Hi Jen,
the T1.mgz is in register with the surfaces by construction, so you
shouldn't need any registration.
cheers
Bruce
On Mon, 14 Feb 2011, Douglas N Greve wrote:
> When you say the original T1, do you mean the data directly from the
> dicom files? FS analysis is generally done in our "confo
When you say the original T1, do you mean the data directly from the
dicom files? FS analysis is generally done in our "conformed" space (1mm
isotropic, 256^3). One of those volumes is called "T1" and one is called
"orig" -- this understandably confuses a lot of newbies (and oldbies).
doug
Je
What volume do you want to project them to?
doug
Jennifer Evans wrote:
> Hi there,
>
> I'm not really familar with freesurfer and am missing the step on what
> to register to create the register.dat file required to use
> mri_label2vol to convert the probabilistic V1 label file outputs from a
>
Hi there,
I'm not really familar with freesurfer and am missing the step on what
to register to create the register.dat file required to use
mri_label2vol to convert the probabilistic V1 label file outputs from a
single subject to a volume. I thought the labels are already on the
surface/vo
Salve!
Sto utilizzando freesurfer per un lavoro di tesi e ho incontrato
problemi per la fase di preprocessing. Allora ho ricevuto dei file in fomrato
".nii" e li ho converiti con il comando: "recon-all -i "file_name.nii" -s
"nuovo_nome". Ora dovrei processarli, tramite il comando "recon-all -i
List the number of conditions as 1 (there is 1 non-null/rest/fixation
condition).
doug
Mandy Nagy wrote:
> Our mkanalysis-sess command:
>
> mkanalysis-sess -analysis mandylh2 -surface fsaverage lh -fwhm 8
> -event-related -paradigm paradigm.par -TR 3 -nconditions 2
> -runlistfile task -gammafi
Am 14.02.2011 18:59, schrieb Douglas N Greve:
> I have created some use cases on how to transform coordinates in one
> space to those in another space (eg, a point on the surface to MNI305
> space or to the col, row, slice of a functional volume). Let me know if
> you have any questions or have ot
Our mkanalysis-sess command:
mkanalysis-sess -analysis mandylh2 -surface fsaverage lh -fwhm 8
-event-related -paradigm paradigm.par -TR 3 -nconditions 2 -runlistfile task
-gammafit 2.25 1.25 -refeventdur 30
Our paradigm file:
0 0301Rest
30 1301Typing
60 0
I have created some use cases on how to transform coordinates in one
space to those in another space (eg, a point on the surface to MNI305
space or to the col, row, slice of a functional volume). Let me know if
you have any questions or have other use cases you'd like me to add.
http://surfer
The aseg.mgz is in the subject's native anatomy (no stretching or
compressing). As Bruce says, if you're just computing volumes, you don't
need to do the transformation. If you want to compute overlap, then you
need them in the same voxel-for-voxel space.
doug
Yolanda Vives wrote:
> But "aseg.
But "aseg.mgz" file comes from a Talairach-registered image and the anterior
and posterior commissures are the standard alignment of the brain for this
atlas. Could I assume that all my caudates come from MRIs that had the same
orientation according to the anterior and posterior commissures?
yolan
Usually this means that there is something wrong with your design or
paradigm files. CAn you send the paradigm files and the mkanalysis-sess
command?
doug
Mandy Nagy wrote:
> Hello,
>
> We are attempting to run an analysis using selxavg3-sess but keep
> getting an error.
>
> We are using:
>
>
It does not take into account any info about the faces or edges. I'm not
sure about your resolution question. Can you elaborate?
doug
Aaron Alexander-Bloch wrote:
> Dear all,
>
> I am hoping to use surf2vol to generate high resolution masks of the
> gray/white surface, so something like the follo
yes, it is.
doug
Yolanda Vives wrote:
> Hi Doug,
>
> I am interested in coming back to rawavg space because we have the
> caudates segmented manually and we would like to compare the
> volumes obtained automatically with those obtained with a manual
> segmentation. In this case, is it necess
no, we don't reorient to avoid additional blurring
cheers
Bruce
On Mon, 14 Feb 2011,
Yolanda Vives wrote:
Ok, I see. Thank you.
Just one more question. MRIs from my "manually segmented" caudates have been
previously reoriented according to the Anterior/Posterior Commissure axis.
Are freesurf
Ok, I see. Thank you.
Just one more question. MRIs from my "manually segmented" caudates have been
previously reoriented according to the Anterior/Posterior Commissure axis.
Are freesurfer segmented images reoriented also in this way?
Cheers,
Yolanda
2011/2/14 Bruce Fischl
> not if you just wa
Hello,
I'm facing the same problem for one of my subjects. Is there a general solution
for this problem or would you solve this problem on a case by case basis? I saw
posts from others with the same problem.
Thanks for your help,
Nasim
On Dec 2, 2010, at 9:18 AM, Jennifer Addicks wrote:
> Hell
Dear all,
I am hoping to use surf2vol to generate high resolution masks of the
gray/white surface, so something like the following command:
mri_surf2vol --sd /subj/dir/ --identity subid --hemi lh --surf white
--mkmask --o volume.mgz --template ./template.mgz
However I'm wondering about what exa
not if you just want to compare volumes. If you want to compute overlap it
would be, but note that you'll probably be biased towards lower overlap as
you will induce some sampling errors mapping the aseg to the original voxel
space.
cheers
Bruce
On Mon, 14 Feb 2011, Yolanda Vives
wrote:
Hi Doug,
I am interested in coming back to rawavg space because we have the caudates
segmented manually and we would like to compare the volumes obtained
automatically with those obtained with a manual segmentation. In this
case, is it necessary to come back to rawavg space, istn't it?
Yolanda
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