Hi Doug,
Sure. I have attached a screenshot of the design tab as well as the terminal
output, mydata.table.dat/Gender.levels/Group.levels files.
Many thanks in advance.
Clare
From: freesurfer-boun...@nmr.mgh.harvard.edu
from the snap shot it does not look like you have selected any factors.
Try clicking on and highlighting Group, for example
On 05/19/2016 04:52 AM, Clare Loane wrote:
> Hi Doug,
>
> Sure. I have attached a screenshot of the design tab as well as the terminal
> output,
please send the command line and all terminal output
On 05/19/2016 05:50 AM, Mahtab Farahbakhsh wrote:
> Dear FreeSurfer,
>
> I have a problem when I use mris_anatomical_stats. It gives me an
> error saying that it couldn't read the input volume which is the
> wm.mgz file. would you please help
Thanks a lot.
Does the snowleaopard version work on El Capitan?
So by replacing the version already found in bin/mrisegstats, with the leopard
one after Chomd +x, it should work?
I thought i would get a link for something like mri_segstats.ElCapitan?
Yas
> To:
Dear Douglas,
To define my new label, I choose the ROI section and choose "New ROI". Then
I save it, but it doesn't work properly. In addition, I cant save it on
fsaverage.
Best Regards,
Mahtab.
On 12 May 2016 at 22:08, Douglas N Greve wrote:
>
>
> On 05/12/2016
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an error
saying that it couldn't read the input volume which is the wm.mgz file.
would you please help me how I should fix this problem?
Best Regards,
Mahtab.
___
Dag Jolijn,
Gegenereerd! En ik heb gezien dat nr 13136 wm_lh_g_temp_sup_plan_tempo ertussen
staat! (output linux) :)
Groetjes, Caroline
-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens
Hi Elijah
no, we don't have the resources to document, test, distribute and support
it. I wish we did
sorry
Bruce
On Wed, 18 May 2016, Elijah Mak wrote:
Hi Martin,
I am also following this thread with interest. Is that multi-modal prototype
Dear Bruce,
This is the input command and the output that I get:
bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon
lh
limiting computations to label anon/label/lh.BA45.label.
reading volume
/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz...
Does it always die like that? It may be out of memory.
On 05/18/2016 01:50 PM, S.V.Shepherd [work] wrote:
> Hello,
>
> When running more than 3 analyses in parallel in FreeSurfer 5.3, I am
> getting matlab crashes. Mathworks has politely declined to provide
> support unless I can replicate
sounds like you are running out of memory, no?
On Wed, 18 May 2016,
S.V.Shepherd [work] wrote:
Hello,
When running more than 3 analyses in parallel in FreeSurfer 5.3, I am
getting matlab crashes. Mathworks has politely declined to provide support
unless I can replicate outside FsFAST.
The
I've refreshed those links
On 05/18/2016 10:44 PM, Dave Yas wrote:
> Dear Doug,
>
> I'm getting mri_segstats error [mghread(...ribbon.mgz) at the end of
> -autorecon2.
> I saw your answer for others about this Q before and i know how to
> solve this *IF* i was able to access to the links you
How did you create the measures? If with mris_anatomical_stats, then use
can use aparcstats2table
On 05/19/2016 03:06 AM, Liu Y wrote:
> Hi Freesurfers,
> I calculated the thicknesses of a cluster for some subjects, and each
> of the measure was saved under each subject' s folder. How to create
Hi Freesurfers
I am doing FSFAST with my own data and have a problem. After I run
mkanalysis-sess command succesfully, I try to run mkcontrast-sess command
but I get an error during the process. The text in my terminal window is
the following:
root@usuario2:/home/usuario2...
mkcontrast-sess
Hi Mahtab
can you please send the screen output of the command you ran and what it
printed, and also what the environment variable SUBJECTS_DIR is?
cheers
Bruce
On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
Dear FreeSurfer,
I have a problem when I use mris_anatomical_stats. It gives me an
Hi Doug,
No that’s not how I usually store my files- I have a folder for the particular
study that I am working on then the dicoms for each subject in that study are
stored in individual subject folders within the study folder.
I got a chance to look around the recon-all logs this morning for
Hi Gaurang,
Can you send me this whole subject case via our filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/
I can take a look and get back to you.
-Ani
On 05/18/2016 05:29 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
> The way I made the changes was that I followed the following
Dear Douglas,
The wm.mgz is in the mri folder so it's in:
Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz.
Best Regards,
Mahtab.
Sent from myMail for iOS
Thursday, May 19, 2016, 16:19 +0100 from gr...@nmr.mgh.harvard.edu
:
>The second one is a
sorry, I have no idea
On 05/19/2016 11:35 AM, S.V.Shepherd [work] wrote:
> It happens when I run more than 3-4 analyses at once. It appears to be
> sensitive to other instances of Matlab being open. however, I don't
> see clear evidence I'm memory limited. for example, I'm currently
> running
do you have permissions to create a folder in that location? Try it from
the terminal to see
On 05/19/2016 11:38 AM, Clare Loane wrote:
> Hi Doug,
>
> Thanks, I have done as you suggested but I am still getting an error.
> I have attached the terminal output but also paste the error below:
>
>
It happens when I run more than 3-4 analyses at once. It appears to be
sensitive to other instances of Matlab being open. however, I don't see
clear evidence I'm memory limited. for example, I'm currently running four
selxavg in parallel, along with a separate melodic analysis. One more would
yea, can you post the log file of both the successful and failing runs?
On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
>
> Hi Doug,
>
> No that’s not how I usually store my files- I have a folder for the
> particular study that I am working on then the dicoms for each subject
> in that study are
Hi Doug,
Thanks, I have done as you suggested but I am still getting an error.
I have attache the terminal output but also paste the error below:
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas
Hi Mahtab
the mris_anatomical_stats help says:
mris_anatomical_stats [options] []
.
.
.
-f
table output to tablefile (different format than -b).
Must use-a or -l options to spec input.
.
.
.
so you are specifycing the name of the table as "anon", the
Hi Freesurfers,
I calculated the thicknesses of a cluster for some subjects, and each of
the measure was saved under each subject' s folder. How to create a table
containing all the measures? What is the command?
Thanks,
Yawu
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