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Thank you Bruce. This really helped.
- Original Message -
From: "Bruce Fischl"
To: "freesurfer"
Sent: Thursday, May 31, 2018 6:40:16 PM
Subject: Re: [Freesurfer] white matter and grey matter
Hi Ritesh
Ruopeng can help you with freeview, but
Dear all,
I am trying to do slicing timing correcting with Siemens’s 3T Prisma data at
acceleration 3. I am told that I can use “-ngroups” when running
"preproc-sess”. How do I use the “-ngroups” flag? Should I do “-ngroups 3”?
Would fs-fast automatically compute the slice timing file and apply
yes, I think contra-lesional might be ok
On Thu, 31 May 2018, Guillaume
Bellanger wrote:
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Hi Bruce,
Thanks for you answer.
I am trying to relate mean cortical thickness with cognitive impairment in a
stroke population (cortical and sub
cortical
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Hi Bruce,
Thanks for you answer.
I am trying to relate mean cortical thickness with cognitive impairment in a
stroke population (cortical and sub cortical strokes).
Should I exclude patients with cortical lesions/ create a mask/ look only on
contro-
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Dear all,
The problem should be fixed in the Linux builds. The MAC update will come in
the next couple of days.
Apologies again for the inconvenience.
/Eugenio
Juan Eugenio Iglesias
Centre for Medical Image Computing (CMIC)
University College Lo
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Hi again,
the binaries are under $FREESURFER_HOME/bin, in your case,
/opt/freesurfer-6.0.0/bin.
After sourcing FreeSurfer, is /opt/freesurfer-6.0.0/bin in your path? If it is,
I can't understand why the code wouldn't find the executables...
Cheers,
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OK. Two follow-up questions.
1. What structures should I add up to get supratentorial? Are they just in
aseg or do I also need aparc?
2. Isn't supratentorial volume calculated differently than simply adding up
individual aseg lables? The reason I ask i
Hi Fred, you mention that the fs environment variables are accessible within
MATLAB, but is freesurfer fully sourced in your MATLAB environment? I’m
guessing this is an issue with your DYLD_LIBRARY_PATH not being set correctly.
You should check to see if the DYLD_LIBRARY_PATH env variable in you
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*Postdoctoral Fellowship in Spinal Cord and Parkinson's Disease*
We are looking to recruit a post-doctoral fellow in Dr. Julien Doyon’s *Motor
Learning and Plasticity Laboratory*, at McGill University. The suitable
candidate will join a team of post-do
No, you'll have to pick out each of the segmentation numbers and use
mri_binarize with the --match option
On 5/31/18 3:27 PM, James Gullickson wrote:
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Sorry I wasn't clear. Yes, I would like to see it with all the non-STV
removed, in order to see exactly
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Greetings freesurfer folk,
Following previous posts here, as well as the freesurfer v6.0 release notes, I
have disabled SIP (I'm in Mac High Sierra 10.13.4), updated my installation ($>
sudo -E fs_update), and rebooted my computer, but I still get t
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My freesurfer home is /opt/freesurfer-6.0.0 which contains all the
necessary freesurfer binaries, .sh files etc in order for freesurfer to
run. I always include this in my shell script
export FREESURFER_HOME=/opt/freesurfer-6.0.0
source $FREESURFER_HOME
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Hello all,
I noticed that after I ran recon-all -autorecon2-wm -autorecon3 to incorporate
manual edits from a white matter surface inspection, many abnormal hard
failures occurred.
First, upon checking to see if my subject successfully ran through
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Hello,
I was able to solve the previous error (not finding the sources.sh)
however, i have encountered another error (please find the attached
hippocampal-subfileds-T1.log file). In this case, line 3 of kvlAutoCrop has
a problem with kvlAutoCrop.bin...
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Sorry I wasn't clear. Yes, I would like to see it with all the non-STV
removed, in order to see exactly what the supratentorial segmentation is
including. So creating a mask would be ideal. Is there a match # for
supratentorialvol and supratentorialvoln
Hi Doug,
I will definitely analyze the lesion load vs mean cortical thickness for each
ROI. I was just trying to think of whether there was a way to also depict those
results in a figure as well. In that case though, I'll just stick with the
statistical analyses!
