cat (so
> there's no real concatenation). Also, make sure that the bad subject in
> the mri_concat output is the same subject that you are looking at
> individually; you could be off by 1.
>
> doug
>
> Agnieszka Burzynska wrote:
>>
>> Dear experts,
>> I used
Dear all,
I have 2 questions:
1) I created labels for some ROIs on fsavgerage (qdec analysis). I got
statistics from these rois for each individual subject (by map-to-subjects,
etc.), but what I am now interested in is to know the size of the ROI on the
group level (so on the fsaverage surface).
Dear experts,
I have 2 questions:
1) I created labels for some ROIs on fsavgerage (qdec analysis). I got
statistics from these rois for each individual subject (by map-to-subjects,
etc.), but what I am now interested in is to know the size of the ROI on the
group level (so on the fsaverage surface
ote:
>
> Try something like this
>
> mri_segstats --slabel fsaverage lh path/to/lh.yourlabel.label --sum
> lh.yourlabel.sum
>
> The 4th column of the summary file will have the Area in mm^2
>
> doug
>
> Agnieszka Burzynska wrote:
>> Dear experts,
>> I ha
Dear all,
I am trying to figure out how to bring my fMRI data from FSL to the
freesurfer surface.
The way I understood it from the tutorial "3.0 Surface-based Group
Functional Analysis"(
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat)
There are two possibilities of combining mu
Dear all,
I have a follow-up question to the previous discussion ("correction for
behavioral varialbles in qdec" Tue, 04 Aug 2009.
Is there an option to extract the average p-value from a ROI? After a group
analysis I specified ROIs at p < 0.001 and extracted the mean cortical
thickness, the peak
the same sign, then look through the
> log file and find the flirt command. Run that command by itself (you may
> need to run reg-feat2anat with --nocleanup to keep it from deleting the
> files). If that fails, then contact the FSL people
>
> doug
>
> Agnieszka Burzynska wro
Dear all,
For one of my subjects I had to correct the Talairach step manually. My
manual correction, however, may not be perfect. Is it possible to re-run
autorecon1 using the Talairach correction to GUIDE (but not REPLACE) the
automatic registration?
Thank you!
Aga
_
Dear Doug,
Thank you a lot for your reply!
Yes, I did use reg-feat2anat and registered example_func to the subject's
anatomical. As far as I understand it, then the registration matrix can be
used for a contrast of interest.
That's great news that the software version will not be a problem.
I wi
Dear Doug,
Thank you again very much for your help. I am replying with a delay because
I was travelling. Please see my questions& comments below in the text:
On 5/10/11 5:48 PM, "Douglas N Greve" wrote:
>
>
> Agnieszka Burzynska wrote:
>> Dear Doug,
>
Dear all,
I created a 3-frame image using a command similar to:
mris_preproc --target fsaverage --hemi lh --fwhm 5 \
--out xrun/lh.cope1.mgh \
--iv fbert1.feat/stats/cope1.nii.gz
fbert1.feat/reg/freesurfer/anat2exf.register.dat \
--iv fbert2.feat/stats/cope1.nii.gz
fbert2.feat/reg/freesurfer
Dear Doug,
Yes, it works, thank you so much!
Cheers,
Aga
On 7/7/11 3:57 PM, "Douglas N Greve" wrote:
> Hi Aga, try View->Configure->Overlay. The config window will have a time
> point entry at the top.
> doug
>
> Agnieszka Burzynska wrote:
>> Dear all,
Dear all,
I am combining 3 runs of a subject using fixed effects GLM and I wanted to
make sure I am doing the right thing.
For each subject I use:
mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof
126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label
$SUBJECT
than you should. At the group level, this is not such a big deal because
> you're either not using the varcope or you are using it as a weight.
> doug
>
> Agnieszka Burzynska wrote:
>> Dear all,
>> I am combining 3 runs of a subject using fixed effects GLM and I wante
Hi,
During running fixed effects glm to combine runs, the analysis of all but
one subject went fine.
The log file contains this error message:
mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval
3runs/tmp.mris_prep
Dear experts,
I am using reg-feat2anat to register my functional data from FSL to
anatomical and starndard space in Freesurfer.
For some subjects the registration is bad.
I can easily fix anat2exf.register.dat. However, as specified in
reg-feat2anat ‹help, I know that the registration failed as
our advice!
Best,
Aga
On 7/7/11 5:14 PM, "Agnieszka Burzynska"
wrote:
> Thank you! I think I will just try it out: now run it as it is but also run
> the 1st level with smoothing, as I need to add some contrasts anyway. Then I
> should also know the difference between volume an
Hi,
I am sorry to re-post this problem, but I cannot find the source of my
problem:
During sampling the feat data to fsaverage using for example:
mris_preproc --target fsaverage --hemi lh --out 3runs/lh.cope1.mgh --iv
run1.feat/stats/cope1.nii run1.feat/reg/freesurfer/anat2exf.register.dat
--iv
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