hello doug,
Thank you.
1) where can i find this lta file? I looked for it in the mri and surface
folders but it wasn't there. do i need to run another command in order to
generate it?
2) Is this the right command? mri_compute_volume_fractions --o pvf --reg
filename.lta (location of .lta)
3)Also, Is
Hi Doug,
Yes i was visualising it on fsaverage. I switched to sub003 and the ROI looks
perfect. What a simple mistake, thanks for your help.
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australi
Are you visualizing the output on subject sub003? It looks like fsaverage
On 01/26/2017 06:23 PM, Bronwyn Overs wrote:
> Hi Mailing list,
>
> I have been running the mri_label2label command and have encountered a
> problem with the newly generated label. The command I am running is as
> follows
Run it something like
mri_compute_volume_fractions --o pvf --reg register.dof6.lta
where the lta file is a registration file between the FS anat and the
volume that you want to get the PVFs for. The output will have a base
name of pvf, eg,
pvf.cortex.mgz pvf.csf.mgz pvf.subcort_gm.mgz pvf.w
Hello Douglas,
Thank you. When I looked up the command with --help, it said " computes partial
volume fractions for cortex, subcortical GM, WM and CSf". What volume do I give
the command as an input? T1, orig.mgz .
Best,
Miracle
Sent from my BlackBerry 10 smartphone.
Original Message
Fro
ps, it is not a probability map per se but the volume fraction (0-1) map
On 01/26/2017 05:52 PM, Douglas N Greve wrote:
> Try mri_compute_volume_fractions
>
>
> On 01/26/2017 05:49 PM, miracoo...@gmail.com wrote:
>> Hello Freesurfer,
>> Is there a way to extract tissue probability map for white
Try mri_compute_volume_fractions
On 01/26/2017 05:49 PM, miracoo...@gmail.com wrote:
> Hello Freesurfer,
> Is there a way to extract tissue probability map for white matter
> in FS. Thank you
> Best,
> Miracle
> Sent from my BlackBerry 10 smartphone.
>
>
>
> __
Hello Freesurfer, Is there a way to extract tissue probability map for white matter in FS. Thank you Best, Miracle Sent from my BlackBerry 10 smartphone.
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hi, please include previous correspondence so that we know what you are
referring to
On 01/26/2017 04:10 PM, Anderson Napolitano wrote:
> Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces
> and removing the spaces all together doesn't seem to resolve the said
> error.
>
>
>
>
?Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and
removing the spaces all together doesn't seem to resolve the said error.
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Hello Lilla,
Thank you very much for the suggestion. Here then are my attempts at putting
what you said into two sequential commands:
mri_vol2vol --targ $SUBJECTS_DIR/$subj/mri/norm.mgz \
--m3z
$SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \
--noD
Ciao Stefano,
You have currently no permission to write in the FreeSurfer directory.
Try:
1. sudo -s
2. Enter your password
3. Run the curl and tar commands as explained in the wiki
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College L
Thank you Doug,
Actually I was trying to apply what was mentioned in this link by replicating the method on the command "mri_glmfit" and not using the command "mri_mcsim".
I tried to use for example the label "BA4a" (it is available in the folder/fsaverage/label), but the command "mriglm_fit f
Ok sure, I will do it tomorrow as I don't have access to the stats file right
now
Many thanks!
From: Eli Johnson
Sent: Thursday, 26 January 2017 6:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical volume from masked region
Hi Doug,
Yes, I h
In that case please upload the actual data that is failing.
On 01/26/2017 01:22 PM, Eli Johnson wrote:
> Hi Doug,
>
> Yes, I have a series of masks that I have created to cover the whole cortex,
> but I want to examine the regions separately. Each region outputs a volume
> much smaller than I w
Hi Doug,
Yes, I have a series of masks that I have created to cover the whole cortex,
but I want to examine the regions separately. Each region outputs a volume much
smaller than I would expect given the volumes from aseg stats for the whole
cortex. That is to say, when I combine the volume fr
Sorry, we don't have any tools to do ICA. The FSL/HCP group might have
some thing that will do it on the surface.
