Never mind, I believe I fixed the issue. Just missed a step. Thanks!
--Rebecca Sheley
On Wed, Oct 25, 2017 at 12:14 PM, Rebecca Sheley
wrote:
> Hello Freesurfer Team,
>
> I'm having trouble running preproc-sess, but only with the
> mkbrainmask-sess step. I tried just running this step and g
Hello Freesurfer Team,
I'm having trouble running preproc-sess, but only with the mkbrainmask-sess
step. I tried just running this step and got this output. Do you have any
insights on why this might be happening?
My tmp folder is empty.
The cwd directory is the folder where my data are located.
Yes, it does. Prior to v6, the brain mask was created by the FSL BET
program, which did not depend on the registration. V6 now maps the
brainmask from the FS analysis into the subject space, which does depend
on the registration
On 07/11/2017 02:36 PM, Li Guo wrote:
> Dear freesurfer developer
Dear freesurfer developers,
I’d like to ask about an error I encountered in Freesurfer v6.0 with
mkbrainmask-sess. I am using macOS Sierra.
Here is the error:
error:"ERROR: cannot find
/Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you
might need to run register-ses
Run preproc-sess instead. inorm-sess is no longer used
On 03/04/2016 05:18 PM, Ji Won Bang wrote:
> Thanks for your help!
>
> I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0
>
> What I used to run are:
> mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd
> bold_reti
Thanks for your help!
I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0
What I used to run are:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino
inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd
bold_retino
However, since version 5.3.
You specify it when you run mkanalysis-sess
On 03/04/2016 04:36 PM, Ji Won Bang wrote:
> In a simple word, my question is:
>
> under version 5.3.0, how can I specify funcstem (stem of functional
> volume)? I don't see any argument for that..
>
> Thanks a lot.
>
> Best,
> Ji Won
>
> 2016-03-04 16:
The functional stream changed a lot from version 4 to version 5. The
commands and workflow are very different now
On 03/04/2016 04:31 PM, Ji Won Bang wrote:
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive question.
>
> When using version 4.5.0 I used the command:
> mkb
In a simple word, my question is:
under version 5.3.0, how can I specify funcstem (stem of functional
volume)? I don't see any argument for that..
Thanks a lot.
Best,
Ji Won
2016-03-04 16:31 GMT-05:00 Ji Won Bang :
> Dear. Freesurfer experts.
>
> Hi. How are you?
>
> It might be very naive que
Dear. Freesurfer experts.
Hi. How are you?
It might be very naive question.
When using version 4.5.0 I used the command:
mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino
However under the version 5.3.0, mkbrainmask-sess does not have -funcstem.
May I use -maskstem in
I imagine this issue has been solved by now but just for the record I ran into
a similar issue. In my case the problem turned out to be that FSL installs by
default in /usr/local/fsl/bin but FSFAST was looking for it in /bin
This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesu
It could be. It uses fsl only to create a mask of the brain, so it
probably does not need a full fsl install, but it might need more than
you have.
doug
On 3/25/12 7:05 AM, Kiley Seymour wrote:
Hi again,
Could this error be due to the fact that I don't have a full version
of fsl installed and
Hi again,
Could this error be due to the fact that I don't have a full version
of fsl installed and configured on my ubuntu virtual machine? i.e.
does fsfast require fsl to be installed?
Thanks
K
From: Kiley Seymour
To: "freesurfer@nmr.mgh.harvard.edu"
Sen
Dear Freesurfers,
I am currently trying to do some retinotopic mapping. I have been successful in
running the reconstruction commands and setting everything up for the analysis,
but I have run into problems when using the selxavg3-sess command. i.e.
selxavg3-sess -a rtopy.self.lh -s IFEE2211 -n
Hi Doug,
On 26. Jun 2006, at 21:19 Uhr, Doug Greve wrote:
HI Sebastian,
I made a mod to this in development version, but it operates slightly
differently in that you set the "nth" run with -run. Eg, -run 2 would
mean to use the 2nd run. Otherwise, if you run it on more than one
session, th
HI Sebastian,
I made a mod to this in development version, but it operates slightly
differently in that you set the "nth" run with -run. Eg, -run 2 would
mean to use the 2nd run. Otherwise, if you run it on more than one
session, the run that you specify might not exist. Would this work for y
Hi List,
to follow up my mail from several days ago, all mkbrainmask-sess
(v3.0.2 centos4 x86_64) really needs to be able to select the run from
which to take the run-number are the following lines:
case "-run"
set run = $argv[1]; shift;
breaksw
somewhere between the label "pa
Hi All,
just a quick note to let you know that 3.0.2's (centos4 x86_64)
mkbrainmask-sess does not really parse the "-run nth" parameter it
specifies in its help text. Haven't found time to implement a fix yet,
but it is a minor issue anyway...
Ahoi
Sebastian
--
Sebastian Moeller
Tel
Dear all,
When I used mkbrainmask-sess, an error occurred shown
below. I am using the latest FreeSurfer, and the bet command is included in the
distribution. Could anyone tell me how to fix it? thanks,
Jia
++begin of error
message+
mkbrainmas
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