Thanks again,
Panos
Panag
It is not so easy to do because you have to map the lesions to the
closest cortical voxel then use the per vertex regressor (--pvr) in
mri_glmfit (and the whole process might be iffy). why not just analyze
the lesion load vs mean cortical thickness for an ROI?
On 5/31/18 3:07 PM, Fotiadis, P
Hi Doug,
No worries at all! Thanks for your input, I will go ahead and do that.
In addition to calculating the number of WM hyperintensity voxels in each
adjacent cortical label, I was also interested in creating a figure depicting
the potential significant correlations between regional WM hy
sorry, fell through the cracks!
The easier way to do this is to use the wmparc.mgz. This is a
segmentation where the WM is labeled based on the adjacent cortical
label. You can run something like
mri_segstats --i wmhyper.mgz --seg wmparc.mgz --ctab-default
--accumulate --sum sum.dat
The su
Hi Rachel,
This appears to be some kind of openGL rendering artifact that we are
not able to reproduce nor find a definitive solution, unfortunately. It
happened to some of us over the years but very very rarely and we were
never able to replicate it. It may be a hardware/system glitch. Would
if you are using version 6, then you can just specify the number of
slice groups (-ngroups) when running preproc-sess.
doug
ps. Please post to the FS list.
On 5/31/18 1:33 AM, Xu, Yaoda wrote:
> Dear Dr. Greve,
>
> I am trying to do slice timing correction for multi-band data. Is there a way
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I probably shouldn’t say this, but I will, anyway: It’s coming soon!
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
O
not yet, sorry. We are working on it
Bruce
On Thu, 31 May 2018, Erik O'Hanlon
wrote:
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>
> Dear FS Experts,
>
>
> Is it possible to use the labels found in the FreesurferColourLUT.txt for the
> Thalamus parcellations (8001-8014) using the mri_extract_label
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Dear FS Experts,
Is it possible to use the labels found in the FreesurferColourLUT.txt for the
Thalamus parcellations (8001-8014) using the mri_extract_label command? If so,
what is the correct input file to use ?
mri_extract_label 8001 L_Ant_tha
Hi all,
Just wanted to re-circulate this, just in case someone had some input!
Thanks,
Panos
Panagiotis Fotiadis
Senior Imaging Research Technologist
J. P. Kistler Stroke Research Center, Department of Neurology
Massachusetts General Hospital, Boston, MA
T: (617) 643-3869
___
Hi Ritesh
Ruopeng can help you with freeview, but you can always extract any set of
labels from the aparc+aseg and binarize them if you wish
(mri_extract_lables, mri_binarize)
cheers
Bruce
On Thu, 31 May 2018, Ritesh Mahajan
wrote:
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>
> Hello Bruce,
>
> Ye
Hi Guillaume
I certainly wouldn't trust the thickness values anywhere near the lesion.
What exactly are you trying to compute?
cheers
Bruce
On Thu, 31 May 2018, Guillaume
Bellanger wrote:
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Hi Freesurfers users,
I am looking on cortical thickne
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Hey Doug,
thanks for the suggestions!
I have some follow-up questions, also regarding your recently published paper
about false positive rates
(https://www.sciencedirect.com/science/article/pii/S1053811917310960).
1) What will the difference be b
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Hi,
Sorry found it in FreeSurfer package
Best wishes,
Maryam
On 31 May 2018 at 08:46, Maryam Abaei wrote:
> Dear Team,
>
> I have some data that I wan to use gradUnwarp to correct them but I can't
> find the function to download: https://surfer.n
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Dear Team,
I have some data that I wan to use gradUnwarp to correct them but I can't
find the function to download:
https://surfer.nmr.mgh.harvard.edu/fswiki/GradUnwarp .
Is this function in the Freesurfer package?
Many thanks,
Maryam
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