The two formats that you sent are not equivalent.
In the version where the gradient vectors saved in columns, the first 2 columns
are:
0 -0.793264
0 -0.394167
0 0.464074
In the version where the gradient vectors saved in rows, the first 2 rows are:
0 -0.793264 -0.453844
as you note, the gtmseg.mgz has higher resolution and several new ROIs.
the higher res is for partial volume correction. The inclusion of pons
to for the possibility of using it as a reference region, which often
happens in AD studies of FDG. Vermis is for use in serotonin studies so
it can be
On 10/26/2020 3:58 PM, Basavaraju, Rakshathi wrote:
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Dear Freesurfer team,
I have been trying to extract local gyrification index in a dataset
according to a label which I have created.
1) First of all, I extracted lGI as per DKT areas, which one is
It looks like the image darkens a lot at the top. Try putting control
points in the WWM near the start of the gyrus. make sure they are truly
in WM!
On 10/25/2020 9:03 PM, Alexopoulos, Dimitrios wrote:
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Any comments from FS users to best best tackle these
A surface label or a volume label?
On 10/25/2020 2:17 PM, Hua, Jessica wrote:
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Hi FreeSurfer Experts,
How can I convert a .nii ROI into a FreeSurfer label? I was able to
convert the .nii into a .mgh file but could not figure out how to
convert to a label
[tkrR tkrA tkrS 1] would be [10 20 30]
On 10/24/2020 2:54 AM, Kim, Gwang-Won wrote:
Dear sir,
I’m going to process as follows:
I have a point on the surface ("Vertex RAS" in tksurfer) and want
tocompute the Scanner RAS in orig.mgz that corresponds to this
point:ScannerRAS =
Is that using freeview or tksurfer? In any event, "orig" there refers to
the ?h.orig surface
On 10/24/2020 2:10 AM, Kim, Gwang-Won wrote:
Dear expert,
I obtained “sig.mgh” from resting fMRI data using Freesurfer. Then, I
opened the file using tksurfer. I selected vertex 156439 out of 163842
You would just run mkcontrast-sess, eg, if your four conditions are
ordered condA, condAcontrol, condB, condBcont, then
mkcontrast-sess -analysis analysis -contrast contrastname -a 1 -c 2 -c 3
-a 4
If you want it reversed, then just reverse the a's and c's
On 10/23/2020 4:39 AM, Paula Maldonado
You can use mri_binarize with --match to specify the hippo seg id and
--surf to output a surface. You may want to smooth it a little bit with
--surf-smooth
On 10/22/2020 10:31 PM, Gonzalo Rojas Costa wrote:
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Hi:
Which is the best library or software to
Can you send the recon-all.log file?
On 10/22/2020 8:15 PM, Wei Koo wrote:
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Hello FreeSurfer Developers,
I am trying to recompute the surfaces after wm edits using this
command line : recon-all -autorecon2-wm -hires -s subject_id , but
when I do run that
We have not used .w files in years. Try converting the .w file to .mgz
using mri_surf2surf (or even better, don't save them as .w files)
On 10/22/2020 4:03 PM, Yixin Ma wrote:
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Hi Freesurfer experts,
I'm trying to write the normals of the GM/WM meshes to
On 10/22/2020 9:52 AM, 1248742467 wrote:
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Hello, Fs
my freesurfer version is 6, I see others have the view button after
load .annot file, But my version does not have this option.
Do I need to update the version? And I have installed fs6, can I
install
You aren't using 7.1.1, you are using 5.1, or maybe some mixture of
them, which would explain why the --uchar opt is not recognized
On 10/22/2020 6:28 AM, erbilnurhan wrote:
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Hello FreeSurfer Developers,
I'm trying to compute volumetric data from MPRAGE
Yes, based on the surfaces. We use Anderson Winkler's truncated pyramid
method.
On 10/22/2020 5:55 AM, Ian Hardingham wrote:
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>
> Hi Freesurfers,
>
> Is "total cortical gray matter volume" from aseg.stats calculated based
> on the recon-all Surfaces? Or
On 10/22/2020 3:58 AM, Julian Macoveanu wrote:
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>
> Hi,
> I am using FS 7.1.0. After running the surface thickness GLM analysis
> I get one cluster after correction for multiple comparison showing a
> significant group difference. I want to make a plot
You can move the surface around in freeview. Under
Tools->RepositionSurface. Change "Intensity" to "Coordinate", then
Shift+Left click near the surface to select the point on the surface you
want to move (ie, the vertex), then Shift+Ctrol+Left to click on the
location you want it to move to,
Hi Marina,
If you meant to set threshold for surface overlay from the command-line, you
can do it like this:
freeview -f lh.inflated:overlay=overlay_file:overlay_threshold=min,max
For more overlay options, you can run ‘freeview -h’ and look under ‘-f,
--surface’ section.
