Hello,
I tried to get freesurfer's source code after registering and receiving
the password for the read-only-cvs. The login command from
https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS is simply failing
with a timeout like this:
# cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fsc
Hi Christine
this looks to me like a consequence of the high myelin content of motor
cortex.If there really is as little contrast there as seems from your
image there is not much you can do except change the acquisition. If you
give us the details we can help with this.
cheers
Bruce
On Thu,
Hi Hugh
if you mean a single subject map, just bring up tksurfer and load the
thickness as an overlay
cheers
Bruce
On Fri, 24 Jan 2014, Hugh Pemberton wrote:
Hi freesurfer crew,
I found some details through thiswebsite
http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/su
rfs
have you tried mri_surf2vol?
On Fri, 24 Jan 2014, Chris Adamson wrote:
Is there a way of making a volume like aparc+aseg with the defect labels so
that cortical region where the defects are show up red?
Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research
I
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access
to Freesurfer. I already added the "recommended lines" from the homepage to
matlab startup-file, but it is still not working. Im trying to estimate the
local gyrification index. However when I type "reco
Dear Freesurfer experts,
I ran some surface-based group analysis using Qdec. I would like to
re-open those analysis and threshold them using FDR, for example. I read
through the Qdec tutorial and it points out how to do so for new
analysis, however there is no mention on how to open previously
We'd like to map the cortical GM ribbon on our original single volume native
space anatomical T1.
The dataset has been run through recon-all -all.
The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the
cortical GM mask
in freesurfer space, correct?
I converted the ribbon.mg
Hi,
I see that the links off of
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
now provide instructions for editing via Freeview rather than Tkmedit.
I found the older instructions for editing via Tkmedit still available by appending "_tktools" rather than "_freevi
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've installed
the latest version of XQuartz (http://xquartz.macosforge.org/landing/)?
If not, please do that first.
If you installed XQuartz, than can you please type the following on the
command line and provide me with t
yes
doug
On 1/23/14 4:21 PM, Alexopoulos, Dimitrios wrote:
Hi,
We'd like to map the cortical GM ribbon on our original single volume
native space anatomical T1.
The dataset has been run through recon-all -all.
The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz'
is the cor
Have you tried running the defect-seg script? It creates annotations of
the defects. Look at the --help
doug
On 1/24/14 1:03 AM, Chris Adamson wrote:
Is there a way of making a volume like aparc+aseg with the defect
labels so that cortical region where the defects are show up red?
*Dr **C
Michael,
Thanks for pointing out the broken links and your suggestion regarding
the links for editing instructions. We will fix the broken links and
revisit the organization of editing instructions for freeview vs tktools.
It is ok to continue making edits via tkmedit. But just be aware, as you
Thanks for pointing this out. I was able to replicate and it should now
be resolved. I have been able to download the data. Please try again and
let me know if you still have a problem.
-Zeke
On 01/24/2014 03:53 AM, Thomas Frank wrote:
> Hello,
>
> I tried to get freesurfer's source code after
Dear Freesurfers,
I am slightly confused about the monte carlo simulation.
First off, I only find a blob when I run the p<0.05 threshold level and don't
see anything else when I run simulations with p less than that. What does this
mean?
Additionally, when I click on any question of interest
what do you want to do? I think surfstat is for cross subject
statistical analysis
doug
On 01/23/2014 11:19 PM, Hugh Pemberton wrote:
> Hi freesurfer crew,
> I found some details through this website
> http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm
> about
Hi FSL Experts,
I am currently processing a large dataset and would like to seek some
advice regarding parallel processing.
These are the specifications of my iMac:
3.2GHz , Intel Core i5, No. of processor: 1, Total number of cores: 4, L2
Cache per core: 256kb, L3 Cache: 6MB, Memory: 8GB.
Would
Dear Elijah,
If I'm right, there are two options to accelerate FS execution:
1) The first option is using the FS openmp implementation
http://surfer.nmr.mgh.harvard.edu/fswiki/OpenMP. I haven't tested this way
but openmp allows to open multiple processing threads, and it is supported
for the most
Hi list,
SLFP is SLF III?
Is there a way to obtain by TRACULA also SLF I and II, knowing the the cortical
targets of the tracts?
Thanks,
Stefano ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/list
Hallo Zeke,
I did it as you told me and typed "otool -L /opt/X11/lib/libX11.dylib" in the
command line, and got the following output:
Usage: /Library/Developer/CommandLineTools/usr/bin/otool [-arch arch_type]
[-fahlLDtdorSTMRIHGvVcXmqQj] [-mcpu=arg] ... -f print the fat
headers-a prin
Hello Dusan,
Are you sure you typed the entire command? Because your system is
supposed ouput information about that particular file. Instead you got
the help information, which is output when you only type "otool" instead
of ""otool -L /opt/X11/lib/libX11.dylib"
Also, did you install XQuartz?
Hi Bruce,
I used that command and I got the same errors when I ran -qcache again. I
also found that my colleague, who did the edits, used the same command
after she manually edited the recons.
I re-ran the subject with the following command recon-all -autorecon2-cp
-autorecon3 -subjid and, when i
Hi Zeke,
sorry, I did it again and got the following output:
/opt/x11/lib/libx11.dylib: /usr/X11/lib/libX11.6.dylib (compatibility
version 9.0.0, current version 9.0.0)/usr/X11/lib/libXau.6.dylib
(compatibility version 7.0.0, current version 7.0.0)
/usr/X11/lib/libXdmcp.6.dyl
Hi Zeke,
I have one more question: It seems that I did not copied the the "recommended
lines" from thehomepage to matlab startup-file correct. when I type "recon-all
-lgi -s G01" Im getting the following message:
ERROR: Matlab is required to run mris_compute_lgi!
When Im trying to run Qdec, the
Dear Freesurferexperts,
I still have the Problem because I can not run the the mris-command to estimate
the gyrification-index, because Freesurfer is not recognizing Matlab: "ERROR:
Matlab is required to run mris_compute_lgi"Im not sure why this is happening?
Does someone have an idea???
Im star
it's possible that the timestamps on your system are wrong I guess. Did
-make all run anything?
On Fri, 24 Jan 2014, Mihaela Stefan wrote:
Hi Bruce,
I used that command and I got the same errors when I ran -qcache again. I
also found that my colleague, who did the edits, used the same command
Yes, -make all ran for about 7 hours and it exited without errors. How
should I fix this?
What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid
? Can I use that if it exited without errors? Can I assume that
the subject has all the correct files and continue my analysis?
Thanks!
yes, although why -make all didn't fix things is a mystery to me.
On Fri,
24 Jan 2014, Mihaela Stefan wrote:
Yes, -make all ran for about 7 hours and it exited without errors. How
should I fix this?
What about -qcache after recon-all -autorecon2-cp -autorecon3 -subjid
? Can I use that if it
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