The fsaverage surface does not intersect very well with the MNI brain
(the problem is that the average surface does not have as deep folds as
an individual). You can see what is going on if you convert your label
to fsaverage space with
tkmedit fsaverage orig.mgz -surfs -fmin 0.5 -overlay 1.
Hi Yuko, i'm guessing that something is fishy with your bval and bvec
files. Make sure that there is a new line after the last entry. How did
you make the files?
doug
On 12/13/11 11:22 PM, Yuko Yotsumoto wrote:
> Hi Doug,
>
> I thought I figured this out, but I was wrong...
>
> my b-values are
Hi Doug,
I thought I figured this out, but I was wrong...
my b-values are 700, and number of directions is 64.
Number of images with b=0 is 1.
Text file for bvals has 65 rows, first row has 0, followed by 64 of 700.
0
700
700
700
...
Text file for bvecs has 65 rows and three columns. The first
Is your register.dat correct?
On 12/13/11 10:33 PM, vin . wrote:
Thanx Doug,
atleast I see, now something. (see attached "seg.mgh -annot
seg.annot.tiff)
> tksurfer Sub_ID lh inflated -annot seg.annot -ov lh.seg.mgh -fthresh
0.01 -fmid 0.3 -fslope 1
just to check, I also summed, all binary f
Try tksurfer Sub_ID lh inflated -annot seg.annot
doug
On 12/13/11 9:39 PM, vin . wrote:
no, in tksurfer, just inflated lh appears (no overlay). so, I viewed
lh.seg.mgh in freeview and converted it to .nii and viewed in fslview.
On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl
mailto:fis...@nmr
no, in tksurfer, just inflated lh appears (no overlay). so, I viewed
lh.seg.mgh in freeview and converted it to .nii and viewed in fslview.
On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl wrote:
> oh, so you mean you see a line on the surface?
>
> On Wed, 14 Dec 2011, vin . wrote:
>
> Thanx Bruc
oh, so you mean you see a line on the surface?
On Wed, 14 Dec 2011, vin .
wrote:
Thanx Bruce for quick reply.
you are right, it's surface based file after mri_vol2surf. yeah, tried with
following command.
>tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov lh.seg.mgh -fthresh
0.01 -fmid 0
Thanx Bruce for quick reply.
you are right, it's surface based file after mri_vol2surf. yeah, tried
with following command.
>tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov lh.seg.mgh -fthresh
0.01 -fmid 0.3 -fslope 1
On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl wrote:
> Hi Vin
>
> it lo
Hi Vin
it looks like your lh.seg.mgh is a surface-based .mgz not a volume one. Did
you try loading it into tksurfer?
cheers
Bruce
On Wed, 14 Dec 2011, vin . wrote:
Thank you Doug,
>tkregister2 --mov $d/T1.nii.gz --targ $d/mri/brain.mgz \
--regheader --reg $d/register.dat --noedit
after
Thank you Doug,
>tkregister2 --mov $d/T1.nii.gz --targ $d/mri/brain.mgz \
--regheader --reg $d/register.dat --noedit
after creating register.dat, I followed the explained procedure,
Which resulted in "lh.seg.mgh". can't view this file. ( appears a line )
>mri_info lh.seg.mgh
Volume informat
a-ha! I forgot to add .gz
sorry for the silly error.
thanks.
michelle
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It really thinks that eccen/real.nii does not exist. What does
ls -l eccen/real.nii
return?
Michelle Umali wrote:
> Hi Doug,
> Here is the output
> Thanks. -Michelle
>
> BOTANICA:/usr/local/freesurfer/subjects/retinotopy/sj25/bold/rtopy.self.rh>
> rtview.sh --debug --s sj25 --lh --eccen --real ecc
Hi Antonella,
> I will appreciate a lot if you can help me understand what is the meaning of
> the results after running after running mri_cvs_register and the GLM group
> analysis.
>
> More exactly, I followed all the instructions from the webpage:
>
> http://surfer.nmr.mgh.harvard.edu/fswik
The easiest thing is to use mri_label2vol, something like
mri_label2vol --label yourlabel.label --temp functemplate.nii --reg
register.dat --proj frac 0 1 .1 --hemi lh --subject subject --o
yourlabel.nii
doug
Zhangyuanchao wrote:
> Thanks for your response!
>
> In fact, the label that I want to
The threshold is a significance threshold, ie, -log10(p), so sig=2.3 ->
p < 10^-2.3 = .005. This will not work for fsaverage5. You can try
generating a new set of tables for fsaverage5 with mri_mcsim.
doug
Xinian Zuo wrote:
> Thank you, Doug! Found the CSD file. Just want to make sure that I
>
It's a little involved but possible.
1. Binarize Nth cluster to have a binary value of N
mri_binarize --i N.nii --min 0.5 --binval N --o Nb.nii
2. Sample Nth cluster to the surface
mri_vol2surf --reg register.dat --mov Nb.nii --interp nearest
--hemi lh lh.Nb.mgh
After doing that will a
Hi Doug,
Here is the output
Thanks. -Michelle
BOTANICA:/usr/local/freesurfer/subjects/retinotopy/sj25/bold/rtopy.self.rh>
rtview.sh --debug --s sj25 --lh --eccen --real eccen/real.nii --imag
eccen/imag.nii --fsig eccen/fsig.nii
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while (
You can try specifying the functional stem in mkanalysis-sess with
-funcstem yourfuncstem (assuming your data are yourfuncstem.nii). This
will cause selxavg3-sess to bypass the preprocessing.
doug
Thunell Evelina wrote:
> Hi Doug,
> I might try to do it in SPM but it requires some more work I th
Run mris_preproc with the --meas volume option. Make sure to get an
up-to-date version of mris_preproc
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
doug
Lindsay Ercole wrote:
> What is the current opinion on using cortical volumes rather than
> reporting on thickne
Hi Lindsay
they are both biologically relevant measures, it's just a question of
what you are investigating. If you are doing volume it's probably worth
decommposing it into surface area and thickness though to understand the
underlying neurobiology better
Bruce
On Tue, 13 Dec 2011, Lindsay E
What is the current opinion on using cortical volumes rather than reporting
on thickness?
Sincerest thanks,
Lindsay
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The information
Can you run it with --debug and send me the terminal output?
Michelle Umali wrote:
> Dear All,
> I am still having trouble generating polar and eccen maps with rtview.
>
> I did this:
> cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh
> rtview.sh --s sj07 --lh --eccen \
> --real eccen/real.n
Dear All,
I am still having trouble generating polar and eccen maps with rtview.
I did this:
cd $SUBJECTS_DIR/retinotopy/sj07/bold/rtopy.self.lh
rtview.sh --s sj07 --lh --eccen \
--real eccen/real.nii --imag eccen/imag.nii --fsig eccen/fsig.nii
The subjectname file is in $SUBJECTS_DIR/retinot
Hi Doug,
I might try to do it in SPM but it requires some more work I think - The
Freesurfer retinotopic mapping analysis is automatic and easy to use.
Evelina
On Dec 12, 2011, at 10:51 PM, Douglas N Greve wrote:
> Hi Evelina, why don't you do the whole analysis in SPM then map the results
>
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