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Postdoctoral Position in Contemplative Neuroscience
at McLean Hospital/Harvard Medical School
A postdoctoral position is available under the mentorship of Drs. Matthew D.
Sacchet, David H. Rosmarin, and Diego A. Pizzagalli within the Laboratory for
Affec
you have a typo in fast_fratio. The first argument (beta) should not be
transposed
On 8/13/2020 3:40 PM, Eric Cunningham wrote:
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There's a minor bit of confusion with the code you sent.
[F p] = fast_fratio(beta,X,rvar,C); gives the error "inner error
dimen
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FS editing experts, I have a subject with enlarged ventricles and processed
the subject with recon-all -bigventricles flag.
The surfaces look good but the subcortical segmentation and some WM around the
ventricles , especially for the right hem, are
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Hello Alex,
Obtaining a license.txt file (and optionally using FREESURFER_HOME to point to
its location) is listed here,
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstalland here,
https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads
- R.
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Hi Freesurfer,
can't find if this was reported.
This refers to freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551.
seems that in the new 7.1.1 version the required license file is located at
FRESURFER_HOME/license.txt (instead of previous version
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There's a minor bit of confusion with the code you sent.
[F p] = fast_fratio(beta,X,rvar,C); gives the error "inner error dimensions
must agree" on the line "ces= C*beta".
size(C) = [1 9]
size(beta) = [1 9]
should this be
[F p] = fast_fratio(beta',X,rva
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I will send the password to your email shortly.
- R.
mudassar liaqAugust 13, 2020 at 10:19
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CautionHi,
I followed the given instructions on page
(https://surfer.nmr.mgh.harvard
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Thanks Douglas
On Thu, 13 Aug 2020 at 18:08, Douglas N. Greve
wrote:
> We also have serotonin atlases. You can get them from here
> https://xtra.nru.dk/FS5ht-atlas/data/5-HT_atlas.zip
>
> On 8/13/2020 11:59 AM, Fischl, Bruce wrote:
>
> Hi Shreyas
>
>
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Dear Bruce,
Greetings!
Thanks for prompt reply.
Which surface atlas do you mean?
For example: Juelich, Desikan, Brodmann !!
We have several and they are stored in different formats.
preferred in GIFTI format, however i can try out also other formats
We also have serotonin atlases. You can get them from here
https://xtra.nru.dk/FS5ht-atlas/data/5-HT_atlas.zip
On 8/13/2020 11:59 AM, Fischl, Bruce wrote:
Hi Shreyas
Which surface atlas do you mean? We have several and they are stored
in different formats. The folding ones are stored as mult
Hi Shreyas
Which surface atlas do you mean? We have several and they are stored in
different formats. The folding ones are stored as multi-frame spherical tif
files, while the parcellations are in an internal format (.gcs). The are all
freely available and included with every FreeSurfer install
Probably your model in R is not the same as the model in FS. First, see
if you can replicate using
X = load('Xg.dat')
C = load('contrast/C.dat');
[beta rvar] = fast_glmfit(X,y); % y is the data at your vertex
[F p] = fast_fratio(beta,X,rvar,C);
p should be the same as in the .sig file
Generally
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Dear Freesurfer Experts,
I came to know that freesurfer software contains atlas/atlases in surface
format (.gii or similar). If yes, how is it possible to get access to these
atlases?
Thank you
Sincerely,
Shreyas Indurkar
Max Planck Institute for Bi
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Firstly, yes. I was making that error, and many thanks for catching it!
Unfortunately, even after applying that fix, the problem remains, but it
does explain why some of my earlier attempts to figure things out on my own
failed. I will try to duplicat
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Hi,
I followed the given instructions on page (
https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) but could not find the
README file to find the password to log in to the developer account. I've
seen that other users in the archive received the password
send your command line and terminal output
On 8/10/2020 2:00 PM, Erin Moe wrote:
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Hi Doug,
That would do it. Thanks! However, I ran bbregister, got out the
register.dat file, input that into the vol2subfield command and now
it’s giving me an error stating:
--pdf delta expects the column row and slice indices of the vertex where
you want the delta to go (you are supplying an RAS). You need to
determine the index
On 8/12/2020 8:22 PM, Mauricio Watanabe Ribeiro wrote:
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Hi Freesurfers,
I'm trying to create a ROI
Do you have a 1-off error? Ie, FS starts counting at 0 and matlab starts
counting at 1. So vertex 53263 is vertex 53264 in matlab.
On 8/12/2020 5:31 PM, Eric Cunningham wrote:
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Hello Freesurfer Experts,
I am trying to plot the ${meas} values at the maximum
You can look in the recon-all.log file to see how wmparc.mgz is created.
Which version of FS are you using? If V6, then the command will be
mri_aparc2aseg. If V7, then it will mri_surf2volseg. Either way, modify
the command to use your annotation.
On 8/12/2020 5:18 AM, Ellen Ji wrote:
On 8/12/2020 2:44 AM, 정현우 wrote:
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Hello Freesurfer Developers,
I'm trying to do permutation simulation on 50 subjects to find brain
region clusters of which cortical thicknesses have significant
association with clinical parameters while controlling for
I don't think there is one "right" way to do it. The choice of
normalization changes what you are testing, so you have to figure out
whether it makes sense based on your hypothesis of what is going on.
On 8/11/2020 1:24 PM, Haewon Roh wrote:
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Hi. team!
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