Hi Wanda,
You should have this function in $FREESURFER_HOME/matlab, the same way you
should have compute_lgi.m and many other matlab functions there. Are you sure
that you are looking at the correct location and / or that you didn't delete it?
Marie
On Jan 31, 2014, at 11:32 AM, Wanda Truong
that looks like the right size. I am stumped. What version of FS are you
using? Do you have access to other versions?
On 01/31/2014 02:50 PM, Wanda Truong wrote:
> This is what I get:
> [Vinas-iMac:Wanda_SFS/qdec/Untitled] vinagoghari% ls -l y.mgh
> -rw-r--r-- 1 vinagoghari staff 1055844047
Emad, please run
mri_converrt
/Users/louispuybasset/Desktop/Zebouni_Fadi/T1/IM-0002-0001.dcm junk.mgh
and send us the terminal output
On 01/31/2014 03:28 PM, Emad Ahmadi wrote:
> Hello,
>
> I am using recon-all, and it gives me error and exits and I cannot
> understand why. I would appreciate
Hello,
I am using recon-all, and it gives me error and exits and I cannot
understand why. I would appreciate it if you give me a clue why it's not
working.
I've written a piece of script (recon.bash attached) to be copied to the
subject's folder, and when run it should automatically go through th
OK, it is y.mgh that is definitely wrong. Can you send me the result of
ls -l y.mgh
On 01/31/2014 02:37 PM, Wanda Truong wrote:
> Hi Doug,
>
> Here's what I get for mri_info lh.area.fwhm10.fsaverage.mgh:
>
> [Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_info
> lh.area.fwhm10.fsaverag
Hi Marie,
Yes, I'm using matlab R3013a. In $FREESURFER_HOME/matlab folder I don't
have a file called SearchProjectionOnPial.m. Should I create it and paste
the updated function?
Thanks for your help!!
Wanda
On 30 January 2014 15:09, Marie Schaer wrote:
>
> Hi Wanda,
>
> I'm not sure to u
Dear Freesurfer Experts,
Is there a way to create custom color scale - like “Heat”, “Jet”, etc - for use
in Freeview?
Thanks,
Fred Lado
Montefiore Medical Center
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https://mail.nmr.mgh.harvard.
what is your mri_convert command line. Send the terminal output too.
doug
On 01/31/2014 12:14 PM, Daniel Carey wrote:
> Dear All,
>
> We have been using mri_convert to convert .nii format quantitative
> scans (specifically R1 volumes) into .mgz (float) format, so they can
> be used as input to
Dear All,
We have been using mri_convert to convert .nii format quantitative scans
(specifically R1 volumes) into .mgz (float) format, so they can be used as
input to mri_vol2surf. Inputting the .nii files to mri_vol2surf has produced an
error in values in the output paint file, whereas this is
Hi Dan
I think specifying -ns 1 will do the trick
cheers
Bruce
On Fri, 31 Jan 2014, Daniel Carey
wrote:
Dear All,
We have been using mri_convert to convert .nii format quantitative scans
(specifically R1 volumes) into .mgz (float) format, so they can be used as
input to mri_vol2surf. Inputti
On 01/30/2014 06:34 PM, Ajay Kurani wrote:
> Hi all,
>I used freesurfer to process my anatomical scans, followed by
> BBregister to align my resting state scan to the anatomical and
> finally afni to process the resting state fmri scans. After recon-all
> I used bbregister:
> *
> *
> *bbre
Hi Elisa
it's tough to tell from just the wm.mgz image. Are the voxels excluded
from the pial brain or are they dura? What does the orig surface show? If
the orig doesn't follow the wm.mgz and you think it should, that means
there is a topological defect that was inaccurately corrected and you
Given the different time distances, the best would be mixed effects models. The
2 stage model should also work as it incorporates time (but not different
correlations according to time distance).
Again I don't see what you are analyzing with only one group. There will always
be thinning, and yo
Hi Janosch
there should be some corrected subjects in the tutorial. The white matter
surface shouldn follow the perceived boundary, although it may look wrong
when it is when it is curving sharply out of plane. I don't have much
experience with MDEFT, so I can't comment on the parameters
che
Ok, thanks Martin for your advice. Is good to have it in mind for long
designs.
Best
Daniel
---
Daniel Ferreira
NVS Department, Div of Clinical Geriatrics (Karolinska Institute,
Sweden)
Department of Clinical Neuroscience (Karolinska Institute, Sweden)
danif...@gmail.com | daniel.ferreira.pad
Dear Doug and Martin,
Thanks a lot. I just have one group including 20 subjects. The scans have
been done in a range of 0.9 to 1.5 years difference (tp2-tp1). Is ooh if I
use the instructions from Paired Analysis :
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis ?
Regards,
Best regards,
A
Hi Daniel,
I'd also include 24 month into both the processing and analysis. It is not
really that we are trying to improve a registration here. We are trying to
improve segmentation and surface placement of each time point.
I'd aways use all data, except there are good reasons to drop (eg strong
Hi Bruce,
thanks for your answer!
Am 30.01.2014 um 14:40 schrieb Bruce Fischl :
> Hi Janosch
>
> it's impossible to tell from a single slice whether those points should be
> added or not. The white matter in your image is *very* dark in these regions,
> do you know why?
No, I don't know why,
Thanks Martin for your reply,
I am agree with you on point 1. What would you say in the case that we are
interested in rates of decline from baseline to 12 months, but besides 6
months follow-up we also have 24 months?. Here I see more conceptual
problems. In an hypothetical context of severe atro
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