Thank you Doug, that worked a treat! I knew it must have been something
simple I was missing.
Best.
LT
On Tue, Nov 19, 2013 at 8:45 AM, Douglas N Greve
wrote:
> The problem is with the mat file, not the input. The matrix should be an
> ascii text file.
> doug
>
>
> On 11/18/2013 12:09 PM, Laur
Thanks! so this is the command I've used:
mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o
freeSurfer_Results/P2/labels/freeSurfer_lobes.nii.gz
a couple of question I have now:
1. what lables (numbers) correspond to the 5 main lobes? looking at the
"FreeSurferColorLUT.txt", I'm assuming the l
I think the best thing to do is to just run recon-all on the FSL
standard brain
doug
On 11/21/2013 04:08 PM, Kirstie Whitaker wrote:
> Hi Freesurfer and FSL communities,
>
> Firstly, I apologise for the double posting. I suspect there are
> experts in both groups that can help me.
>
> I'd lik
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am
wondering up to how many recon -all for separate subjects I can run in
parallel. With the version of Snow Leopard 32b I was running two at a time and
it took around 20 hours. Would I be able to run 6 subjects in parallel
Hi Freesurfer and FSL communities,
Firstly, I apologise for the double posting. I suspect there are experts in
both groups that can help me.
I'd like to be able to visualise the Destrieux atlas that freesurfer uses
at the same time as my MNI standard space results in FSL.
Is that possible? I'm a
Hi Rujing
run:
recon-all -s -make all
that will figure out what needs to be rerun and do so.
cheers
Bruce
On Thu, 21 Nov 2013,
Rujing Zha wrote:
Dear all,
I have run recon-all for some subjects,but this code is unexpected
terminated before it normally end. Can I run the code agian directl
Hi all,
I figured I would have some luck tapping expertise on using optseq2 in
this mailing list. There are 8 trials times 8 conditions in an
event-related design. We are using a 1-back task just to keep
participants paying attention. Thus, we are not attempting to match the
number of 1-back-y
Dear professor Bruce,
Thanks for your precious prompt. I will try it.
All the best.
Rujing Zha
发件人：Bruce Fischl
发送时间：2013-11-21 21:39
主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination
收件人："Rujing Zha"
抄送："freesurfer"
Hi Rujing
run:
recon-all -s -make all
that will f
Hi Pablo
it depends on how many cores you have
Bruce
On Thu, 21 Nov 2013, pablo najt wrote:
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am
wondering up to how many recon -all for separate subjects I can run in
parallel. With the version of Snow Leopard 32b I was ru
Hi all,
I want to convert the cortical labels I get in freeSurfer to volumetric
ROIs in the subject space and I've followed the steps mentioned in:
http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/
except since I'm interested in lobe m
Dear doug:
Thank you for your reply ,and it looks good now.But I meet a question
when I am ready to write in my paper,that is how to decribe the annotation of
my effect size maps ,I found two papers that were described as follows:
1、Cohen‘s d for the difference between two means was based o
Dear all,
As we know, recon-all is a integrated code. I have read this code process flow
in the website http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. Can I
run the a series of command which are presented in command line step by step to
realize all the function of recon-all?
All the
The "Vertex RAS" is a FS internal coordinate system
"Vertex MNI Talairach" is the MNI305 coords
"Vertex Talairach" is an estimate of talairach coords based on a
transform from Matthew Brett
see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
On 11/18/2013 08:39 AM, Anita van Loenhoud wrote
If you don't have any covariates, you can use --osgm. If you have
covariates, then they need to go into an FSGD file.
doug
On 11/15/2013 04:12 PM, Govindarajan, Koushik Athreya wrote:
>
> Hi all,
>
> I am trying to compute differences between 2 runs of my same set
> of subjects (repeatabil
Do you mean the aseg.mgz for an individual? If so, you can run mni152reg
to register that subject to mni152space. Next you can run mri_label2vol
to map the aseg to the 152 space.
doug
On 11/17/2013 07:26 PM, ebell...@uwm.edu wrote:
> Hello,
>
> I plan on using the aseg.nii to create a grey mat
Hi Rujing
sure, you can run them individually if you want. Just make sure it is in
the right order and you don't skip any or they will fail
cheers
Bruce
On Thu, 21 Nov 2013, Rujing
Zha wrote:
Dear all,
As we know, recon-all is a integrated code. I have read this code process
flow in the we
No idea why. What is the difference in the headers? Can you post the
terminal output of both your mri_vol2surf commands? Also, you can try
using MRIread.m and MRIwrite.m (these use load_nifti and save_nifti
under the hood but also do some things to the header).
doug
On 11/20/2013 08:46 AM, L
btw, you should not need to run mri_annotation2label twice.
On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote:
> Hi all,
>
> I want to convert the cortical labels I get in freeSurfer to volumetric
> ROIs in the subject space and I've followed the steps mentioned in:
> http://brainybehavior.com/neuroimag
use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is
created. Look in the recon-all.log file for the command line used.
doug
On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote:
> Hi all,
>
> I want to convert the cortical labels I get in freeSurfer to volumetric
> ROIs in the subj
I don't follow the two examples you have there. Why are you reporting a
map of Cohen's d?
On 11/21/2013 09:40 AM, cj wrote:
> Dear doug:
> Thank you for your reply ,and it looks good now.But I meet a
> question when I am ready to write in my paper,that is how to
> decribe the annotation
This means that there are not enough voxels in the mask to compute the
intervoxel correlation needed to compute the FWHM from the residuals.
The FWHM is needed for clusterwise correction. What does the mask look
like? Does it have a "funny" shape? If you just want to run mri_glmfit
without the
Which "above process" do you mean?
On 11/17/2013 04:57 AM, Anna Jonsson wrote:
> Thank you. I have tried to write a script to make this above process
> automatic but it doesn't work. Any tips on how to make the above
> process into a script for a number of subjects ?
>
> Kind Wishes,
>
> Anna
>
hi , I have run this subject again, checking all the processing
stages, and still get the same issues. I have placed the
new output from the preprocessing stage (this is only
1.4 megabytes as the previous one had 2 preprocessing jobs
appended)
you can find it here:
https://dl.dropboxusercontent.com
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