other directory and restart recon-all.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Suman Saha
Sent: Monday, November 27, 2023 11:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: ERROR reading
/usr/local/freesurfer/subjects/fsaverage
External Email - Use Caution
Have you looked at this page
https://secure-web.cisco.com/1BV2hYoaSBjdqCI3ji_zfSci2RFzSKvskUEpLSzz9KZZmJ3W692xmbGJZYtcILbXwSeNGChMfif4QJenV0WIKvqU9-y6rwrLkf3PY6_kwKAA0UMsTELNqJZjOgJBdeZO_ohao1RiTq7M-MGJ54JDw6BQyJbBIkgZZ28P8CWJqFlnQxggUkQBtLaA1W-aXp2lULZ
not sure what is going on. It received a kill signal (the 9 mentioned at
the end). This often means that it was killed externally. Does this
happen repeatedly? Does this happen on other subjects? How much memory
did you allocate to your virtual box?
On 9/23/2022 1:04 AM, Ahmad Khan wrote:
External Email - Use Caution
-- Forwarded message -
From: vittal korann
Date: Tue, Nov 17, 2020 at 1:16 PM
Subject: Error in longitudinal pipeline
To:
Hi FreeSurfer experts
Recently I started working on the longitudinal data.
I followed the pipeline described i
External Email - Use Caution
Hi FreeSurfer experts
Recently I started working on the longitudinal data.
I followed the pipeline described in the below link.
Also, I attached my longitudinal table along with freesurfer data.
https://secure-web.cisco.com/10GeKQWbNwmdQQgtn3lkt2V_V6C
External Email - Use Caution
TO: freesurfer@nmr.mgh.harvard.edu
SUBJECT: Error in Monte Carlo simulation: Error running mri_surfcluster
Hello FreeSurfer Developers,
I'm attempting to run a longitudinal analysis on structural T1 images for a
sample, as described on the freesurfer
did you run recon-all -qcache ... on all your subjects?
On 7/25/19 3:35 PM, Renew Andrade wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts:
> I am processing in qdec 3 subjects with the GUI and I have this
> terminal output.
>
>
> Error in Analyze: Couldn't open
> /App
External Email - Use Caution
Dear FreeSurfer experts:
I am processing in qdec 3 subjects with the GUI and I have this terminal
output.
Error in Analyze: Couldn't open
/Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file.
lh-Avg-
External Email - Use Caution
Hello,
Can anyone help me with this? I think it got lost in the pool of email.
Best,
Paul
-- Forwarded message --
From: miracle ozzoude
Date: Thu, Jul 5, 2018 at 12:23 PM
Subject: error with mri_ca_register in long
To: Douglas N Greve
Hello FreeSurfer Developers,
I am attempting to repeat the group analysis with the tutorial data on
FreeSurfer website, as described on the FsTutorial/GroupAnalysis (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). But I
received an error message when running the mri_glmfit co
Dear Freesurfers,
I wonder if you could please help me with this issue, it may be similar
to this post?
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40092.html
Ran it just fine a while back, but now it is failing with this error.
Thank you very much,
Best wishes,
Barbara
Thanks a lot Martin. I was running it on cluster and my quota was exceeded.
You saved my day.
Regards,
Nabin
On Thu, Dec 17, 2015 at 3:04 PM, Martin Reuter
wrote:
> Hi Nabin,
>
> maybe you run out of disk space at different places?
>
> It should print the command that it was trying to run befor
Hi Nabin,
maybe you run out of disk space at different places?
It should print the command that it was trying to run before it prints
the error, try running that command manually from the command line to
get more info on what happens.
Best, Martin
On 12/17/2015 08:52 AM, Nabin Koirala wrot
Hi all,
I am doing longitudinal analysis (recon-all) and while running the
long_mri_slopes using the following command, I am getting different errors
for each run and its driving me crazy.
The command I am running :
long_mris_slopes --qdec ./qdec/long.qdec.Sub_7_t0t1.dat --meas thickness
--hemi
-- Forwarded message --
From: Timothy Le
Date: Tue, Oct 6, 2015 at 10:33 AM
Subject: Re: [Freesurfer] Error Messages for Accessing Bin
To: dgw
Cc: Freesurfer support list
Hi,
We have a 64 bit system. We chose to install 5.0 because we already have
data processed in 5.0 and want
Thanks a lot Anastasia for your help. I will install the new version and run it
on my data.
Best wishes
Lucia
Inizio messaggio inoltrato:
> Da: Anastasia Yendiki
> Oggetto: Re: [Freesurfer] Error running TRACULA
> Data: 02 ottobre 2013 17:23:42 GMT+02:00
> A: Lucia Billeci
> Cc: freesurfer@
Hi Joshua, you do not have samples for all of your groups (eg,
group0bp2-2-1).
doug
On 04/04/2013 11:59 PM, Joshua deSouza wrote:
> Hello Douglas,
>
> I have done as you have suggested and have created 16 classes with 2
> different groups, and 3 discreet variables. However, I seem to be
> getti
Hi Joshua, you should start by not coding gender and handedness as
continuous variables. In doing this, you are saying that you expect
right handers to have 2x the thickness as left handers (or females to
have 2x the thickness as males). You need 8 classes. If your "voxel"
variable is discrete,
Hello Sir/Madam,
I am currently running a statistical test using the FSGD method. I am
encountering a problem in relation to the creation of the glmdir folder
when I run the mri_glmfit function. I recieve an ERROR message that tells
me that the design matrix (automatically generated) is ill condit
Catherine,
Thats odd, can you email me your qdec.table.dat file? qdec parses
'discretes' if they're non-numerical, so maybe there is a stray character
thats messing it up.
Nick
> Sorry, just to clarify; it lists age as a discreet variable rather
> than continuous for some reason, not the other
Catherine,
Is your SUBJECTS_DIR enviro var setup properly prior to starting qdec?
That is, set to your own writable subjects directory? I noticed in the
error message that it looks like the subjects dir is the default one under
the /freesurfer dir, which is read-only.
One option is to put this
Sorry, just to clarify; it lists age as a discreet variable rather
than continuous for some reason, not the other way round as I
accidentally wrote=)
Regards
Quoting Catherine Bois on Tue, 12 Feb 2013
14:58:45 +:
>
> Dear all,
>
> I have a question;
>
> I am trying to load data into
Dear all,
I have a question;
I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set th
Hi Maryam, I don't know what is going on. Does 006/mcparams2extreg.log
have anymore information? Can you run
cd 110419_xu_PDM1_02_PDM/bold
mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg
doug
On 4/24/11 9:01 PM, Maryam Vaziri Pashkam wrote:
Hi,
I am running into troubl
Hi,
I am running into trouble with motion correction on my Mac and freesurfer
4.5.
Originally I ran preproc-sess and got an error from mc-sess in the part (i
think) that runs the mcextreg. I ran mc-sess and the same error happened (I
have copy pasted the log bellow).
It seems like the matlab progr
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