On 01/26/2017 01:13 PM, David Baric Parker wrote:
> Hello!
> I tried to look through the history but couldn't seem to find
> exactly what I was looking for.
> Is there a recommend
Sent from my iPhone
> On 26 Jan 2017, at 18:11, Douglas N Greve wrote:
>
> In looking at your mask, it covers only half (or less) of the brain.
> This would explain why the total volume you get from the mask is much
> lesss than the total gm volume reported in aseg.stats.
>
>
>> On 01/20/2
FS does not come with correction tables for all labels. You'll have to
build your own. here are the instructions:
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On 01/26/2017 01:09 PM, John Anderson wrote:
> Hello Freesurfers,
> I am working on a PET surface based analysis betw
Hello!
I tried to look through the history but couldn't seem to find exactly
what I was looking for.
Is there a recommended way to run ICA on vertex data? For example, I've
transformed my raw fMRI data to surface space using fsfast, and would like
to extract group level IC's from this data. Tha
In looking at your mask, it covers only half (or less) of the brain.
This would explain why the total volume you get from the mask is much
lesss than the total gm volume reported in aseg.stats.
On 01/20/2017 12:08 PM, Eli Johnson wrote:
>
> *Hi Doug,*
>
> *
> *
>
> *Thanks a lot for your help!*
Hello Freesurfers,
I am working on a PET surface based analysis between two groups. I did the following:
1. I concatentaed the PET images using the command "mris_preproce" and I got the file (lh.mgh) for left hemisphere and (rh.mgh) for right hemisphere.
2. I smoothed "lh.mgh and rh.mgh) using
Hi Tamara
we don't use an intensity threshold as such. If you are looking for CSF,
why not use our aseg and erode it once to avoid border voxels? Or twice if
you want to be really certain.
I'll leave (2) for one of our longitudinal processing experts.
cheers
Bruce
On Thu, 26 Jan 2017, Tama
Hi list,please see the error reported below.ThanksStefano
curl
"http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bMAC.tar.gz";
-o "runtime2012b.tar.gz"
% Total% Received % Xferd Average Speed TimeTime Time Current
Hello,
I have two questions which I was hoping to get some help with.
(1) I was wondering whether there was a intensity threshold for grey matter
and CSF. I know that Freesurfer scales the intensity so white matter has an
intensity of 110 (as can be seen at the bottom of Freeviewer when I open
th
Dear Batool,
Sorry for missing your message.
And dear Adam:
Thanks for covering me! That’s exactly my standard answer to that question ;-)
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
I believe Dr. Iglesias previous responses on this exact question have been,
"yes it's possible, but your results may be harder to reproduce"
e.g. If someone wanted to replicate your study they may have a harder time
having to download 2 different versions of freesurfer to achieve comparable
results
Hi,
Can anyone comment on my question below?
I think the FAQ page mentions that the same version should be used to process
all cases within a dataset, but my question is whether I can have the same
dataset used for two different versions for separate analyses? This is
considering that I've alrea
Hi Doug,
In order to compute and apply the inverse of an m3z transform you would
need to use the --inv-morph flag instead of the --m3z and reverse your
targ and mov inputs. With the current implementation of mri_vol2vol though
I do not think that you can specify the order of the transforms (w
Glad to hear it, thanks for checking! If the final 6.0 works, there's no need
to dig up the beta.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira
[barbara.avelar.pere...@ki.se]
Sent: Thurs
I have never tried this. Does the rest of recon-all -all run without errors?
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/
On 25 Jan 2017, at 11:45, Michel Hu mailto:a
Dear FS's experts,
I have run all my cross with v5.3 and hesitate to run all longitudinal
process with v6. Does that make sense and will improve the process or would
it be risky to do this ?
Many thanks for your lights !
Best regards,
Matthieu
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Free
Hi Anastasia,
Thanks so much for your help! Sorry for the delay in replying -- just wanted to
make sure the was problem was indeed solved. Since I'm using a server for which
I have no administrative rights, I had to wait before the update was installed.
It seems to run perfectly now.
I can't fi
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