Hi,
I have used make_average_subject and made a new average subject form my N
subjects, now I want to load one overlay form a single subject on this new
average subject, how should I do that?
Regards,
Fariba
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Fariba Sharifian, PhD Student.
Hi Catherine,
it shouldn't be necessary, but you should be very careful that any
effects you find are biological ones and don't simply reflect acquisition
differences.
cheers
Bruce
On Wed, 14 Dec 2011, Cat Chong wrote:
Dear Experts,
I am sorry for the basic question but we have a dataset
Hello,
Just a quick question.. when is the file (within the bold subdirectories)
fmcsm5(4)-all.txt made? Is it created as a result of running func2roi?
Thank you!
Sandra
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue
volume/estimated ICV) as an estimate of global atrophy. In previous
versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not
Hi Fariba, use mri_surf2surf to map individual data to another subject
(individual or average).
doug
Fariba Sharifian wrote:
Hi,
I have used make_average_subject and made a new average subject form my N
subjects, now I want to load one overlay form a single subject on this new
average
That is the fill threshold. It indicates how many label points must
fall into a voxel in order for that voxel to be considered part of the
label. By default it is just over 0, meaning that even one label point
falling into the voxel will make that voxel labeled. I would leave it
like, look at
Hi Sandra, I'm not sure I know what file you are talking about. What is
its exact name?
doug
swood...@nmr.mgh.harvard.edu wrote:
Hello,
Just a quick question.. when is the file (within the bold subdirectories)
fmcsm5(4)-all.txt made? Is it created as a result of running func2roi?
Thank
Have you tried to change the threshold to see if you see more colors?
Don't load it as a segmentation, just look at the overlay.
doug
vin . wrote:
Thank you so much Doug,
you are right, it doesn't match exactly, however there is some match.
so, now I am running recon-all T1_1mmMNI.nii,
Hi Doug,
the file fmcsm4-all.txt,
.../bold/tap_lh_long_CD_R01BTX_pat6_sess1_sm4/caud_LH_t3_5_sm4_75thresh.
I think tool using the command 'func2roi-sess' produces this file, but I
would like to confirm. An example command we use is:
func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis
Hi Cheryl,
You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject
mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum
stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
--supratent --subcortgray --in mri/norm.mgz
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We are having a difficult time getting the ICV to fit correctly in our sample,
but the segmentions and parcellations look accurate. I believe that the ICV is
generated from the talairach.xfm early on in the processing stream, but then
further processing for segmentations/parcellations is done.
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get
the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from
recon-all, could whole brain parenchymal volume be calculated as
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