help!
*Bryna Goeckner* (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing"
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list
Message-ID:
Co
for your help!
Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program
Date: Fri, 10 Feb 2023 20:48:26 +
From: "Huang, Yujing"
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list
Message-ID:
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors
External Email - Use Caution
Hi All,
I am using FS 7.2.0 and have one subject that exited recon-all with errors
(looks like for talairach issues) but I am not able to use tkregister2 to view
and make
Not sure what you are trying to do. Usually we do not do voxel-wise
analysis on the asegs (eg, like with a vbm)
On 8/29/2021 2:52 PM, guang wrote:
External Email - Use Caution
At 2021-08-05 08:44:11, "guang" wrote:
Hello FreeSurfer Developers,
I'm trying to analyze
External Email - Use Caution
At 2021-08-05 08:44:11, "guang" wrote:
Hello FreeSurfer Developers,
I'm trying to analyze aseg.mgz files for each subjects though i have segmented
hippocampal subfields and nuclei of the amygdala. Can I make the voxel-by voxel
External Email - Use Caution
If you are running Virtualbox to host linux on a windows machine sharing a
folder from a windows NTFS file system, then it may not work to create soft
links in linux on the mounted share w/o setting some things on the Windows
side. I’m not up on
External Email - Use Caution
Hi,
I think the problem is caused because Zhaoguang uses a VirtualBox share
folder.
The path "/media/sf_T1/" indicates the path is a shared folder of
VirtualBox.
Symbolic links can be used on some certain conditions.
Source:
Look in /media/sf_T1/recon/demo3/surf
Does lh.white.preaparc.H exist?
If so, does lh.white.H exist?
If not, what happens when you run
ln -s lh.white.preaparc.H lh.white.H
in that folder?
On 8/5/2021 1:41 AM, guang wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm
External Email - Use Caution
Thanks Douglas. I downloaded and installed the latest version 7.1.1 and
recon-all with no errors.
On Tue., Sep. 1, 2020, 10:21 a.m. Douglas Greve,
wrote:
> Try looking at our wiki
>
>
Try looking at our wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 8/30/20 7:16 AM, Vinny K wrote:
External Email - Use Caution
Hi,
I've tried to process a scan but it gets hung up on a particular large
defect and then exits with error. I've
Date: *Thursday, 7 May 2020 at 15:59
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
No all, just one. And try running it with just the -parcstats3 flag
(ie, don't use -all or -autreconX). You should have an answer in se
ardiff.ac.uk>
*Reply to: *Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, 4 May 2020 at 20:01
*To: *Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors
6 May 2020 at 23:11
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Recon-all exited WITH errors
It looks like that command finished without error. Have you tried running it in
recon-all again to see if it fails again? You can just run that command with
-parc
on behalf of Mason
Wells
*Reply to: *Freesurfer support list
*Date: *Monday, 4 May 2020 at 20:01
*To: *Freesurfer support list
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
*External Email - Use Caution *
Ah yes. I just set the SUBJECTS_DIR correctly, Terminal out bel
Ffôn: 02920 879628
From: on behalf of Mason Wells
Reply to: Freesurfer support list
Date: Monday, 4 May 2020 at 20:01
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Disarmed}
External Email - Use Caution
Ah yes. I just set the SUBJECTS_DIR cor
ls...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
From: on behalf of "Douglas N. Greve"
Reply to: Freesurfer support list
Date: Monday, 4 May 2020 at 19:56
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Recon-all exited WITH errors {Di
879628
*From: * on behalf of "Douglas
N. Greve"
*Reply to: *Freesurfer support list
*Date: *Monday, 4 May 2020 at 18:54
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] Recon-all exited WITH errors
Unfortunately, the log file does not indicate what went wr
d.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628
From: on behalf of "Douglas N. Greve"
Reply to: Freesurfer support list
Date: Monday, 4 May 2020 at 18:54
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Recon-all exited WITH errors
Unfortunately,
Unfortunately, the log file does not indicate what went wrong. But it
does show that the error happened on the LH (so it is not just RH). Run
the command below and send all terminal output
cd
/home/c1749990/Documents/Analysis/Data/freesurfer/subjects/PPT_001/scripts
mris_anatomical_stats
: Re: [Freesurfer] Recon-all exited with errors
Hi Lily
that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine? It looked like half of it was in use when you
ran recon-all. If you want you
Fischl
Sent: Monday, March 30, 2020 5:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all exited with errors
Hi Lily
that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine
-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, March 30, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all exited with errors
It looks like there might be a very large defect. Try looking at the wm.mgz
and brainmask.mgz
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, March 30, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all exited with errors
It looks like there might be a very large defect. Try looking
It looks like there might be a very large defect. Try looking at the
wm.mgz and brainmask.mgz and the lh.orig.nofix surface to see if there
is a large part of skull or cerebellum that is encompassed in the
orig.nofix surface
On 3/30/2020 11:26 AM, Wang, Lily wrote:
Hi All,
I have a subject
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: 12 March 2020 22:07
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
Hi Frank
sorry, I've been busy with local deadlines that are over now. Can you send
us
urfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
it should not really affect it
On 3/10/2020 10:22 AM, Tim Schäfer wrote:
External
rds
Frank
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: 11 March 2020 21:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
it should not really affect it
On 3/10/2020 10:22 A
?
