Hi Freesurfer,
How can I get the LGI measurements for each brain region in Desikan atlas?
Instead of getting thickness with aparcstats2table, I want the gyrification
instead.
Thank you.
Cheers,
Shane
--
Shane Schofield___
Freesurfer mailing list
Fr
Dear Shane,
use this command:
mri_segstats --annot my_subject_id lh aparc --i
$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
Look at the info on FreeSurfer wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/LGI
Antonin Skoch
Hi Freesurfer,
How can I get the LGI meas
Hi Arno,
This is fascinating stuff. In my research, I have come across instances when I
felt that a hybrid of ANTS and freesurfer would be very useful. Is this
pipeline possible for data processed with the earlier versions of freesurfer
say 5.1 ? FS6 just got released in Jan 2017 and I am sure
Hello,
Thanks. Seems very interesting!
Is there any way to run this on Mac?
Cheers
--
Shane Schofield ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in t
try making it executable,
chmod a+x mri_binarize
then run rehash and see if it work
On 2/24/17 12:13 AM, Jinsong Tang wrote:
Dear all,
I am trying to run a mri_binarize command on FS 5.3
mri_binarize --i aparc+aseg.mgz --gm --o gmmask.mgz
I obtain this:
ERROR: Option –gm unknown
Based on the subtle issues that arose with previous releases of VirtualBox FS
images, it was decided that a better solution was to simply have users install
a Linux VirtualBox image themselves (e.g. Ubuntu 16) and let them install the
Linux release of FS in that image. This is a much more flexib
Hi Flavia
can you send us the reon-all.log and also what version you are trying to
run?
cheers
Bruce
On Wed, 22 Feb 2017, Flavia Arduini wrote:
> Hi,
> I try tu run this code:
> recon-all -s CAROFILO -i
> /home/matlab/Scrivania/SEGMENTAZIONE/CAROFILO/T2/Phase2/c2scCAROFILO.nii
> -autorecon2-wm
Hi Trisanna
are you sure you aren't running out of disk space? If not, what happens
when you run the mri_convert command directly on the command line?
cheers
Bruce
On Thu, 23 Feb 2017,
Trisanna Sprung-Much wrote:
> Hi All
>
> I am trying to run a subject in 6.0 (it ran perfectly well in 5.3)
HI Yusif
you can read our 1999 paper (Anders Dale first author) for the basics,
although it has evolved considerably since then
cheers
Bruce
On Thu, 23 Feb 2017, yusif
Al-kheder wrote:
> Hello,
> I was wondering how does Freesurfer segment the white matter from the grey
> matter.
>
>
> __
Dear FreeSurfer Experts,
I want to compute some intensity information (e.g., mean and std) of each
Hippocampal subfields (similar to aseg.stats file).
I think one option could be mri_segstats command, but I am not sure.
If it works, what are the inputs of this command?
Thank you in advance for a
Dear Freesurfer experts,
I have used the following commandline to generate the final statistics in my
analysis:
mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum
stats.dat
The final output of this command is (attached). Depedning on the anatomical
location of the ma
Thanks to Docker, you can run it on a mac, it's all explained on the
Mindboggle website.
Olivier
Shane Schofield a écrit :
Hello,
Thanks. Seems very interesting!
Is there any way to run this on Mac?
Cheers
--
Shane Schofield
___
Freesurfer mailin
That is everything that has a segmentation number = 0. You can exclude
it with, --excludeid 0
On 02/24/2017 10:08 AM, John Anderson wrote:
> Dear Freesurfer experts,
> I have used the following commandline to generate the final statistics
> in my analysis:
> mri_segstats --seg aseg.mgz --ctab-
The basic command is
mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
where seg is the hippo sub field seg and input is the input where you
want to get the intensities from (probably norm.mgz). Note that you need
to use the hipp sub field output that is 1mm (not the high re
Great question! You can certainly run Mindboggle on FreeSurfer output for
earlier versions of FreeSurfer. In fact, we did this for part of the work
described in the PLoS Computational Biology article:
"For this study we used FreeSurfer v5.1-derived labels and meshes, but the
recently released Fr
Hi Bruce
I tried and still get the same error. Would this mean a space issue? I'm
not sure how this is possible as I'm working off a 2Tb drive
trisanna@kaplan:~$ mri_convert ./tmp.mri_nu_correct.mni.1798/nu1.mnc
orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.1798/n
Dear TRACULA experts
I run TRACULA FS 6.0 on a Mac and get the following error:
#@# Priors Fri Feb 24 17:11:18 CET 2017
/tmp/subj33.interpreter_control_01/.15208.txt: No such file or directory.
In the FS archive I found the following email
https://www.mail-archive.com/freesurfer@nmr.mgh.harvar
Hi Freesurfer Team,
I am running recon-all on Freesurfer version 6. A few of my subjects have “XL
defect detected …” and their recon-all have been running for more than 20
hours. I hope this is not a silly question, but will this XL defect be
corrected eventually…?
Another question, what are
Hello all,
I recon-all'd ~40 different subjects. I have been going through all the
images to make sure they were processed correctly. Most required no no
editing and recon-all did a very good job.
But for one scan in particular, it looks like Freesurfer thinks the top
of the spinal cord is the br
Hello FreeSurfer Team ,
I was wondering if you could explain to me what the “Left-Hippocampus” and
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail
of the hippocampi? Or everything that is not assigned to one of the other seven
labels?
Additionally I am wondering
Hello Freesurfer Experts,
I received this error while running the make_avg_subject script. I would
greatly appreciate it if you can point me in the right direction.
Also, I do not know how the aparc.annot file is supposed to be created.
not aligning hemispheres before averaging.
zeroing medial
As far as I can tell, everything looks OK up until brainmask.mgz. The
skullstrip step seems to have cropped out the brain and left the neck...
On Fri, 2017-02-24 at 12:58 -0600, Elijah Rockers wrote:
> Hello all,
>
> I recon-all'd ~40 different subjects. I have been going through all the
> images
OK, sorry for spamming the list. I fixed the the faulty skullstrip by using
recon-all -skullstrip -clean-bm -no-wsgcaatlas -subjid
Currently redoing the surface reconstructions, but it should be OK now.
Thanks for the nice documentation.
Eli
On Fri, 2017-02-24 at 15:30 -0600, Elijah Rockers wr
Hi Jessica,
I believe that those are the old labels. What version of FreeSurfer are you
using? 5.1 - 5.3? If so, you should upgrade to 6.0.
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmic
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