Thank you Doug, I think that my question was not precise enough. I would
like to know which function I can use to obtain a vector with the number of
vertices and the corresponding MNI coordinates.
Regards,
Yolanda
2012/6/19 Douglas N Greve gr...@nmr.mgh.harvard.edu
For fsaverage, the
hello!
i have saved a couple of .label files and am trying to convert them to a
.annot file with:
mris_label2annot --h lh --s MMRR-21-1
--l lh.superiorfrontal.label
--l lh.superiorparietal.label
--ctab FreeSurferColorLUT.txt --a output
the stdout is:
ColorTable atlas_colortable.txt
AnnotName
We run things on an Xgrid cluster that is now a mixture of Macs running Snow
Leopard (10.6.8) and Lion (10.7.x). We found the results given from
asegstats2table and aparcstats2table are identical after running 100 subjects
on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also ran a
Dear Freesurfer experts,
I have a fairly simple question, but it is not immediately clear to me how to
solve it.
I have a statistical parameter map representing the results of a group-level
analysis. After thresholding the map (p.05), several significant clusters
remain, and I want to
Hi Peter
thanks for the info. Feel free to post this on one of the *many* blogs
howling for our blood :) I think that the effects in the paper reflect
default floating point settings in gcc on 32-bit vs. 64-bit, although we
haven't really investigated as it doesn't seem like a wise use of
p.s. I should add that we've known about this effect for a while (as the
authors in the paper state), but haven't had the time to track it down.
Since it's an avoidable source of variance (by controlling what computers
you run the analysis on), it's lower on our list of priorities than other
I'm curious: For comparison to the results in that paper, has anyone
quantified the variability that results when one runs the same FS
version repeatedly on the same subject, but with a different random seed
each time? That is, how much of the difference is related to math
libraries vs.
Nick might have, not sure. Are you volunteering Mike :)
On Wed, 20 Jun 2012, Michael Harms wrote:
I'm curious: For comparison to the results in that paper, has anyone
quantified the variability that results when one runs the same FS
version repeatedly on the same subject, but with a
Please post it on PLoS One homepage. According to the policies of this
journal, you are allowed to respond to each paper directly on the same page
as the article. You don't need to submit it as a paper and won't go through
a review process.
On Wed, Jun 20, 2012 at 10:28 AM, Peter J. Molfese
Hi,
I run -corr and -intra with no errors. -inter finishes without errors if
does not use doregcvs.
When I want to use cvs for registration, I get error:
iterating
done with candidates
Active BCs = 91494
Total BCs = 548640
no-eqs = 245610
surf2vol(26656) malloc: *** mmap(size=295714816)
Hi Maria - Do you at any point get the following warning?
WARN: CVS template is not unavailable in the current version
Thanks,
a.y
On Wed, 20 Jun 2012, Maria Gemzicka wrote:
Hi,
I run -corr and -intra with no errors. -inter finishes without errors if
does not use doregcvs.
When I
Dear all,
For a number of my participants, Freesurfer's automated segmentation of
the putamen appears to include brain matter that isn't putamen - this
problem persists across 5-6 slices, on average.
I was wondering what people would recommend - should I edit the aseg?
Thank you in advance
Oops, that's a typo, meant is unavailable. In any case something like
this should show up early in the logs.
On Wed, 20 Jun 2012, Bruce Fischl wrote:
not unavailable
On Wed, 20 Jun 2012, Anastasia Yendiki wrote:
Hi Maria - Do you at any point get the following warning?
WARN: CVS
Hi Kristin
yes, if you care about putamen volume I guess you should. you can optimize
the acquisition for this, or acquire multispectral (e.g. PD-weighted) data
to help segment pallidum/putamen
cheers
Bruce
On Wed, 20 Jun
2012, Kristin Javaras wrote:
Dear all,
For a number of my
Arno, you need to create a custom color table (--ctab).
doug
On 06/20/2012 12:05 AM, Arno Klein wrote:
hello!
i have saved a couple of .label files and am trying to convert them to
a .annot file with:
mris_label2annot --h lh --s MMRR-21-1
--l lh.superiorfrontal.label
--l
Hi Jenny, Martin will be the best person to answer your question.
Unfortunately, he is in China now. I think he's back next week.
doug
On 06/20/2012 01:37 AM, Jenny Liu wrote:
Hello,
I am attempting to use the Qdec Analysis for longitudinal data.
