you can try
tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3
you may have to adjust the thresholds (fminmax)
On 6/26/18 10:43 PM, srishti goel wrote:
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Hello Bruce,
You had mentioned about loading the volumetric maps with the surface
t
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Hello Bruce,
You had mentioned about loading the volumetric maps with the surface to
check that all my clusters are contained within the surfaces. Since I am
very new to freesurfer, could you please guide to where I can find an
appropriate command to d
FYI
-- Forwarded message --
Date: Tue, 26 Jun 2018 22:35:08 +
From: "Amir Shmuel, Dr."
To: "Amir Shmuel, Dr."
Subject: Resting-State and Brain Connectivity in Montreal: Early registration
deadline is July 10
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The Sixth Bi
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Hi Rob,
It works. Many thanks for your kindly help.
All the best
Shize
At 2018-06-27 05:01:37, "Dicamillo, Robert" wrote:
Hello Shize,
Try downloading the following zip archive, and double click on it to uncompress
it
https://drive.google.com/
Hello Shize,
Try downloading the following zip archive, and double click on it to uncompress
it
https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing
There is a README file in the archive describing how to update a couple of
files. Please try to
apply the updates,
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Hi Ruopeng,
Thanks for your reply. I have tried many types of volume file, including the
example files. Freeview all quit unexpectedly. I am not sure if there are
still something wrong with the volume file itself.
Many thanks for your help
Shize
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Hi Rob,
Thank you for your kindly help. This is the log file from terminal. could you
helps me to figure out what was wrong with it. Many thanks.
Shize
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro loginwindow[95]:
-[SFLListManager(ServiceReplyPr
Hi Sara
check out the help (with --help). For example you could use:
--projdist-avg min max del : average along normal
cheers
Bruce
On Tue, 26 Jun
2018, Sims, Sara A wrote:
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Bruce,
Thanks! So if I set it to say 4mm would it sample from 0-4mm or just fro
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Bruce,
Thanks! So if I set it to say 4mm would it sample from 0-4mm or just from
exactly 4mm and ignore things slightly closer to the surface?
My problem would be somethings could be 2mm or 3mm etc. and it's not exactly
the same all the way around th
Hi Sara
you can use a negative projdist in mri_vol2surf
cheers
Bruce
On Tue, 26 Jun 2018, Sims,
Sara A wrote:
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Hello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer
surfaces. If I
put the volume into freesurfer sp
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Hello,
I have outputs from FSL probtrackx that I would like to display on Freesurfer
surfaces. If I put the volume into freesurfer space how can I get it to sample
onto a surface when the values are in white matter and not grey matter? To
rephrase, h
Hi Doug and Freesurfers,
I am using fcseedcor to compute the correlation between two time courses for
each subject in my group. The command that I run is as follows:
fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat -xreg
global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -x
Would it be possible for you send us the volume file that caused the crash?
Best,
Ruopeng
On 06/26/2018 01:30 PM, 姜时泽 wrote:
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Hi Rob
Many thanks for your feedback. There is no notification pop up. The
GUI of freeview just quit. I am not sure what was wro
Hi Shize,
You could try looking at the system log. Before you launch Freeview open a
terminal window and do,
$ tail -f /var/log/system.log
There will be some output there already from the last recorded system events.
Then launch Freeview, load your file, and when it crashes, see if anything
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https://github.com/Jfortin1/ComBatHarmonization
-joost
Op di 26 jun. 2018 18:50 schreef Heidi Lindroth :
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>
> Hi there,
>
> Is there a standard method to use for adjusting for between scanner
> variance? In the
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1st scanner - 34
2nd scanner-1
3rd scanner-4
4th scanner-15
Heidi Lindroth BSN RN
PhD Candidate| School of Nursing
Program Assistant | School of Medicine and Public Health, Department of
Anesthesiology
Predoctoral Fellow | Veterans Administrati
That is what it means to add scanner as a nuisance variable. How
unbalanced is the design?
On 06/26/2018 01:30 PM, Heidi Lindroth wrote:
>
>
> Hi Bruce,
>
>
> It is a cross-sectional, descriptive analysis. The data has already
> been collected. The participants are not evenly distributed. Would
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Hi Bruce,
It is a cross-sectional, descriptive analysis. The data has already been
collected. The participants are not evenly distributed. Would it be appropriate
to regress out scanner type if I am using the raw data (extracted via DKT
atlas)?
t
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Hi Rob
Many thanks for your feedback. There is no notification pop up. The GUI of
freeview just quit. I am not sure what was wrong with this. DO you have any
ideas about this? Thank you .
Best wishes
Shize
At 2018-06-27 00:54:45, "Dicamillo, Rob
Hi Heidi
what kind of study are you doing? Usually scanner is included as a nuisance
regressor, but you also want to make sure that you balance your subject
population across scanner as much as you can
cheers
Bruce
On Tue, 26 Jun 2018, Heidi Lindroth wrote:
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Hello Shize,
Did you see the Finder bring up a window with a notification that Freeview quit
unexpectedly, with some choices to
click on for “ignore”, “report”, or “reopen” Freeview?If so, it could help
if you select report, cut and paste (or take a screenshot)
of the first page of the crash
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Hi there,
Is there a standard method to use for adjusting for between scanner variance?
In the sample I am analyzing, 4 different scanners were used.
Thank you,
Heidi Lindroth BSN RN
PhD Candidate | School of Nursing
Program Assistant | School of Me
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|
|
Dear fresurfer experts,
I am currently using freeview 2.0 to check some data. I am not sure why it
always quit unexpectedly when I try to load a volume. my freeview is installed
on OS 10.11.3 system. Would you please help me to solve this problem.
Each contrast is a test, so you have 8 tests. Like I said, the ultimate
right thing to do is to correct for all your tests, but this might not
leave you with anything if you do. This is often a judgement call. I
rarely, if ever, see people correct over multiple tests. However, if you
try to pub
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Hi Freesurfer community,
I have an issue in adding a surface label to an annot file.
I had a manually drawn .nii mask in native space for each subject which I
have used mri_vol2surf to create a surface overlay and then mri_vol2label
(with the surf
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Hi Niels,
The atlas is the same, so you’ll get the same regions, but the actual
segmentation code has improved since FS6.0 – therefore the 1.1 and 1.2
versions. The results should not be wildly different, though.
Cheers,
/Eugenio
--
Juan Eugenio Igle
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Hi I see on the website of brainstem substructures that the
'-brainstem-structures' option in freesurfer 6.0 stable release produces
brainstem segmentations that are labeled v10 whereas the script
'segmentBS.sh' available in beta versions of freesurfer
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Hello Doug,
We are doing one test I supposed. Because we inputted all covariates into
glm_fit.
This is our command line.
We entered all behavioral scores as covariates and obtained each folder
named as covariate's name with sig.mgh in each folder.
Hi Ottavio,
you can also install gnu parallel
(https://www.gnu.org/software/parallel/) and run in parallel on all your
cpus with just one parallel command line:
export SUBJECTS_DIR=/home/my/study/fs60/MRIstudy/sMRI/native
cd /home/my/MRIdata/sMRI/native
ls *.nii | parallel --jobs 8 recon-
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