The unsegmented is all the WM that is further than 5mm from cortex. You
can change the threshold so that it labels all of WM regardless of the
distance. Other than that, I don't have much to suggest.
doug
On 11/18/14 6:13 PM, Michele Cavallari wrote:
Hi, I am planning to perform some regional
I'm not sure what you mean by that, but I'm pretty sure the answer is no :-)
doug
On 11/17/14 3:01 PM, ye tian wrote:
Hello Doug and Bruce,
Thank you!
Another quick question, is there an option to select bandwidth using
cross-validation?
Sincerely,
Ye
On Mon, Nov 17, 2014 at 9:40 AM, Dou
Hi there,
Just trying out the QAtools and I notice that there are a number of
"(standard_in) 1: syntax error" reports for each subcortical label:
checking subcortical label: Endosteum, . +/- .
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in) 1: syntax error
(standard_in)
Hi, I am planning to perform some regional analysis of the frontal white
matter as a whole, and asking here for suggestions/help.
>From the FS output wmparc.mgz I could select and merge the following labels
to define my ROI
parsorbitalis [4019, 3019]
parstriangularis [4020, 3020]
lateralorbitofron
That's super!
Thanks again Martin
Best regards
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter
[mreu...@nmr.mgh.harvard.edu]
Sent: 18 November 2014 18:07
To: Freesurfer support list
Subject:
Ok, I go through that.
Thanks,
Gunjan
On Nov 19, 2014 12:37 AM, "Bruce Fischl" wrote:
> Hi Gunjan,
>
> it's all on the wiki. You should go through our tutorials
>
> cheers
> Bruce
> On Wed, 19 Nov 2014, Gunjan Gautam wrote:
>
>
>> Thank you
>>
>> I will be thankful if you could let me know about
Hi Gunjan,
it's all on the wiki. You should go through our tutorials
cheers
Bruce
On Wed, 19 Nov
2014, Gunjan Gautam wrote:
Thank you
I will be thankful if you could let me know about the link related to
recon-all, in order to know about the parameters(input volume info etc)
associated to
Thank you
I will be thankful if you could let me know about the link related to
recon-all, in order to know about the parameters(input volume info etc)
associated to it and other usage.
On Nov 19, 2014 12:18 AM, "Bruce Fischl" wrote:
> Hi Gunjan
>
> just run recon-all and it will do everything
Hi Gunjan
just run recon-all and it will do everything that we know how to do
(including those steps)
cheers
Bruce
On Wed, 19 Nov 2014, Gunjan Gautam wrote:
Ok, I try this tomorrow morning.
I will be thankful if you could tell me about getting brain mask and
performing skull stripping oth
Ok, I try this tomorrow morning.
I will be thankful if you could tell me about getting brain mask and
performing skull stripping otherwise I'll have to wait for 12 hours to get
your replies as our working hours doesn't match.
On Nov 18, 2014 8:45 PM, "Z K" wrote:
> Gunjan, this may be related
Hi Erik,
no need to re-run . no need even to do -all, just do the subfields.
Best, Martin
On 11/18/2014 12:57 PM, Erik O'Hanlon wrote:
Thanks Martin,
Could I also ask that if the -long command was run without the
subfield option, is it best to delete the dir and rerun it or simply
recur the
Thanks Martin,
Could I also ask that if the -long command was run without the subfield option,
is it best to delete the dir and rerun it or simply recur the command with the
subfields option included (and that will continue on and run the remaining
hippo camp things?).
Thanks again for your he
Hi Shahin, I finally tracked it down. The problem is that in the
analysis you specified -native but after that you specified -per-run.
These two are incompatible, so it uses whatever is specified last. This
caused it to take the intersection of all the run masks. But the run
masks are not regi
Hi Erik,
yes, you would do the subfields only in the -long. No need currently to
include it in cross (independent) or base.
Best, Martin
On 11/18/2014 11:41 AM, Erik O'Hanlon wrote:
Dear FS Experts,
I'm running a longitudinal analysis and have run the individual time
points using the hippo
Dear FS Experts,
I'm running a longitudinal analysis and have run the individual time points
using the hippocampal subfields. Do I also need to include the -hippo-subfields
in the recon-all -long command too?
Thanks in advance for any input.
Kind regards
Erik
Erik O'Hanlon
Postdoctoral rese
Solved it, thank you
-- Forwarded message --
From: Octavian Lie
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: "freesurfer@nmr.mgh.harvard.edu"
Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the following error.
Hello Freesurfer Gurus,
I am trying to compute LGI analysis using Qdec and have successfully loaded
my qdec.table.dat file as well as created .Qrecrc to include the new
pial_lgi measure. However, when I try to analyze using this measure (or
with any measure for that matter), an error pops up saying
Gunjan, this may be related to an Ubuntu specific issue we address on
the Freesurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Specifically the part thats states the following:
***
On Ubuntu, you might have to do this if qdec or freeview complain about
libjpeg or libtif
Hi Gunjan
if you are using bash, you need to run the instructions for bash at:
http://freesurfer.net/fswiki/SetupConfiguration
for example, it says:
If using bash or sh, type:
export FREESURFER_HOME=/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
cheers
Bruce
On
Tue,
18 Nov 2014, G
I followed the installation process from
http://freesurfer.net/fswiki/LinuxInstall.
while running "setenv FREESURFER_HOME /usr/local/freesurfer" it shows that
setenv command not found.
Is it necessary to place FreeSurfer directory in to /usr/local ? I have it
on my desktop.
On Tue, Nov 18, 2014
I think if the file existed you would have gotten a syntax error. Does it
exist? If not, then either you didn't install FreeSurfer there or something
went wrong with your installation
cheers
Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
I ran but its showing error like below:
bibl04@BIBL0
I ran but its showing error like below:
bibl04@BIBL04:~/Desktop/freesurfer$ source
/Desktop/freesurfer/SetUpFreeSurfer.csh
bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory
May be due to the shell. What should I do now?
On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl
wrot
Hi Areti
Ruopeng (ccd) should be able to help you. You probably don't have the
correct version
cheers
Bruce
On Tue, 18 Nov 2014, Smaragdi A. wrote:
Dear Freesurfer mailing list,
I am having the same problem with the missing recon edit button, and I have
posted two times about this- please
Hi Gunjan
FREESURFER_HOME should be an environment variable, not the name of a
directory. It should point to the directory that you installed FreeSurfer
in. You should run:
source /SetUpFreeSurfer.csh
before trying to run anything
cheers
Bruce
On Tue, 18 Nov 2014, Gunjan Gautam wrote:
H
Dear Freesurfer mailing list,
I am having the same problem with the missing recon edit button, and I have
posted two times about this- please can someone advice us if we need the recon
edit, what the difference is to voxel edit and how we could get the recon edit
function.
Many thanks,
Areti
Hello Sir,
I have place the "license.txt" in the same directory that contains
build-stamp.txt as there were no directory with name "FREESURFER_HOME".
freeview command is not working and showing below message
"freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
open shared obj
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