No, don't try to register them directly to fsaverage. Create a
registration matrix for each 1st level (sounds like you've done this),
then use mri_vol2surf with "--trgsubject fsaverage". This will sample
the CON to the subject's individual surface, then use the surface-based
registration to map
That is the right way to map it to the volume. Does the activation
disappear in the volume? If you want to go to the fsaverage surface, you
should use mri_vol2surf and spec "--trgsubject fsaverage"
doug
casp...@clipper.ens.fr wrote:
> Hi!
>
> This is maybe something very easy: but I am not sure
It is not really possible in QDEC. You can use the command-line stream
to do this. Do a search for "paired" on the wiki to find the page.
doug
Mira Michelle Raman wrote:
> Hi,
> I have a group of siblings (one disorder, one unaffected).
> Is it possible for me to set up the group analysis
> i
I'm not that familiar with the parametric modulation option in SPM. Is
it changing the height of the HRF on an event-by-event basis or is it
changing the HRF parameter (eg, delay dispersion) on an event-by-event
basis? The former we can do, the latter we cannot.
doug
Andrew Jahn wrote:
> What
Thanks for the help, will try lh.sulc, for proxy 'depth' measure
cheers
On 18/06/2010 19:50, "Donna Dierker" wrote:
> I would think lh.sulc might be better for this purpose.
>
> If neither works, you can try importing into Caret and using sulcal
> depth. Hopefully lh.sulc will do the job.
>
just run
recon-all -s subject -segstats
Gonzalo Rojas Costa wrote:
> Hi:
>
> I deleted the aseg.stats file by mistake (only that file)... How can I
> regenerate that file ?... I have the complete processing of that patient...
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
>
>
>
> _
Hi:
I deleted the aseg.stats file by mistake (only that file)... How can I
regenerate that file ?... I have the complete processing of that patient...
Sincerely,
Gonzalo Rojas Costa
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htt
cat $FREESURFER_HOME/build-stamp.txt
It's good that it's something you care about!
doug
Dalwani, Manish wrote:
> Sorry for this lame question but how can I check the current version of
> freesurfer?
>
> Regards,
> Manish Dalwani
> ___
> Freesurfer m
Sorry for this lame question but how can I check the current version of
freesurfer?
Regards,
Manish Dalwani
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The information in thi
You can create a binary ribbon mask with
mri_binarize --i ribbon.mgz --match 3 --match 42 --o ribbon.mask.mgz
doug
Andrew Ward wrote:
> Hi all,
>
> This may be a bit elementary, but I have been unable to figure it out.
> I would like to create a structurally defined binary gray matter mask
>
You can do it this way, but it will be inferior to using a
subject-specific label (why use freesurfer in the first place?). You can
map a label from fsaverage to the mni152 with mri_label2vol, specifying
$FREESURFER_HOME/average/mni152.register.dat as the registration.
doug
mmoay...@uhnres.ut
The 4th column is the gray matter volume ("GrayVol").
doug
Ed Gronenschild wrote:
> Doug,
>
> I don't understand this since the ?h.aparc.stats file doesn't
> contain volumes.
>
> Ed
>
> On 18 Jun, 2010, at 15:56, Douglas N Greve wrote:
>
>
>> Yes, the difference is partial volume correction. B
Doug,
I don't understand this since the ?h.aparc.stats file doesn't
contain volumes.
Ed
On 18 Jun, 2010, at 15:56, Douglas N Greve wrote:
> Yes, the difference is partial volume correction. But you should
> use the
> values from the ?h.aparc.stats file for cortical parcellations as it
> uses
Try the group analysis tutorial on our wiki.
doug
Joana Braga Pereira wrote:
> Dear Freesurfers,
>
> I'm a new/inexperienced user. I've just run a thickness comparison
> between two groups with qdec and got several differences throughout
> the brain.
