Dear List Members,
I converted my data from .dcm to .nii and than from .nii to .mgz volume, after
that I have run the following command to calculate the cortical thickness;
recon-all -s sub01 -all
but I have not get ".thickness.fwhm15.fsaverage.mgh" files in the surf folder
after recon-all
Dear experts!
I have a question.
I have run recon-all on a cluster , and I am editing on my local machine. I
just checked the versions and I see that I have:
freesurfer-x86_64-redhat-linux-gnu-stable5-20110522 at the computing
cluster and
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on my
Dear FreeSurfers,
I’m comparing two groups (patients (N=45) and controls (N=93)) on
cortical thickness using 34 parcelated areas in each hemisphere (i.e.
68 areas in total). When correcting for multiple comparisons using
Bonferroni, only one area remains significant. Bonferroni is quite
conservati
Dear FS experts
When extracting cluster information using mri_surfcluster, there is a
problem with the --fixmni option. By default, FixMNI is 1 but it reports
Talairach coordinates as confirmed by tksurfer. When using the option
--nofixmni (FixMNI is zero) it reports MNI Talairach coordinates.
Th
because every time I try to run
recon-all -autorecon-pial -s 101
it seems to hang up here and nothing more happens :
#@# Sphere lh Wed Aug 14 14:42:06 CEST 2013
/media/Secure_HDD/patients/101/scripts
mris_sphere -seed 1234 ../surf/lh.infl
you need to run specify -qcache on the recon-all command line. You should
be able to just run it now that -all has finished and it will be pretty
fast.
cheers
Bruce
On Wed, 14 Aug 2013, Muhammad Naveed Iqbal Qureshi wrote:
Dear List Members,
I converted my data from .dcm to .nii and tha
hi'm trying to download the trac-all file from the site in the tracula
release notes, it is the download from 2012/1/09 recommended for all, but
hen i click it open a page and gives me an error
should i do something different than just click?
thanks
___
F
how long do you wait? In general it's a bad idea to mix version
Bruce
On Wed, 14 Aug 2013, Cristian Paz wrote:
because every time I try to run
recon-all -autorecon-pial -s 101
it seems to hang up here and nothing more happens :
#@# Sphe
Hi Eli
I don't think that's an error, just an arcane warning that some open
source numerical minimization code complains about sometimes. Looking at
the log it seems like it completed ok, although this is the version of 5.3
without the segstats/ribbon patch, which you will probably want to dow
Thanks for the quick response Bruce. Is that missing patch the reason that
it did not create a wmparc.mgz file in any of our cases?
On Wed, Aug 14, 2013 at 10:47 AM, Bruce Fischl
wrote:
> Hi Eli
>
> I don't think that's an error, just an arcane warning that some open
> source numerical minimizat
Hi Alan - I'm not sure where the output from the one subject ends the the
other starts. For future reference, it's best to attach the entire
trac-all.log files instead of copying and pasting parts of them into your
message.
I see two error messages here:
1. "ERROR: must specify as many DW
Hi Ana - If you notice the release notes, this was relevant to an old
version of tracula. You should now be using the latest version of tracula
that's included in freesurfer 5.3, in which case you don't need any extra
downloads.
a.y
On Wed, 14 Aug 2013, ana ;osp wrote:
> hi'm trying to downl
yes, probably
On Wed, 14 Aug 2013, Eli Fredman wrote:
Thanks for the quick response Bruce. Is that missing patch the reason that
it did not create a wmparc.mgz file in any of our cases?
On Wed, Aug 14, 2013 at 10:47 AM, Bruce Fischl
wrote:
Hi Eli
I don't think that's an error, ju
Hi Corinna
how does the rest of the aseg.mgz look? Is it accurate?
Bruce
On Wed, 14 Aug 2013,
Corinna Bauer wrote:
> Hello all,
> I am examining diffusion tracking in the corpus callosum of individuals with
> periventricular leukomalacia (PVL). The corpus callosum is particularly
> small and the
Dear Support,
I am trying to use fcseed-sess to create a ventricle and CSF regressor for
my resting state analysis. I have encountered an error running
fcseed-sess.
fcseed-config -vcsf -fsd Bold1 -mean -cfg vcsf_bold1_config -overwrite
works, but then the following command fails:
fcseed-sess -s
Hi Anastasia:
I fixed that problem - thank you. However, I have another question. i am
trying extract trac data but when I set environment, I get an error message:
csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: setenv SUBJECTS_DIR $FreeSurfe
Dear Freesurfer experts,
I am needing to manually re-set T1.mgz intensity ranges in recon-all,
because, currently, only voxels under 80 are getting segmented as gray
matter, which is generally outside of the brain. Additionally, all voxels
with an intensity of 80 or more are segmented as wm. I hav
Where did you get this command line? You should set the SUBJECTS_DIR to
the location on disk where your freesurfer recons are.
