Hi,
thank you very much for providing the lectures of the last Freesurfer course as
videos! I am just watching them, and it seem that the .ppt file provided for
the troubleshooting lecture does not match the slides used in the video.
It would be great if you could provide the slides used in the
Hi Janosch,
The link on the course schedule page should point to the correct version
now.
http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.failure_modes.ppt
-Louis
On Wed, 27 Nov 2013, Janosch Linkersdörfer wrote:
Hi,
thank you very much for providing the lectures of the last
Hi Doug,
I sidestepped the registration issue because I am performing the analysis on 5
ROIs per subject (5x1x1 volumes), which are aligned by design. I'm doing this
using the lab's semi-manual NHP processing stream, so usual assumptions you
have about which FS-fast steps have been performed m
Hmm, it looks like my formatting didn't survive the internet (at least in my
e-mail program). . I'm going to try it one more time (I'm going to include the
complete original message).
Hi Doug,
I sidestepped the registration issue because I am performing the analysis on 5
ROIs per subject (5x1x
Dear freesurfer experts,
when running the createMorph function an error of shared libraries occur.
createMorph: error while loading shared libraries:
libboost_program_options.so.5: cannot open shared object file: No such file
or directory
I searched for such shared library and although I have a
Hi Andre,
I posted the below on Monday on the list:
The boost library is installed by default on CentOS platforms. If a user
gets the libboost error then they are using a different platform which
doesn't have boost installed by default. On RedHat systems libboost can be
installed by typing t
Hi,
I previously installed set-up and have successfully used freesurfer to run
recon-all and visualize my results in tkmedit and tksurfer. However when I
went to analyze my data and also view it in freeview I have run into a
problem with what my home directory is considered for these applications
Hi Laura
freeview by default doesn't use any of the environment variables. You
need to give it the full path to the data you are trying to visualize. It
included your home dir in the path probably because that was your pwd.
cheers
Bruce
On
Wed, 27 Nov 2013, Laura Taylor wrote:
Hi,
I prev
Freesurfer experts,
I am interested in converting functional ROIs defined by the Greicius lab (
http://findlab.stanford.edu/functional_ROIs.html) into individual subject
space. Originally I had converted the fROIs from an FSL-based MNI152 to
Freesurfer-based MNI305 space. To do this I used this co
Hi all,
I'm running a retinotopy analysis. I was wondering if there was a way for
me to ignore the last x seconds/TRs of a given run. I want to ignore this
bit of time because each run started and ended with a 'blank screen'
period.
I appreciate any tips you guys might give me.
Cesar
Hi all,
I'm running a retinotopy analysis and I was wondering if there was a way
for me to ignore the last x seconds/TRs of a given run. I want to ignore
this bit of time because each run started and ended with a 'blank screen'
period.
I appreciate any tips you guys might give me.
Cesar
_
Dear FS experts,I am forwarding a message I sent yesterday that my got lost in
the long list of email. My question is as follow:
As far as I understood the FS version for Mac snow Leopard is not compatible
with FS version 5.3 CentOS 6 (see response I got below). Is this correct or I
could combin
Hi Lilla,
Thank you for your reply. I have boost installed, yet it is not the version
required (v. 1.49). Although, even after installing an older version such
as the 1.41 it is not straightforward to use this libboost with freesurfer.
The doc from libboost is not easy to understand and even if do
Hi Cesar, you can use a time point exclude file. Run mkanalysis-sess
with -help to get more info. Make sure to put the time in seconds in the
file where t=0 is the first time point.
doug
On 11/27/2013 03:29 PM, Cesar Echavarria wrote:
> Hi all,
>
> I'm running a retinotopy analysis and I was wo
Does it happen on every subject? Any chance that the disk is full?
On 11/27/2013 07:43 AM, Johnson, Eileanoir wrote:
>
> Hi there,
>
> I am currently trying to run freesurfer version 5.3.0 on a cluster and
> am encountering an error when running recon-all.
>
> The error is:
>
> Writing to ./tmp.
Are these this right one?
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/freesurfer.failure_modes.ppt
On 11/27/2013 03:55 AM, Janosch Linkersdörfer wrote:
> Hi,
>
> thank you very much for providing the lectures of the last Freesurfer course
> as videos! I am just watching them, a
Not sure if it's relevant, but the syntax for mris_calc in this case is:
mris_calc -o mul
Your log is missing so the syntax doesn't make sense and
mris_calc will fail...
On 11/27/13, 18:10 , Douglas N Greve wrote:
>
> Does it happen on every subject? Any chance that the disk is full?
>
> On
yHi Pablo,
yes, we don't recommend mixing version. We try as hard as we can to make
sure that you get the same answers from different versions, but it's
pretty hard and not always in our control (e.g. when 3rd part libraries
we use give different answers, which is what causes the discrepencies
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