Hi Sara
no worries. The units are mm, and use -avg averages the values and max
takes the max over them (which is a somewhat dicey thing to do if you are
going to do stats afterwards).
cheers
Bruce
On Wed, 11 Jul 2018, Sims, Sara A wrote:
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Bruce,
The
there is some code around to display each parcel with a different value,
but I'm not sure exactly what it is. YOu could certainly do it in matlab
if you wanted to (use read_annotation.m to read in the .annot file)
Cheers
Bruce
On Wed, 11 Jul 2018, Ben Smith wrote:
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Bruce,
The help file and wiki don't explain the units of the min, max, and del. I
still can't get the data to sample onto the surface correctly and so I'm
wondering if it has something to do with my assumptions about how this command
flag is
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Hi Bruce,
Some background:
I have already extracted ROI timeseries using the following method:
- use mri_vol2vol to transform the functional images to structural space
(yes these were very large images; I did it one at a time)
- use
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Hello FreeSurfer Developers,
I am attempting to perform group analysis on a group of subjects. However, When
I am trying to create an average subject I get the following error.
mghRead(mri/norm.mgz, -1) could not open file
I went into the average
I suppose you could look for voxels that outside of the cortex and
adjacent to it
On Wed, 11 Jul 2018, John Anderson wrote:
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Dear Dr Bruce,
Thank you for the response. Indeed, I was completely wrong, these represent a
pathology and should
not
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Dear Dr Bruce,
Thank you for the response. Indeed, I was completely wrong, these represent a
pathology and should not correct for!
Kindly, I have one additional question not relevant to the subject of this
email. Is there any way in Freesurfer to
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All,
I am comparing cortical thickness between subjects with and without mild
traumatic brain injury (mTBI). So far the contrasts in QDEC have not been
significant after correcting for multiple comparisons. I am not necessarily
surprised at this due
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This works! Thank you so much for your help.
-Seonjoo
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Boyd, Emma
Sent: Wednesday, July 11, 2018 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
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jesus almost panicked there
haha
cheers mate
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Wednesday, July 11, 2018 4:41 PM
To: Freesurfer support list
Subject: Re: [Freesurfer]
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Hello,
I am running a dataset through version 6.0 of Freesurfer on Linux,
extracting results for both the Desikan atlas and our own atlas. When
extracting the stats for our atlas, the results were varying considerably
(sometimes up to 10%) in
no, you can just run with -qcache for each subject. Don't include -all or
-autorecon2 or anthing, just subject id and -qcache. It should be fast
On Wed, 11 Jul 2018,
Mr. Tass wrote:
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Hello
just a quick question
i didn't run recon-all using the
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Hello
just a quick question
i didn't run recon-all using the -qcache
do i have to start all over ? the initial run took a week
Please advise if there is a way to fix that without having to restart recon-all
again
thank you
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And yes, pwd and dirname are both in my path.
m-100205:bin PageLab$ pwd
/Users/PageLab/Documents/freesurfer/bin
m-100205:bin PageLab$ dirname
usage: dirname path
m-100205:bin PageLab$ dirname path
.
On Wed, Jul 11, 2018 at 9:25 AM, Iglesias
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Hello Eugenio,
I noticed Matlab doesn't open when I run the hippocampal analysis, so when
I tried to click on the file, segmentSubjectT1_autoEstimateAlveusML,
I encountered the following error:
Check with the developer to make sure
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Sorry, I meant pwd, dirname, etc
--
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/
From: on behalf of Jasmin Alves
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Hello Eugenio,
Thank you for the reply. The script, segmentSF_T1.sh is found in
/Users/PageLab/Documents/freesurfer/bin
The freesurfer environment has been set to
/Users/PageLab/Documents/freesurfer
So, I am not sure why the script is
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Dear Jasmin,
The script segmentSF_T1.sh does not seem to be able to find basic commands like
pwd and dirname. Are these in your path?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
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Hello:
I have a problem when running trac-all preprocessing. I have X11 and FSL
installed. Not Matlab I don’t know if I need it I think only for fMRI.
Sincerely,
Andrade.
Renes-MacBook-Air-2:diffusion_tutorial andraderenew$ trac-all -prep -c
Hello Daniel,
The docker container may not be properly supporting symbolic links, i.e.,
apparently you can write files inside the container, but in your log that error
is the first instance of the ln command.
Could you try running it w/o using a container and see if it gets past the ln
Hello Daniel,
The docker container may not be properly supporting symbolic links, i.e.,
apparently you can write files inside the container, but in your log that error
is the first instance of the ln command.
Could you try running it w/o using a container and see if it gets past the ln
Hi John
why do you want to correct for them? They likely represent a pathological
process, so correcting for them may remove whatever effects you are looking
for, no? The space between the sulci and the ventricle volume won't
directly affect surface-based analysis, but of course the sulcal
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Dear Freesurfer experts,
I have two groups of subjects (healthy and patients). The patients have
different degrees of atrophy. Looking into the individual scans, the subjects
are largely different in the space between the sulcuses and the size of
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Hello FreeSurfer Developers,
I am trying to analyze the subfields of the hippocampus using FreeSurfer
6.0 based on the tutorial, "Segmentation of hippocampal subfields".
However, several errors come up when I run:
recon-all -s 102
Dear FreeSurfer experts,
I would like to understand better the principle of eddy_correct:
-in which way the eddy currents caused by motion are set apart from the eddy
currents caused by fast switching diffusion-encoding gradients?
-and then, how are the affine registration matrices reflecting
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Dear experts,
following on this old thread, do you have any new knowledge on the possible
severity of non-stationarity in cortical-thickness maps and its effect on
permutation-based cluster-extent inference? Given current status of
development,
Hi Seonjoo,
What directory are you in when you run preproc-sess? You should run this
command from the data/ dir.
Emma
-
Emma Boyd
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
From:
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Dear Freesurfer experts,
I tried to run preproc-sess but did not have much luck to make it work.
I converted resting fmri file into .nii, and I created the following directory
structure and it’s stored under /data/sub1/rest/001/fMRI.nii:
/data
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Hi Freesurfer Team and Doug,
Is there any way to derive the gtmstats from Petsurfer within a longitudinal
design?
Could I get your take on the steps below?
1. Extract GTM stats from each PET time-point (registered to the closest
structural MRI in
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