Hi, Just wanted to follow up on the issue below regarding the dimension of the
mri_label2vol output.
Hi,
I'm using mri_label2vol with the parameters below but the output .nii volume
has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension
mismatch is causing issues in our
I'll take a stab.
On Mon, Mar 28, 2016 at 10:13 AM, Afzal, Afsana wrote:
> Hi, Just wanted to follow up on the issue below regarding the dimension of
> the mri_label2vol output.
>
>
> Hi,
>
> I'm using mri_label2vol with the parameters below but the output .nii volume
> has the shape 163842x1x1 w
Hey Bruce,
The scans are done on 3T Siemens TRIO and 8 Channel head coil with a GRAPPA of
2.
Here is the screen shot of protocol used.
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=VJ0QiLxUz9fI6GCUofGHq7IAQY6k4uG50U0ic0zBkHE%3d&
Sorry, what are you trying to do? mri_label2vol maps a label (ie, ROI,
segmentataion, annotation) into a volume space. Do you just want to map
the surface overlay (fmcpr.sm4.fsaverage.lh.b0dc.nii) into the volume
space? If so, use mri_surf2vol. You can use the version below (using
method1 from
It automatically performs highpass filtering using a 2nd order
polynomial. You can increase the order to make the cutoff higher. You
can also use cosine filtering to set up a bandpass filtering with -hpf
and -lpf as inputs to mkanalysis-sess
On 03/26/2016 06:11 AM, std...@virgilio.it wrote:
> H
Hi Lara, what do you mean? Are you asking if the dev version and the
final v6 will be compatible? I would not rely on that.
doug
On 03/25/2016 06:51 PM, Lara Foland-Ross wrote:
> Hi Freesurfer experts,
>
> We'd like to begin a cortical thickness and hippocampal subfield analysis in
> the most re
What command did you use to visualize? There are no significant clusters
so the brain should have been totally blank
On 03/25/2016 05:42 PM, Miracle Ozzoude wrote:
> Hello Douglas,
> I just sent you the current file. Thank you.
> Best,
> Miracle
>
>
> From
Hello Douglas,
this was the command i used "Freeview -f $ SUBJECTS_DIR / fsaverage / surf /
lh.inflated -viewport 3d
Once I opened freesurfer, I viewed lh.secondsessionscore1.glmdir-->
cache.the30.pos.sig.cluster.mgh using the overlay icon ; and
lh.secondsessioncore1.glmdir ---> cache.the30.po
please also include all previous correspondence. We get a lot of emails
here and we can't keep track of each person's case, so we have to look
at the previous email chain. thanks!
doug
On 03/28/2016 02:00 PM, Miracle Ozzoude wrote:
>
> Hello Douglas,
>
> this was the command i used "Freeview -f
This were the conversations leading up to it
"Hello Bruce and Douglas,
This is what my design looks like.
GroupDescriptorFile 1
Class Group1
Class Group2
Variables Age Firstsessionscore
Input subj1 Group1 72 0.76
Input subj2 Group1 67 0.43
Input subj3 Group2 80 1.23
The contrast matrix i used was
Hello Freesurfer Experts,
I processed all of my brains through freesurfer 6.0 dev for Linux and
warped the surfaces to standardized space. For a handful of subjects I
want to perform a left right flip of the cortical thickness files
(standardized space) for a group analysis. What is the best
Hi Freesurfer Experts,
In testing mris_reverse, there seems to be a voxel shift. In looking up
other freesurfer utitlites I came across xhemireg and surfreg.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-September/040573.html
Does xhemireg or surfreg call out mris_reverse, causin
what do you mean by a voxel shift?
On 03/28/2016 04:03 PM, Ajay Kurani wrote:
> Hi Freesurfer Experts,
>In testing mris_reverse, there seems to be a voxel shift. In
> looking up other freesurfer utitlites I came across xhemireg and surfreg.
>
> https://mail.nmr.mgh.harvard.edu/pipermail/frees
Try changing the threshold. I think the threshold is set to 0 by default
so you are seeing all the 0-valued voxels and it looks like the whole
brain is active
On 03/28/2016 02:14 PM, Miracle Ozzoude wrote:
> This were the conversations leading up to it
> "Hello Bruce and Douglas,
> This is what
hard to say - they are low contrast and at least one has pretty bad
movement artifacts. I would try setting the various gray and white matter
thresholds to mri_segment and mris_make_surface in the expert opts stuff.
If you can't figure out how to do that, send me the recon-all.log from a
good s
Hello,
I have used label_area to compute the surface area of a desikan label on
fsaverage. Is the correction factor taken into account during computation with
this function?
Thanks,
Jaiashre.
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Hi Doug,
I am carrying out some correlations between cortical thickness and
cognitive ability, and had a question about the use of DODS vs DOSS for my
analysis with Qdec. From reading some of the forums, it seems as though
DOSS should be used when there are no interactions present. I am including
Hi Jaiashre,
yes, it should do the correction for average surface area, and should
print out a message indicating it is doing so. Something like:
adjusting for group surface area ...
cheers
Bruce
On Mon, 28
Mar 2016, Jaiashre Sridhar wrote:
Hello,
I have used label_area to compute the
Hello,
I installed the Freesurfer tool several months ago. Today when I run the
"recon-all" command, it showed the error
"ERROR: Invalid FreeSurfer license key found in license file
/usr/local/freesurfer/.license
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvar
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