Hi
I found out the way to calculate global cortical mean. The procedure is
as following just use
mris_calc.
mris_calc lh.avg_thickness stats in the fsaverage.
Knut J
On 07/27/2011 03:43 PM, Knut J Bjuland wrote:
Hi. I am trying to extract the mean cortical thickness in a group, and
the
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run mri_label2label to all the subjects of my comparison
- To run mris_anatomical_stats. I would obtain the volume of the labels in
each subject
- Mean volume of all the subjects
Hi Yolanda,
you need to email us the screen output with the error so we can diagnose
it.
cheers
Bruce
On Thu, 28 Jul 2011, Yolanda Vives wrote:
Thank you Douglas for your suggestions!
If I use mris_anatomical_stats, would I perform the following procedure?
- To run mri_label2label to
Hi Jessica,
I'd recommend to run the -base and the -long on these and see what
happens. If you then still see these differences, maybe we can take a
look at your data to figure out what causes this. It could be that the
WM segmentation fails somewhere. Anyway, the longitudinal stream should
help
Hi Bruce,
Thanks again for your valuable information. I was trying to click on my orig
surface button in the interface but it is not active. Is there a way that I
can enable this option/button? I see more buttons are not active. How I can fix
this?
Second, using tkmedit, how I can see the
Hi Antonella,
if it's not active then it probably failed loading the orig surface. Can
you send us the output of the tkmedit command? There is a multi-view button
you can click in tkmedit to show 3 orthogonal views at the same time.
cheers
Bruce
On Thu, 28 Jul 2011, Antonella
Kis wrote:
Hi Antonella,
When you load the files that those buttons are associated with, then they
become active. When you loaded the orig surfaces, the orig surface button
still was not active?
If you choose any button besides the Navigate button, when you left click,
that will move the cursor (red
Hi Bruce,
That's the error:
limiting computations to label
fsaverage/label/grouplabel_concro_rh-0001.label.
reading volume
/nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz...
ERROR: cannot find
/nfs/arpon/PROJCT/DEPR/proc/FREESURFER/WithModif/fsaverage/mri/wm.mgz
Yolanda, don't run mris_anatomical_stats on fsaverage. You should map
the label to each individual with mri_label2label, then use
mris_anatomical_stats. Sorry for not being clearer eariler.
doug
Yolanda Vives wrote:
Hi Bruce,
That's the error:
limiting computations to label
Hi,
I have two questions regarding ICV correction for total hippocampal volume
(from aseg.stats) and for hippocampal subfield volumes.
1) Total hippocampal volume: I am using the mri_label_volume script that
uses the atlas normalization factor as an estimate for total ICV two
T1-weighted scans
Dear Bruce,
In fact, when I run:
tkmedit subject2 brainmask.mgz lh.orig lh.white -aux wm.mgz -aux-surface
rh.orig rh.white
it
gave me an error saying that tkmedit does not recognize lh.orig but the
green line pops up and the orig surface button is now active. Why I
still get the error message
On Thu, 28 Jul 2011, Antonella Kis wrote:
Dear Bruce,
In fact, when I run:
tkmedit subject2 brainmask.mgz lh.orig lh.white -aux wm.mgz -aux-surface
rh.orig rh.white
it gave me an error saying that tkmedit does not recognize lh.orig but the
green line pops up and the orig surface button is
Hi Martin,
When I did longitudinal analyses in the past, the output was very strange
even though I think I did everything correctly. If it's not too much
trouble for you, could you please take a look at my data and tell me what
I've done wrong? Since the files are so large, how would I send
Hi Jessica
the problem may be data quality! At 1.5T with a volume coil we would
typically get 2 scans to average. A TR of 14 is pretty short and will
reduce the SNR, and a TE of 6 is quite long and will reduce contrast. Can
you send us a tif of one slice to look at?
Bruce
On Thu, 28 Jul
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