Hi,
if I apply the following command:
preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm
-fwhm 0 -per-run -nosmooth -force
The preprocessing runs into trouble at the following point
mri_vol2vol done
mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii
/usr/local/
Hi,
Is there a way to create and save multiple ROIs given there RAS coordinates in
tkmedit and then plot them and measure the distance between them onto an
inflated brain surface? Thanks!
~Rayna~
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Freesurfer@nmr.mgh.harvard
Hi Negar, sorry about the delay. The first thing to do is to look at the
orig.mgz to see if there is anything funny going on, maybe most of the
image is dark with one very bright spot or some other distortion. If
that looks ok, please tar up the subject and drop it to me at our file
drop (url
Hi,
I work in the area of longitudinal shape analysis, and have used the
longitudinal OASIS data in the past. I was trying to find freesurfer
segmentations of structures for the OASIS data, but could only find them
for cross-sectional ones.
I write to you to ask if you're aware of segmentations ma
Yep, that's a bug. I've fixed it in my version. To fix it in yours, do
the following two steps:
Step 1:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz
cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri
Step 2: In rawfunc2tal-sess, change:
set subcortma
Note that each of those set commands should be a single line. The file
to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess
doug
On 11/27/2012 01:23 PM, Douglas N Greve wrote:
> Yep, that's a bug. I've fixed it in my version. To fix it in yours, do
> the following two steps:
>
> Step 1:
>
Hi,
Thanks for the reference and explanation of the subtle statistical inferences.
It was very useful.
You are right in what i am trying to show (c- controls, p1 to p4 patients with
varying levels of endogenous factor) which is that when patients are subdivided
into levels of endogenous facto
Hi Mahinda,
make sure to include previous correspondence so that we know what
previous the previous suggestions are. Your analysis sounds technically
correct if you can justify the 1, 2, and 5 values for the covariate.
This design will give you a little more power.
doug
On 11/27/2012 01:28
Hi Parsanna,
I am not aware of any publicly available segmentation of the
longitudinal oasis data using the longitudinal freesurfer stream. I have
done some of that for my longitudinal paper but did not use all time
points for that. I may have run all somewhere else, but need to double
check.
Any
On Tue, Nov 27, 2012 at 1:28 PM, Mahinda Yogarajah wrote:
>
> Hi,
>
> Thanks for the reference and explanation of the subtle statistical
> inferences. It was very useful.
>
> You are right in what i am trying to show (c- controls, p1 to p4 patients
> with varying levels of endogenous factor) whi
Hi Doug,
Sorry the previous suggestion referred to a suggestion from Donald earlier in
the thread as follows:
"You might consider the contrast
[0 1.5 .5 -.5 -1.5] across all 5 groups showing a linear effect of
disease severity. The first column being controls."
I will try that suggestion out,
Hi Doug and Freesurfers,
I recently used mergecontrasts-sess to merge two contrasts of an analysis
in 50 different subjects. The command ran on each subject individually and
created a sig.nii and sig.ovpl file within a merged contrast folder for
each subject. I'd now like to look at an average map
sorry, what I meant to request is that you keep everything in a single
email. If they are spread out over multiple emails, then we have to go
back and find the relevant ones. As you know, we answer many emails, and
it is burdensome to have to keep track of particular emails.
thanks!
doug
On
Hi FS community,
I was trying to view the results of the hippocampal subfield segmentation
but had trouble overlaying the subfields on the nu.mgz file. I tried
letting it run for a while but it still does not work. Below I have
included the commands I used in Terminal:
[dyn-128-59-230-112:subject
Hi Doug,
I am afraid the p values are still too small in Free Surfer
Linux-centos4_x86_64-stable-pub-v5.1.0-full.
I redid
mkanalysis-sess
mkcontrast-sess
selxavg3-sess
in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
the center of the cluster.
Any further advice?
Thanks,
Caspa
Hi Hugh
how far is the closest visible white matter? Do you have any other image
types (e.g. a FLAIR)?
Bruce
On Wed, 28 Nov 2012, Hugh Pemberton wrote:
Hi freesurfers,
Just want to ask how I might go about including parts of the temporal lobes
that have been left out of the the surfaces due
What version are you running?
On Nov 27, 2012, at 8:51 PM, Hugh Pemberton wrote:
> Generally about 4 or 5 slices away, no other images unfortunately! Any ideas
> or is the atrophy just too great?
>
> Also meant to ask about another control point based issue I've had -
> occasionally, if I'v
5.1.0
On 28 November 2012 13:59, Bruce Fischl wrote:
> What version are you running?
>
>
>
> On Nov 27, 2012, at 8:51 PM, Hugh Pemberton
> wrote:
>
> Generally about 4 or 5 slices away, no other images unfortunately! Any
> ideas or is the atrophy just too great?
>
> Also meant to ask about an
Try it with nicks control point-fixed recon-all and see if it works better
On Nov 27, 2012, at 10:44 PM, Hugh Pemberton wrote:
> 5.1.0
>
>
>
> On 28 November 2012 13:59, Bruce Fischl wrote:
> What version are you running?
>
>
>
> On Nov 27, 2012, at 8:51 PM, Hugh Pemberton wrote:
>
>>
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