>>
>> Regards
>>
>> Frank
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> on behalf of Frank Chau
>>
>> Sent: 06 March 2020 22:17
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] freesurf
gt; Sent: 06 March 2020 22:17
> To: Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Tim,
>
> The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 se
...@nmr.mgh.harvard.edu
on behalf of Frank Chau
Sent: 06 March 2020 22:17
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
External Email - Use Caution
Dear Tim,
The FOV of my T1 series is 256 x 240. Is it the FOV of the T1 series wi
...@nmr.mgh.harvard.edu
on behalf of Tim Schäfer
Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
External Email - Use Caution
Thanks for providing the image. Looks fine to me as well.
What is a bit strange is
Sent: 05 March 2020 2:25
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
External Email - Use Caution
Thanks for providing the image. Looks fine to me as well.
What is a bit strange is that when running `mri_info` on th
Freesurfer support list
> Subject: Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"
>
> External Email - Use Caution
>
> Dear Frank,
>
> if you search the log in your Dropbox for 'error', this comes up:
>
>
> ERROR! FOV=2
External Email - Use Caution
Dear Frank,
if you search the log in your Dropbox for 'error', this comes up:
ERROR! FOV=284.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
Did you have a look at the orig.mgz?
External Email - Use Caution
Hello FreeSurfer Developers,
I ran a recon-all on a recent batch of T1 Nifti files and all ended with
"exited with ERRORS". For example: "recon-all -s Chan_Pui_Kim_42M_T1 exited
with ERRORS at Sat Jan 11 01:32:55 HKT 2020".
I've searched the email
THe last command run is
ln -s lh.white.preaparc.H lh.white.H
So I'm guessing that the error comes when the symbolic link is created (and it
would not be captured in recon-all). That link is the first created in the
stream, so it would not necessarily have shown itself before then. Try this:
cd
hmmm, what system are you running on in terms of software and hardware? I
don't see any errors in the log file so I'm not sure why it stopped. You
should be able to rerun these subjects with -make all to complete them
cheers
Bruce
On
Sat, 3 Aug 2019, Kuo Li wrote:
External Email -
-rootless-system-integrity-protection-mac-os-x/
best
Andrew
From: on behalf of Ryan Flores
Reply-To: FS Help
Date: Monday, June 18, 2018 at 1:07 PM
To: FS Help
Subject: [Freesurfer] Recon-all exited with errors
External Email - Use Caution
Dear FS developers,
I tried
u>>
Subject: [Freesurfer] Recon-all exited with errors
External Email - Use Caution
Dear FS developers,
I tried running recon-all using the -parallel flag over the weekend, but to my
surprise they all exited with errors. I’m hoping the problem is something
subtle, but I’m having t
Flores
Reply-To: FS Help
Date: Monday, June 18, 2018 at 1:07 PM
To: FS Help
Subject: [Freesurfer] Recon-all exited with errors
External Email - Use Caution
Dear FS developers,
I tried running recon-all using the -parallel flag over the weekend, but to my
surprise they all exited
oun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, June 4, 2018 6:11:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all exited with errors
It is not clear what the actual error is. Is there anything that gets
printed out to the terminal that is not in the
It is not clear what the actual error is. Is there anything that gets
printed out to the terminal that is not in the log? Also, can you verify
that the disk is not filling up?
