Hi Will
not if the dicoms have the correct ras2vox matrix (which they should).
Try visualizing them in freeview and see if the anatomical labels it
shows are correct
cheers
Bruce
On Tue, 11 Nov 2014, will brown wrote:
> Hi all,
>
> I have files that are 2D axial slices that are left-right inv
Hi all,
I have files that are 2D axial slices that are left-right inverted, so the
left side of the brain is on the right side of each slice. Do I need to do
anything to the dicoms before importing them into freesurfer?
Thanks,
Will
___
Freesurfer maili
Hi Nick,
I downloaded the most recent version of freeview.bin using wget as you
suggested and ran it on two different machines.
It appeared to load a volume file fully whereas before it was crashing when
showing it had loaded only 1%.
But it still crashes after that with the message below my
Hi Doug,
thanks for your reply. I would like to feed the differences into a FFX
group analysis, so I think I will need to resort to your workaround. It
would be great if you could provide that. Thanks! Caspar
2014-11-10 13:45 GMT-05:00 Douglas N Greve :
>
> To get sig maps for an individual, thi
To get sig maps for an individual, this is problematic but I could
probably come up with a work-around. For a group analysis, you can
simply compute each taskreg separately, then subtract the two prior to
running mri_glmfit.
doug
On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
> Hi!
> A
Check in the rtopy.par file for the polar and make sure it actually says
polar (and not eccen) inside
On 11/10/2014 01:23 PM, Francesca Strappini wrote:
> Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and
> 2 of eccentricity.
>
> Francesca
>
> On Monday, November 10, 2014,
Hi!
A quick follow-up:
I have a taskreg file with 6 continuous predictors. I would like to run
specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
>From what I gather, selxavg3-sess will run automatic contrasts on taskregs,
but the automatic contrasts are against baseline. This is not wh
Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and 2 of
eccentricity.
Francesca
On Monday, November 10, 2014, Douglas N Greve
wrote:
>
> There are a bunch of columns in the design matrix that are 0, meaning
> that it expects some kind of stimulus to be there but it was not i
Dear Bruce,
It worked, I transferred it and is ready for view.
The original recon was with the command
recon-all -3T -openmp 8 -notal-check (the raw volume was analyze).
I noted a small gyrus excluded from the surfaces, located in the right
hemisphere posteriorly; the recon also did not include tw
Can you upload the gtlmdir and I'll take a look?
On 11/06/2014 08:19 PM, Bronwyn Overs wrote:
> I believe it is the cluster-forming threshold. I was running the
> following:
> mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache
> 1.3 abs --cwpvalthresh 0.05 --2spaces
> mri_g
The messages don't look problematic. What do you mean it goes into an
infinite loop?
doug
On 11/10/2014 12:14 PM, Nooshin Zadeh wrote:
> Dear FreeSurfer experts,
>
>
> I get a new message when I use "mri_convert" command to convert dicom
> to mgz. I used to apply this command before and there w
Hi Nooshin
if you upload the dicoms we will take a look
Bruce
On Mon, 10 Nov 2014, Nooshin
Zadeh wrote:
Dear FreeSurfer experts,
I get a new message when I use "mri_convert" command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
what is the r
Dear FreeSurfer experts,
I get a new message when I use "mri_convert" command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
what is the reason that I receive the following message. In addition, it
does not create mgz file, and goes to infinite loo
There are a bunch of columns in the design matrix that are 0, meaning
that it expects some kind of stimulus to be there but it was not in the
parfile. Do you only have eccen for this or do you also have polar?
doug
On 11/08/2014 11:25 AM, Francesca Strappini wrote:
> Hi, I attached the file, t
try changing the local dir to /usr/local/fs5.3/freesurfer/subjects and just
putting the file without a path
cheers
Bruce
On Mon, 10 Nov 2014, Octavian Lie wrote:
> Thank you, Bruce
>
> I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
> instructions
>
> ftp surfer.nmr.mgh.h
There is not an explicit program to do this. You can re-run
mri_surfcluster with a lower threshold and mask to the big cluster to
force all the results to be within that cluster.
doug
On 11/06/2014 04:29 AM, Sophie Maingault wrote:
> Dear FS experst,
>
> I used the command mri_surfcluster. For
Thank you, Bruce
I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
instructions
ftp surfer.nmr.mgh.harvard.edu
anonymous
my email
cd transfer/incoming
put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
and I get this:
local: /usr/local/fs5.3/freesurfer/subjects/
yes, that is correct.
Bruce
On Mon, 10 Nov 2014, Jürgen Hänggi wrote:
Dear FS experts
There is a reviewer question with respect to the voxels/vertices used to
compute the SNR and CNR with FreeSurfer's mri_cnr function.
Do we right that SNR/CNR computation is based only on the voxels that are
lo
Dear FS experts
There is a reviewer question with respect to the voxels/vertices used to
compute the SNR and CNR with FreeSurfer's mri_cnr function.
Do we right that SNR/CNR computation is based only on the voxels that are
located at the interface between the white and pial surface?
Thanks in adv
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