Best,
Ruopeng
On
Hi Mel, sorry just getting to this and now the subject.tar.gz does not
exist. Can you reupload and/or send the recon-all.log file?
doug
On 10/6/2020 9:24 AM, Melanie Ganz wrote:
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>
> Dear FS list,
>
> as soon as samseg was available in FS v6dev we used it
Yes, that is all correct. I only have a few comments. One is that 15mm
is a lot of smoothing; this is not wrong, just more than the 5-10 that I
usually use. Second, you might want to use permutation instead of MCZ;
the threshold of 4 should make MCZ control the false positives
adequately, but
I'm not sure what you mean by the mean area for the different LGI
values. Can you elaborate?
On 10/20/2020 6:46 PM, Lab of Autism and Developmental Neuroscience, Lab
of Autism and Developmental Neuroscience wrote:
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Dear Freesurfer experts,
I have
Sorry for the delay. I actually don't have any programmatic way to force
this change. You can move the surface around in freeview. Under
Tools->RepositionSurface. Change "Intensity" to "Coordinate", then
Shift+Left click near the surface to select the point on the surface you
want to move (ie,
Not sure. Ruopeng (cc'ed) can comment on the control of the color bar
On 10/20/2020 5:05 AM, Marina Fernández wrote:
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Thanks for the reply Doug,
We used the tksurfer command lines because they were run in matlab
after performing some analysis to obtain
When you run your original analysis, you probably smoothed the map
before doing the group analysis. This smoothing would not be in your ROI
analysis, and the difference could be pretty big if the label is small.
Also, the area map will have a jacobian correction that will not be in
the raw
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Dear Dr. Yendiki,
Thank you very much for your reply. Is it correct to assume then that the
FA/MD/RD/AD values that are averaged over all the voxels for a given tract do
not necessarily have a ‘precise’ relationship to one another?
With warm
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Also, I am not sure if these are helpful for you to give me a suggestion-but I
have attached here our original bvals and bvecs text files and the text files I
have formatted according to configuration file tutorial.
I have tried with them both but
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Hi Anastasia
Thanks so much- it worked! just now.
But I have this error with trac-preprocessing I get "Error: data and
bvals/bvecs do not contain the same number of entries"
As far as I know all my files have 66 entries so I am not sure what causes
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Thank you!
This has been super helpful.
Sincerely,
James Park
From: freesurfer-boun...@nmr.mgh.harvard.edu
Date: Tuesday, October 27, 2020 at 2:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question
Hi Oshadi - Yes.
For future reference, if you have any doubts about command line usage, you can
1. run "trac-all", without any arguments, and/or 2. read the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
Anastasia.
From:
Hi Cat - I am not sure what precise means. If the effects on these measures are
the same over the entire tract, averaging the measures over the tract would
actually increase SNR and make the effects (and their relationship) cleaner. If
there are opposing effects in two different parts of the
Hi James,
Rsync is a very common unix command for syncing/copying across filesystems.
There’s plenty of information about it online, and you can access the help text
through `man rysnc`. This might be useful
https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/
Best
Andrew
Hi Julia,
The -tp flags for the base creation require a subject ID as input, but you
supplied a nifty file. That’s why it can’t find any subject files. See
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing.
Best,
Andrew
From: on behalf of Julia Lam
Reply-To: FS Help
Date:
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Hi Andrew,
Thank you so much for your prompt response.
Our IT department was unfortunately a bit unfamiliar with these types of files.
We were not using rsync to move our files but instead just copying the files
over through a file explorer.
Could
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Hi everyone,
We have been fortunate to obtain funding for a postdoctoral position. A
brief description is enclosed. Please feel free to pass this along to
anyone who might be interested.
--ron
--
Ronald J. Killiany, Ph.D.
Center for Biomedical
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Hi there!
thanks for the answer and your searches.
Actually I solved my issue, basically the last upgrade created a
circular depency issue in my nvidia driver packages, causing issues
with graphical applications. I think this, in the end, is
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