On 06/04/2018 04:53 PM, Hanna Vasilevskaya wrote:
>
>
> Good afternoon all,
>
>
> I am new to Freesurfer (using
gt;> best
>>
>> Andrew
>>
>>
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anna Daniels
>> <anna.dani...@fu-berlin.de>
>> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
>> Date: Monday, April 9, 201
vard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at
110, cannot allocate
memory)
Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into
rvard.edu>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at
110, cannot allocate memory)
Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-c
7 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "Dicamillo, Robert" <rdicami...@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at
110, cannot allocate memory)
If you are running on Ubuntu, I have a build of the freesurfer source checked
o
esurfer@nmr.mgh.harvard.edu>>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at
110, cannot allocate memory)
Hi Bruce,
thank you f
f Anna Daniels
<anna.dani...@fu-berlin.de>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at
110, cannot allocate
Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna
Hi Anna
no attachments :<
Srishti's issue stemmed from
Hi Anna
no attachments :<
Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we
Hi Bruce, hi Srishti,
I have exactly the same problem with several subjects rerunning recon-all
and there was sufficient memory available. I also tried out the last
command directly which resulted in the same error log.
mri_normalize -f /home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_
can you email us the input file and the full command line you ran?
On Thu, 5
Apr 2018, srishti goel wrote:
So it gave this error:
3d normalization pass 1 of 2
white matter peak found at 110
HISTOalloc(-2147483648): could not allocate histogram
Cannot allocate memory
Best,
Srishti
So it gave this error:
3d normalization pass 1 of 2
white matter peak found at 110
HISTOalloc(-2147483648): could not allocate histogram
Cannot allocate memory
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at
let's see if it works. If it does, you should be able to run
recon-all -s SUBJID -make all
cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:
Should I re-run the recon-all after running the last command from recon-all.cmd?
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging
Should I re-run the recon-all after running the last command from
recon-all.cmd?
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12
On Thu, Apr 5,
Hi Srishti
if you look in the subject's scripts dir there should be a file named
"recon-all.cmd". Try rerunning the last command in it (probably from the
mri dir)
cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:
I am sorry, I am not sure what do you mean by running the command line
I am sorry, I am not sure what do you mean by running the command line
directly?
I use the following command:
sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
srish...@email.unc.edu --wrap "export
SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
recon-all -s 13166
if you run the command that failed again on the command line directly (that
is, not in recon-all) does it fail again?
On Thu, 5 Apr 2018, srishti goel wrote:
Hi Bruce,
The machine definitely hasn't run out of memory. Here is the memory usage
from recon-all.log
total
Hi Bruce,
The machine definitely hasn't run out of memory. Here is the memory usage
from recon-all.log
total usedfree
shared buff/cache available
Mem: 26372696834330048 152102696 1294477294224
191963372
Swap: 2097148
Hi Srishti
are you sure that your machine didn't just run out of memory? The
recon-all.log file includes the amount of free (and total) memory at the
time the process was started.
cheers
Bruce
On Thu, 5 Apr
2018, srishti goel wrote:
Hi,
I have been trying to edit structural brains and
Hi,
I have been trying to edit structural brains and very few times I would get
the following error while running recon-all -s subjID
white matter peak found at 110
cannot allocate memory
Upon looking at the archive, there was only one similar issue and it was
recommend to check mri_info as the
What edits did you make to it? Can you check the T1.mgz to see if it
looks ok?