Specifically, each subject has two
Hi Yolanda, you can run
mris_convert lh.white lh.white.asc
to produce a text file of the vertices and their coordinates. We also
have a matlab function to read in surfaces.
doug
On 06/20/2012 02:44 AM, Yolanda Vives wrote:
Thank you Doug, I think that my question was not precise enough. I
Use mri_surfcluster (or mri_volcluster if a volume).
doug
On 06/20/2012 10:41 AM, John Richey wrote:
Dear Freesurfer experts,
I have a fairly simple question, but it is not immediately clear to me
how to solve it.
I have a statistical parameter map representing the results of a
Peter,
Thanks for this info. The Mac OS versions compared in the paper were 10.5
and 10.6 (Leopard and Snow Leopard). One of the major changes between
these two versions was the switch from a 32b kernel to a 64b kernel
(whereas Snow Leopard and Lion both use a 64b kernel). I havent been able
Freesurfers-
For pre-smoothing subject surfaces for qdec using:
recon-all -s subjid -qcache
Is it necessary to have all the variations of smoothing done (ie - fwhm
0,5,10,15,20,25) or is it possible to run with only a subsection of these?
Best-
Michael
--
Michael D. Kruepke
PhD - University
Mike,
I have run such tests in the past (which showed about 2-3% variability in
hippo volume due to randomness) and Doug has done similar tests, but
admittedly running a large scale analysis and showing the results on a
wiki page would be useful. Something like running our Buckner40 and/or
Hi Bruce et al,
I may be late to the discussion, but wanted to share some insights given
that we've had some headaches trying to get identical results
on presumptively identical systems for FreeSurfer and other tools, I wanted
to add my two cents. Ultimately, of course, the systems were not 100%
Does anyone have a mapping of the Allen Brain Institute labels to the
freesurfer parcellations? Just the labels would be sufficient for these
purposes.
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of
Perfect that should make things a bit easier on me, also according to this
post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
it is not possible to run multiple subjects with this set up (recon-all -s
(subjectid) -qcache -fwhm 10, however this was from 2009, so not
HI
I believe that recon-all -s subjid -qcache
will pre-cache smoothing from 0 through 25 fwhm. You can howevere select
a small subjection of this by issuing recon-all
-s subjid -qcache -fwhm desired smoothing.
-measure surfmeas can follow -qcache, where surfmeas is one of:
thickness,
curv,
nope, can't run multiple subjects
On 06/20/2012 01:43 PM, mdkrue...@uwalumni.com wrote:
Perfect that should make things a bit easier on me, also according to
this post
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12406.html
it is not possible to run multiple subjects with
for multiple subjects to run for -qcache, i wud suggest use this
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two
substitute -all with -qcache..you can also pick specific measure and
fwhm if you dont want all others to be ran.
hope this helps
kk
- Original
bottom line is can we trust freesurfer cortical thickness results
and a recent paper my group published seems to give very strong
positive answer to the question.
paper - cortical thinning in psychopathy, it's on the wiki publication list.
All of the areas reported
overlap with the areas that
Kushal -
This helps immensely! Just have to get this working now
So my understanding is that after setting my subject dir in terminal, and
creating a txt file with the list of my subject id numbers (list.txt) i
would type into terminal
foreach list.txt `cat list.txt` echo $list.txt recon-all -s
Are you using tcsh/csh as your shell? Also you type the foreach line and
hit return. It will prompt you for commands, a separate one on each
line, when you're done with the commands, type end and hit return
foreach list.txt `cat list.txt`
echo $list.txt
recon-all -s $list.txt -qcache
1- if u want fwhm=10mm just across thickness, include the flag -measure
thickness, this saves lot of time, unless you prefer to do across all measures
2- this is how i made command line for my multiple subject -qcache
for i in `cat list.txt`; do echo $i; recon-all -s $i -qcache -measure
Dear FreeSurfer,
I am emailing you to ask for your help with the qdec_glmfit command (I
got the command from the following link:
http://www.freesurfer.net/fswiki/qdec_glmfit).
My issue is that I do not know how to turn my raw data into the .dat
file required by the command (you used
Hi Nicolai, have you looked at the qdec tutorial on our wiki page? It has an
example on how to create the table
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
doug
On 06/20/2012 03:49 PM, Nicolai Grüner-Hegge wrote:
Dear FreeSurfer,
I am emailing you to ask for your
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