Dear Bruce,
thanks for the quick reply! You are right, of course. I do find errors in
lh.inflated.nofix.
I have attached a screenshot of the biggest errors I found..
Can you maybe guide me a little how to fix the issue? Do I just cancel the
running recon-all process, and set control points and r
The answer is yes, indeed.
Just be careful when you report your results, specifying which version you used
for what.
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
Thank you for your answer, Bruce and Eugenio.
Then the way to do that might be,,
1. Install new version of freesurfer to a new location.
2. Move previous data from old version freesurfer path to the new location.
3. Do what I want (hippo subfield)
Right..?
Thanks.
Sincerely,
Joonyoung.
2017
Dear Freesurfer Experts.
Is there a way to create a freesurfer surface label from entering a
MNI152 coordinate? I would like to extract cortical thickness data
from fMRI peak activation coordinates.
I am aware that I can use tcl with tksurfer:
mar_vertex X 1
labl_new_from_marked_vertices
labl_d
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Dear Freesurfer experts,
I ran recon-all with the flag -qcache to generate smoothed cortical thickness
maps.
In order to check how the flag "-qcache" is smoothing the cortical thickness
data. I looked into the file $subj_dir/scripts/recon-all.log" which showed that
the following command was appl
Hi Martin
we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help
cheers
Bruce
On Tue, 12 Dec 2017, Loeffler, Martin wrote:
Dear Bruce,
thanks for the quick reply! You are right, of course. I do find
Hi John
I don't think fslmaths takes a surface topology so they won't be the same
(mri_surf2surf smooths within the surface and fslmaths smooths in the
volume I believe)
cheers
Bruce
On Tue, 12 Dec 2017, John Anderson wrote:
Dear Freesurfer experts,
I ran recon-all with the flag -qcache t
Dear Dr Bruce, I highly appreciate the response.
I want to smooth PET volumetric images, when I use "fslmaths", it shifts the
signal from the cortex to the underlying structures. I think (depending on
wiki) that Freesurfer handles this issue by smoothing on sphere. Which is the
recommendded stre
Yes, Thalamus-Proper is the correct segmentation. We should just change
the name
On 12/09/2017 03:17 AM, 郑凤莲 wrote:
> Hi FS professors,
> I am using FS 6.0 for subcortical structures. I have a doubt
> about thalamus and thalamus-Proper. I added thalamus to brainmask.mgz
> in Freeview, it
Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin
-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2
To reinforce what bruce is saying, mri_surf2surf does surface-based
smoothing (ie, along the cortical surface), whereas fslmaths does
volume-based smoothing which does not take into account the anatomy
On 12/12/2017 10:38 AM, Bruce Fischl wrote:
> Hi John
>
> I don't think fslmaths takes a surf
You have to sample the volumetric PET data onto the surface
(mri_vol2surf) and then smooth it there (mri_surf2surf or mris_fwhm).
On 12/12/2017 11:23 AM, John Anderson wrote:
> Dear Dr Bruce, I highly appreciate the response.
> I want to smooth PET volumetric images, when I use "fslmaths", it
>
Dear experts,
I'm currently trying to import some of my data into Qdec in order to perform a
group analysis on cortical thickness. All of my data was originally in an excel
sheet and it had the following variables (fsid, gender, age, and thickness). I
tried converting it into a file that would
Those files are not named that any more. Now they are just lh.pial, etc.
On 12/11/2017 12:25 PM, Duran, Tugce wrote:
>
> Dear Doug Greve,
>
> Where can I find the rh/lh.pial_avg file in fsaverage/surf/ created in
> freesurfer 6.0?
>
> Is this file named differently in FS 6.0 or do I need to proc
can you send the table?
On 12/12/2017 01:18 PM, Arsenije Subotic wrote:
>
> Dear experts,
>
>
> I'm currently trying to import some of my data into Qdec in order to
> perform a group analysis on cortical thickness. All of my data was
> originally in an excel sheet and it had the following varia
Hello,
I was hoping to get some clarification on how exactly the cortical thickness
number is calculated. In the videos, Doug says it's "the distance between the
vertex on the white to the vertex on the pial, and you go backwards and
forwards to compute the average thickness", and the 2000 pape
Hi Eli,
because the "closest" metric isn't symmetric. White-->Pial != pial-->white
cheers
Bruce
On Tue, 12 Dec 2017, Rockers, Elijah D. wrote:
> Hello,
>
> I was hoping to get some clarification on how exactly the cortical thickness
> number is calculated.
> In the videos, Doug says it's "th
Hi all,
I have processed data using freesurfer and the output for most of my
subjects did not remove all of the eye and dura around it during skull
stripping. When I check the brainmask there is dura (or blood vessel) in
the frontal lobe that is classified as GM.
I am wondering if I have to manua
Hi professors,
I am using Freesurfer 6.0 for calculating LGI. I have done 'recon-all' for
it. When I ran Monte Carlo in qdec (FWHM=10), it has errors:
However, when FWHM=5, It was ok. What led to this result? I don't know why.
Thanks in advance !
Zheng
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