>
> I would like to get the coordinates, mea
You can run mri_surfcluster to get basic statistics. If you want cluster
p-values, you will need to run a simulation (mri_glmfit-sim), or you can
pass mri_surfcluster a simulation table that we distribute here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz
Yes, the difference is partial volume correction. But you should use the
values from the ?h.aparc.stats file for cortical parcellations as it
uses the more accurate surface-based volumetric calculation.
doug
Ed Gronenschild wrote:
> But what about the labels starting with "lh-ctx-"
> and "rh_ct
you can load it as an overlay, then change the thresholds to only
display the deepest part.
doug
Lena Palaniyappan wrote:
> Hi all
>
> I am trying to determine a 'sulcal pit' - the deepest point in central
> sulcus. The lh.curv file gives curv values of all vertices, but how can I
> display the
that's what I thought, but it's the orig, not the nu. I think it's the
histogram in mri_convert. The mdeft looks like it has a lot of very bright
vessels in it, maybe more than we ignore
On Fri, 18 Jun 2010, Douglas N Greve wrote:
> This might be a problem with the way we call nu_correct. I had
This might be a problem with the way we call nu_correct. I had a similar
problem a few months ago. I changed mri_nu_correct.mni, and the problem
went away, so you may need the new version (attached). Make sure to make
a backup.
doug
Bruce Fischl wrote:
Hi Frank,
is it the orig.mgz that is d
Hi all
I am trying to determine a 'sulcal pit' - the deepest point in central
sulcus. The lh.curv file gives curv values of all vertices, but how can I
display the depth as a color map localised to central sulcus only? With such
a display will I be able to identify the zone with maximum 'depth' a
use aseg.stats for the subcortical volumes. There is a difference
between aseg.stats and wmparc.stats for the subcortical volumes because
of the partial volume correction.
Ed Gronenschild wrote:
> Hi,
>
> I tried to find out this from previous contributions
> but got lost.
> There's some confusi
Probably so. Just use the gray matter as seed points
ox...@yahoo.com wrote:
> thank you. I'll try that.
>
> might it be better to use the white matter parcellations (wmparc.mgz)
> as tractography way points and end points instead of gray matter
> parcellations (aseg)?
>
> Thanks!
>
> --- On *Thu
Hi Bruce,
It is the orig.mgz (cannot check right now if the nu is also dark).
Many thanks,
frank
2010/6/18 Bruce Fischl :
> Hi Frank,
> is it the orig.mgz that is dark, or the nu?
>
> cheers
> Bruce
>
> On Fri, 18 Jun 2010, Frank Scharnowski wrote:
>
>> Dear Freesurfers,
>>
>> When importing a 3T
But what about the labels starting with "lh-ctx-"
and "rh_ctx-", like for instance lh-ctx-fusiform (index=1007).
In the wmparc.stats file it has a volume of 8249
voxels and in wmparc.mgz 8752 voxels?
Is the first pve-corrected and the latter not?
On 18 Jun, 2010, at 13:43, Allison Stevens wrote:
Hi Frank,
is it the orig.mgz that is dark, or the nu?
cheers
Bruce
On Fri, 18 Jun 2010, Frank Scharnowski wrote:
> Dear Freesurfers,
>
> When importing a 3T MDEFT structural scan into freesurfer with
> 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark
> (see attached tkmedit
You're right - aseg.stats refers to the aseg.mgz and you should use that.
You would only use the wm parcellations from the wmparc.mgz
--
On Fri, 18 Jun 2010, Ed Gronenschild wrote:
> Hi,
>
> I tried to find out this from previous contributions
> but got lost.
> There's some confusion on which
Hi,
I tried to find out this from previous contributions
but got lost.
There's some confusion on which file(s) to use
for segmented volumes.
FreeSurfer generates the following image and
text files:
- aseg.mgz
- aseg.stats
- aparc+aseg.mgz
- wmparc.mgz
- wmparc.stats
To my best knowledge aseg.stat
Dear Freesurfers,
I'm a new/inexperienced user. I've just run a thickness comparison between
two groups with qdec and got several differences throughout the brain.
I would like to get the coordinates, mean thickness, z or t values of my
results. Would someone tell me how to do this or kindly dire
Dear Freesurfers,
When importing a 3T MDEFT structural scan into freesurfer with
'mri_convert subjectname.nii 001.mgz', the image looks extremely dark
(see attached tkmedit snapshot).
The results of recon all are suboptimal, probably due to the bad
intensity normalization. In SPM the structural lo
Hi Patricia,
when you convert your labels to volume, they will not be actually the cortical
masks, but rather a line of voxels on the junction of GM and WM, which should
be fine for seeding and targeting the tractography.
Best,
Martin
On Friday 18 June 2010 02:24:52 ox...@yahoo.com wrote:
> t
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