thanks Akio
hopefully you will contribute the code back if/when you get it working?
Bruce
On
Wed, 4 Jul 2012, Akio Yamamoto wrote:
> Hi Bruce and Richard,
>
> Yes, as Richard pointed out, I just wanted to know the numbers for input
> to Amdahl's law, if you have already something, to figure out
Hi Bruce and Richard,
Yes, as Richard pointed out, I just wanted to know the numbers for input
to Amdahl's law, if you have already something, to figure out the maximum
expected speedup using multiple processors/cores.
As for improvements of em_reg, I'll try to split each transform as well as
par
On Tue, Jul 3, 2012 at 3:48 PM, Bruce Fischl wrote:
> I think that the theoretical ratio is much bigger than what you would be
> able to achieve in practice. It's hard to compute exactly, but for example
> for em_reg it should be the number of samples (which are processed
> independently), so som
Hello,
I know that we can resume a recon-all command, if it's a cross-sectionnally
process.
In this case the command is:
recon-all -make all -s subject
But I had a power failure during a longitudinal study, when I try to execute :
recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'O
Hi Jay, it is an extension of the one group two covariate
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V (which I just created
just for you:).
doug
On 07/01/2012 08:27 PM, Jay Morozov wrote:
>
>
> Dear Freesurfer experts,
> We are trying to run a statistical analysis for FA in 5 ROIs.
> W
Hi Akio
I think that the theoretical ratio is much bigger than what you would be
able to achieve in practice. It's hard to compute exactly, but for example
for em_reg it should be the number of samples (which are processed
independently), so something on the order of 1000. For ca_reg it should
Those are things that are in your ct.anat.mgz file. It's not a
FreeSurfer problem.
doug
On 07/02/2012 01:23 PM, Borzello, Mia wrote:
> another question, i trying to pick points (electrode contacts) now, so at the
> command line i have:
> tkmedit BWXX_SurferOutput norm.mgz lh.pial -aux ct.anat.mg
On 07/02/2012 12:01 PM, Luis R. Piloto wrote:
> Hi Doug,
>
> Thanks for getting back to me. I'm right around the vicinity of my desired
> results, but had just three more questions.
>
> 1) When running the mri_vol2surf command and specifying --reg, is there any
> way I can pass in a registrati
I'm guessing that the registration failed (spmregister). If you want the
identity, then you can just run tkregister2 with --regheader --reg
reg.dat (It will create reg.dat when you hit the "save" button). But it
will be unlikely that they will actually be in registration.
doug
On 07/02/2012 12:
Hi Nicolai, your first column and second column are redundant. You
cannot have both.
doug
ps. Please remember to send these things to the freesurfer list instead
of directly to me. thanks!
On 07/03/2012 02:55 PM, Nicolai Grüner-Hegge wrote:
> Hi Doug,
>
> I have been trying to run qdec but have
Hi again,
I was able to get help off of the listserv with the answer.
If anyone else is interested, the easiest way seems to be to load the
orig volume in tkmedit, punch in the talairach coordinates, and go to
"tools => save point." From there, open the surface in tksurfer, then
"Tools==> Got
It is ok to do the group analysis using a different version. You should
not mix individual subject data run with different versions.
doug
On 07/03/2012 10:32 AM, L. Koenders wrote:
> Dear Freesurfer people,
>
> We attended the Freesurfer course in Amsterdam last week, thank you so much
> for the
There is only one file in the series. Is that right? It's trying to
compute the slice direction cosine, which it cannot do from one file.
On 07/03/2012 12:36 PM, Chen, Xiaoyan wrote:
> Hi,
> I have the data from one of our collaborators. They are dicom files,
> and they are collected fr
Hi Martin,
lot's of small changes can make a big change but from your phrasing i
assume this isn't the case. what has changed? i would like to have the new
(long_mris_slope) script.
thanks,
-joost
On Tue, Jul 3, 2012 at 6:30 PM, Martin Reuter
wrote:
> Hi Yolanda,
>
> take a look at the longitu
Hi,
I have the data from one of our collaborators. They are dicom files,
and they are collected from GE. I try to use mri_convert to convert the files
from dicom to nifti. However, the following error shows up.
mri_convert 1.2.840.113619.2.135.2025.3762570.5144.1309404440.95.dcm
1.2.8
Hi Yolanda,
take a look at the longitudinal tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
There is a section that hints at the post-processing as far as we have
implemented it. Based on a longitudinal qdec table you can run
long_mris_slopes to create rate or
Hi Brianna
If the white surface is correct and you can't get watershed/graph cuts to
do any better, it may be that erasing voxels from the brainmask or
brain.finalsurfs is your only option. If you had multi-echo MPRAGE you
might be able to get rid of it also.
sorry,
Bruce
On Tue, 3 Jul 2012,
Freesurfers-
When running analysis in qdec is it possible to use each individual
subjects brain volume (white matter + gray matter) as a covariate? If so,
what would be the easiest way to go about getting this information.
Best-
Michael
--
Michael D. Kruepke
PhD - University of Illinois at Urba
Dear Freesurfer people,
We attended the Freesurfer course in Amsterdam last week, thank you so much for
the information! During the course it was mentioned that it is a very bad idea
to mix Freesurfer versions during the analysis. However, we did all the
preprocessing on an external server, usi
Hi Martin,
I would like to compare also a Control vs. an Experimental group
(pre-post), but instead of using ROIs, I am interested in a whole-brain
paired t-test analysis between the two groups. Which data should I take?
Would it be possible to process ?.long.base with qcache and take the
"rh.thic
Anne,
It looks like the diagnosis.levels file has 'MApsychosis' as a level but
the error message says 'Psychosis', so they would need to match.
Nick
On Tue, 2012-07-03 at 15:51 +0200, Anne Uhlmann wrote:
> Hello FreeSurfers,
>
> I have a similar problem as described in an old thread
> (http:/
Hello FreeSurfers,
I have a similar problem as described in an old thread
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12357.html)
- qdec doesn't read my factor.levels properly.
I have checked the files with gedit and can't see any control
characters, which might have caused the
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