Hi Bruce,
Thank you very much for your quick reply. Sorry I hadn't been able to
reply faster as I was trying to figure out the below mentioned issue from
two days.
I have computed surface area of left-hippocampus using the commands
mri_tessellate and mris_info. However I found that in freevi
Dear developers,
Is it possible to check the presence of Matlab runtime right at the start of
recon-all
in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for
a high-res data processing I got this unexpected error message.
Thanks in advance.
Cheers
Ed
___
What is saved in Matlab cell arrays is simply volumetric SPM data for different
subjects, ROIs, and etc. For example I have "data {subject no.,contrast
no.}{roi, hemisphere}" which is a 2D cell with each cell being a cell too. What
I want is run mri_vol2surf for each of these subjects, each of t
Dear FreeSurfer Experts,
Are these coordinates reported in mri_surfcluster in MNI305 space? (with
—fixmni)
Thanks,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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does that file exist? Did you run recon-all -qcache ?
On 11/11/15 7:54 AM, Heidi Foo wrote:
Apologies, the error message should be /Error in analyze: couldn't
open
/Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file./
On Wed, Nov 11, 2015 at 8:48
mri_vol2surrf operates on volumetric data. If your data is not
volumetric, then you can't use it. If it is volumetric but not stored on
disk in a volume format (eg, nii. mgz), then you cannot use it directly.
If you can write out your data in such a format, then you can use it.
On 11/11/15 6
Hi all,
I know there is good evidence to support analyzing and performing edits on the
same version of freesurfer, and the same operating system. However, our systems
are going to be updating to Scientific Linux 7, from Scientific Linux 6 in the
coming weeks. We are planning to keep a legacy bo
If you use --fixmni, then they are reported in approximate talairach space
On 11/11/15 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Are these coordinates reported in mri_surfcluster in MNI305 space?
(with —fixmni)
Thanks,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail
Probably Ruopeng will have to weigh in on freeview.
On 11/11/15 5:57 AM, anirudh nihalani wrote:
Hi Bruce,
Sorry I forgot to attach the files mentioned in my last email. PFA
the files here. Thank you.
Regards,
Anirudh
On Wed, 11 Nov 2015 at 16:18 anirudh nihalani
mailto:anirudhnihal...@
Hi Ed, generally recon-all does not need matlab. Are you running the
gyrification analysis? That should be the only thing that needs matlab.
doug
On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote:
> Dear developers,
>
> Is it possible to check the presence of Matlab runtime right at the start of
>
Thank you for taking the time and responding. I managed to correct my shell
script, and now it works! I would guess running shell scripts from Matlab is
generally not a good idea.
Best,
Fatemeh
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Hi Anirudh,
Label Stats just shows the area of the label in that slice, not surface area
of the entire label (17, Left Hippocampus in your case). So for your slice in
the screenshot, there were 71 voxels labeled 17, so the area is 71. The
mri_tessellate then mris_info commands give the surfa
Thanks, Doug! Got it. So FreeSurfer registers the individual scans to the
MNI305 atlas but mri_surfcluster reports approx. Talairach coordinates with the
default option: —fixmni
I was a little bit confused because this website
(https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) says t
Hi,
How would I make a one sided t-test to see whether group mean is greater than X
(any other number than 0)?
Thanks,
Dace
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The i
Hi Andrew,
that should be OK, as long as there is a clear line between
image processing/editing
vs
post-processing (glm fit, other type of analysis).
Best, Martin
On 11/11/2015 11:00 AM, Andrew Schoen wrote:
> Hi all,
>
> I know there is good evidence to support analyzing and performing edits o
Just look for positive activation. The p-values were computed assuming
two-sided, so if one-sided is really what you want, divide the p-values
by 2. Note that the correction for multiple comparisons (mri_glmfit-sim)
will do this for you automatically when you specify a signed test
doug
On 11/11
Sorry, I was not very clear.
I meant, how do I test whether the group mean is greater than 5, for
example.
The default is 0, but can I change it somehow?
Dace
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I guess you could subtract 5 from the gamma.mgh, then recompute the t =
gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p
or sig given the dof.
doug
ps. Please remember to include previous correspondences so we know the
context of the question
On 11/11/15 4:10 PM, Dace Ap
Could you also just subtract 5 from all your input data? Then when you test
against zero (and only look at positive p values) you'll really be testing
whether the values are greater than 5?
Kx
On 11 November 2015 at 21:35, Douglas Greve
wrote:
> I guess you could subtract 5 from the gamma.mgh,
That's what I will do. Just wanted to enquire whether there is an
option to specify the value directly for the one-sample ttest.
Thank you!
Dace
> Could you also just subtract 5 from all your input data? Then when you test
> against zero (and only look at positive p values) you'll really be test
Hi FS-ers,
I'm a bit stuck trying to compute cortical and subcortical statistics using
the Buckner 2011 Cerebellum mask. I tried using mri_segstats to generate
the .stats file for the provided image:
mri_segstats --seg
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum
Hi Martin:
But, between version 5.3 and 6.0 there are any differences in the
algorithms for subcortical volume, cortical thickness, etc., or only
additions to that, such as the hippocampus or brainstem subfields ?...
and in general, if I segment for example the same healthy control in
freesurfer
Hi Gonzalo,
yes there are changes to many of the algorithms (sometimes bug fixes or
improvements, sometimes parameter changes etc) which will generate different
results. It can happen in individual cases that subcortical volume or cortical
thickness differs a lot between 5.3 and 6.0, even when
Hi Anirudh
sorry, I'm not sure what/how freeview computes things. Maybe Ruopeng
can answer?
Bruce
On
Wed, 11 Nov 2015, anirudh nihalani wrote:
Hi Bruce,
Thank you very much for your quick reply. Sorry I hadn't been able to reply
faster as I was trying to
figure out the below mentio
Hi all,
Is there a tool to surface-dilate all the labels contained within an annotation
file simultaneously, while preserving the non-overlapping nature of the labels?
I saw there is a development version of mri_label2label that works for
individual label files separately, but that gets me into
Hi Doug,
I used mostly the default options, nothing special:
recon-all -autorecon1 -clean-tal -expert my_options.txt -hires
where the file my_options.txt contains some options for nu_correct.
Then I entered
recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires
The error occurred w
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