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia:
I fixed that problem - thank you. However, I have another question. i am trying
extract trac data but when
You can use FDR correction.
On 08/14/2013 08:16 AM, Anita van Loenhoud wrote:
Dear FreeSurfers,
I’m comparing two groups (patients (N=45) and controls (N=93)) on
cortical thickness using 34 parcelated areas in each hemisphere (i.e.
68 areas in total). When correcting for multiple comparisons us
Hi Anastasia/ FreeSurfers
I did not use the conventional path usr/local/freesurfer. since there is
very little disc space in this location. Alternately I set the environment
at a location where is plenty of disc space and then sourced it.
For the SUBJECTS_DIR I set the environment *without using
Dear list,
To obtain the thickness, surface area and volume values for each
hemisphere I ran the command line in the subjdir:
mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats subjid lh white
And did that with the pial surface too. However, the values I get from
the generated cort
Alan - Where is the location that has plenty of space? You should set your
SUBJECTS_DIR to that location, e.g.,
setenv SUBJECTS_DIR
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia/ FreeSurfers
I did no
I have a bash script which calls a .tcl script through which I'm running
tksurfer. It works, except the script is no longer exiting when it reaches
the end. Instead, it displays the tksurfer window and stays open. After I
click the menu option to Quit, the script continues.
Below is the script
op
Why do you want to use a '$'?
On Wed, 14 Aug 2013, Alan Francis wrote:
Hi Anastasia:
Yes the path that you pointed out is the one I presently use. Is there no way
to use the '$' as a substitute?
thanks,
Alan
On Wed, Aug 14, 2013 at 1:46 PM, Anastasia Yendiki
wrote:
Alan - Where
can you send us the screen output? Try using just exit (instead of exit(0))
On Wed, 14 Aug 2013, Greg Book wrote:
> I have a bash script which calls a .tcl script through which I'm running
> tksurfer. It works, except the script is no longer exiting when it reaches the
> end. Instead, it displays
Hi list,
we have a cluster that survived the Monte Carlo simulation for thickness,
and we would like to obtain more data from that exact cluster (volume for
example), is it possible to automatically create a label from that cluster?
If I use mri_binarize or mri_cor2label is not working (I understa
Changing it to just exit instead of exit(0) didn't change anything. I
actually changed it from exit to exit(0) to test it, but that didn't seem
to matter.
Do you want to see a screenshot of tksurfer or output from the shell script?
On Wed, Aug 14, 2013 at 2:24 PM, Bruce Fischl wrote:
> can you
Dear Freesurfers,
Has anyone recently downloaded freesurfer for Mac OS X 10.6? I tried
downloading on two computers, and they gave errors of "no mountable file
systems" and "not recognized" respectively. If someone has happened to
download the same version, would you please let me know whether you
I just completed a successful download of the SnowLeopard version of
freesurfer (freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg).
Are you on a work or guest wifi network? Almost always when people write
to the list saying that downloading freesurfer isnt working for them,
the problem
Dear Zeke,
Actually they have been wired internet connection in both cases. Does this
make a difference?
Thank you very much!
Sincerely,
Ye
On Wed, Aug 14, 2013 at 4:00 PM, Z K wrote:
> I just completed a successful download of the SnowLeopard version of
> freesurfer (freesurfer-Darwin-**sno
If you already have the 5.1 version and have used it on some subjects, you
can of course use the same version on the other subjects. But if you're
going to download something new, that should be the 5.3 version, not an
intermediate update to 5.1. It's highly recommended to use the 5.3 version
Dear Zeke,
Thank you very much!
Now I have downloaded the software.
Sincerely,
Ye
On Wed, Aug 14, 2013 at 4:12 PM, Z K wrote:
> If its a work network there could by any number of possible restrictions
> on the network. Try from a home computer, or any other network, other
> than the one th
Dear Freesurfers,
Tkmedit and tksurfer both return "Bus error" for me. I can even have a
glimpse of the surfaces before tksurfer collapses on me. I checked the
archive
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19422.html
I don't think disc space is an issue for me since the f
Ye,
Please see the following page which may help diagnose your issue:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
Also, please remember to install XQuartz:
http://xquartz.macosforge.org/landing/
-Zeke
On Aug 14, 2013, at 6:50 PM, ye tian wrote:
> Dear Freesurfe
Hi Alan - This appears to be the same error message as the one for subject
118 that you sent yesterday. So I'd try here whatever you did to fix that
one.
a.y
On Wed, 14 Aug 2013, Alan Francis wrote:
> Hi Anastasia:
>
> Sorry to bother you again. Another of my brains gave an error message. I
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