Really? 178 separate anatomical scans of the same person?
On Jan 18, 2013, at 4:31 PM, paul horton wrote:
> Hi Bruce and Martin,
>
> Thanks for your replies.
>
> With regards to the questions from Bruce,
>
> 1.The machine has 72gb of ram
> 2.There are no other processes running
> 3.There
I dont know if this applies but I sometimes have really long run times when
image quality is bad, usually from subject movement. I drop them.
Josh
On Fri, Jan 18, 2013 at 1:31 PM, paul horton wrote:
> Hi Bruce and Martin,
>
> Thanks for your replies.
>
> With regards to the questions from Bruce,
actually, looking at your cmd line more I see that you have slashes (/)
in the subject names. The argument to --subjects should just be a list
of name. See the help (aparcstats2table -h) for examples.
doug
On 01/18/2013 04:58 PM, Nucleos P wrote:
> Hello experts:
>
> Can someone please help me
does the file exist? If so, is it empty(maybe because the disk is full)?
On 01/18/2013 04:58 PM, Nucleos P wrote:
> Hello experts:
>
> Can someone please help me understand what I am doing wrong? This is
> the first time I am trying this command and it will not work...
>
> COMMAND: aparcstats2tab
Hi Bruce and Martin, Thanks for your replies. With regards to the questions
from Bruce, 1.The machine has 72gb of ram2.There are no other processes
running3.There are 178 time points. With regards to the questions from Martin,
1. This is happening in the -long runs, but, only in 1 of the four ru
Hi Christine
it's based on the individual anatomy
Bruce
On Fri, 18 Jan 2013, Christine R
Denning wrote:
> Dear experts,
> I am going to use mris_divide_parcellation with a split file to create
> smaller labels and am curious how the "long axis" of a label is defined. Is
> the long axis defined
Dear experts,
I am going to use mris_divide_parcellation with a split file to create smaller
labels and am curious how the "long axis" of a label is defined. Is the long
axis defined by an atlas so that it is guaranteed to be in the same direction
across subjects, or is it defined based on the
Dear freesurfers,
After reading the documentation on freesurfer web site and searching in the
mail archive I wasn't able to find an answer to my question.
I'm trying to perform cerebellar segmentation on 100 subjects.
The recon-all step went well : every t1 image finished "without error" when
I ch
Hi Paul,
also, is this happening in the -base run or in one of the -long runs (or
in all of the -long runs of that subject). What binary is running so
slowly (you mentioned some output "labelling slice", can you scroll up
in the log and see what exactly is running)?
Best, Martin
On 01/18/20
how much RAM do you have in the machine? And are there other processes
running at the same time? How many timepoints does the subject have?
Bruce
On Fri,
18 Jan 2013, paul horton wrote:
Hi Alex,
Thanks for your reply.
I am also using Linux. I have restarted the analysis a few times but
Petr why do you keep trying to name your input files something.mgz, when you
were in wisconsin i told you the inputs always need to be 001.mgz
at this point i think you need to get invited to upload one of your data sets
to ugh and see if there is a problem
with the data or is it a problem with
Cool, it's running. Hopefully I did that right.
Thanks for your help!
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Friday, January 18, 2013 11:28 AM
To: Borzello, Mia
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] pial not computing
Hi Alex,
Thanks for your reply.
I am also using Linux. I have restarted the analysis a few times but the
process for this particular subject is very slow. When I try the same analysis
on a different subject using the same machine, it only takes a few hours. So
not sure why the analysis is h
Hi Cathy, try removing "--parc --aparc" or changing it to "--parc
aparc". Let me know if that works.
doug
On 01/18/2013 09:26 AM, Catherine Bois wrote:
> Hi, I am trying to extract stats files from my subjects using this command
>
> aparcstats2table --hemi lh --subjects EHRS_* --skip --meas thic
Hi Paul,
I also had such problems previously. My initial analyses were performed
on mac. Though it might seem strange, some analyses resolved after I
just restarted the computer. Other ones I analysed on centos. Now I am
doing all the recons on linux.
best wishes,
Alex.
Le 1/18 9:22, pau
it's run as part of recon-all. If you grab a new one and run
recon-all -make all ...
you should be all set
Bruce
On Fri, 18 Jan 2013, Borzello, Mia wrote:
> great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where
> to run this and I don't see a page on the freesurfer site
great. is there a freesurfer page on mris_topo_fixer? I'm not sure how/where to
run this and I don't see a page on the freesurfer site.
Thanks so much,
m
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 17, 2013 1:30 PM
To: Borzello
For those willing and brave enough, another beta of v5.2.0 has been posted
here for you to download and test:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
The Mac builds should work (note: the lion build is 64b, snow-leopard is
32b).
The final release still awaits some critic
Hi, I am trying to extract stats files from my subjects using this command
aparcstats2table --hemi lh --subjects EHRS_* --skip --meas thickness
--parc --aparc --tablefile lh.thick.table
however I keep getting this error message
Parsing the .stats files
Skipping
/sdata/images/projects/EHRS/2/
> Date: Fri, 18 Jan 2013 08:54:48 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: horton_p...@hotmail.com
> Subject: RE: [Freesurfer] longitudinal analysis
>
> Hi Paul
>
> can you cc the list so that others can answer?
>
> thanks
> Bruce
> On Fri, 18 Jan 2013, paul
> horton wrote:
>
> > Hi Br
Hi Paul
what is the actual binary being run?
Bruce
On Fri, 18 Jan 2013, paul horton wrote:
Hi guys,
I am currently running a longitudinal analysis on a set of scan. It is
currently running and so far it has taken 5 days. It seems to be taking a
large amount of time on a process called label
Hi guys, I am currently running a longitudinal analysis on a set of scan. It
is currently running and so far it has taken 5 days. It seems to be taking a
large amount of time on a process called labelling slice. I have run the same
analysis on other subjects which took about 6 hours to complete
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