the distance between two vertex points on the pial surface using
the cvs_avg35_inMNI152 brain. We are
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Is there a recon-all flag similar to -label_v1 or -ba-labels to automatically
create label and stat files for Yeo network parcellations?
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Dear Freesurfer experts:
I am on ROI analysis tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0
And I am trying to understand the relationship between:
/label/?h.aparc.annot and /mri/aparc+aseg.mgz
/label/?h.a
Hi Yerong
the parcellations are done on the surface to generate the annot files.
These are then sampled into the cortical ribbon to extend the aseg so that
every voxel in the cortex is given a label from the corresponding annot
file (aparc+aseg.mgz from aparc.annot and aparc.a2009s+aseg.mgz fro
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Recon all takes the vertices and assigns them to a parcel using the gcs
atlases ... these labelings are the annot files and they are used to
generate the autoparcellated pial surfaces
Because there are 3 atlases in the recon all pipeline... three
p
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Dear Bruce:
Thank you.
So my question would be if aparc+aseg.mgz is from ?h.aparc.annot and
aparc.a2009s+aseg.mgz is from
?h.aparc.a2009s.annot.
Then how I can find the mapping between labels in aparc+aseg.mgz to
labels in ?h.aparc.annot?
The l
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Dear Freesurfer experts:
In notice "mris_sample_parc" samples a volumetric parcellation onto a
surface, I am trying to find a program that samples "annot" files to
volumetric parcellations. I need to know the connection between labels
in [lh.apar
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Hi! FS Experts!
In the fMRI experiment, there are 2 conditions:
1# 3D picture
2# zero disparity picture
interleaved with fixation block (0).
To compare 3D-vs-zero disparity, I used command:
mkcontrast-sess -a 1 -c 2 -nosumconds
but the results showe
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Dear freesurfer experts,
I would like to do subcortical divide parcellation, such as the hippocampus.
By my understanding in freesurfer, the cortical parcellation can be saved as
vertices but subcortical parcellation is only saved as volumes.
The
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