On 02/15/2017 07:56 AM, Dayanne Ferreira Ayres wrote:
> Good morning, I tried to process a patient with the command below
> after editing it:
>
> Recon-all-all -sd / Applications / freesurfer / subjects
Behalf Of Z K
> Sent: Thursday, October 13, 2016 12:53 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
> I was afraid this was the case. Normally in this situation I would say set up
> a shared fol
13, 2016 12:53 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
I was afraid this was the case. Normally in this situation I would say set up a
shared folder between the host and the virtual machines. But unfortu
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
> Sent: Thursday, October 13, 2016 11:03 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad
> Matushewski <bjmat...@uwo.ca>
> Subjec
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 11:03 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad Matushewski
<bjmat...@uwo.ca>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
I think its referring to t
...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 13, 2016 11:03 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Brad Matushewski
<bjmat...@uwo.ca>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
I think its referring to the hard disk space in the virtual
-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Thursday, October 13, 2016 9:43 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] recon-all exited with ERRORS
>
&
13, 2016 9:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_ev
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October 13, 2016 9:43 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all exited with ERRORS
Hi Brad
it looks like the recon failed as you ran out of disk space:
c
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)
as for
I just tried to run my first recon-all.
What now?
[Logo]
Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP.
Laboratory for Brain & Heart Health
School of Kinesiology
Western University
Room 402, Arthur & Sonia Labatt Health Sciences Building
London, ON, Canada, N6A 5B9
Tel: (519) 661-2111 x
Hello,
I am very new to freesurfer who have been using SPM and FSL, and just started
doing individual subject analysis. I already had an error message on recon-all
step.
I am using:
Vertualbox, OS is RedHat 64-bit
I am using bash (I prefer to do so) so I am not in tsch shell.
The recon-all
Thank you, Zeke for your help!
Best wishes,
Hisako
-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:08 PM
To: Freesurfer support list; Fujiwara, Hisako
Subject: Re: [Freesurfer] recon-all exited with errors
Hello Hisako
Hello Hisako,
This is a recently discovered bug either mni related or VirtualBox
related. The issue is that the mri_nu_correct.mni command will fail
when executed in the VirtualBox environment on a subject whose data
exists on a shared folder between the host and the virtual machine.
Hi Katica
what format was the input image to recon-all? Can you verify that tkmedit
has the directions correct (that is what it labels as anterior is actually
anatomically anterior, etc...). If so, then the talairach just failed and
you will need to either try an alternative (like the MNI or
Happy New Year freesuerfers!
I run into this error while doing recon-all :
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0., pval=0. threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
Dear freesurfer experts:
I am trying to process an MRI using recon-all -autorecon1 -autorecon2
-autorecon3
and exited with errors. Apparently the encoded image data is not supported
(below you can see the recon-all.log)
Is there a way to process this study?
Thank you very much for your
Hi all,
I posted a message regarding this problem a while ago, but still not resolved.
Basically, freesurfer exits with errors in the final (autorecon-3) stages,
because of what must be a problem with the symbolic link lh.EC_average. The
link is created as should be, but I get an error message
Hi Luzia, do you have permission to see that file? Can you send the
recon-all.log file?
doug
On 09/03/2013 07:32 AM, Troebinger, Luzia wrote:
Hi all,
I posted a message regarding this problem a while ago, but still not
resolved. Basically, freesurfer exits with errors in the final
Can you send the recon-all.log file?
Zhangyuanchao wrote:
Dear expert，
We compute the MRI data with FREESURFER using
instruction recon-all -s -all,but some data will show recon
-all exited with ERRORS in the recon-all-status.log. The flowing
display error information :
Dear expert， We compute the MRI data with FREESURFER using
instruction recon-all -s -all,but some data will show recon -all exited
with ERRORS in the recon-all-status.log. The flowing display error information
:status file for recon-allThu Nov 11 19:22:13 HKT 2010recon-all finished
Hi everyone,
I had a recon-all exit with errors, but I can't find a specific error
message that explains what the problem is. This is v4.5.0. The last
several lines of the script are pasted below: Any ideas as to what went wrong?
Thanks,
Dana
gca peak Unknown = 0.94427 ( 0)
gca peak
Hi,
I'm trying to run the command: recon-all -subjid subname -autorecon1. I'm
getting the an error message during skull stripping and the error log reads
as follows:
#...@# Skull Stripping Wed Oct 28 12:29:47 PDT 2009
/space/raid7/data/london/data/
hi all,
I ran recon-all on a case, and it exited with errors, and the error message
looks like this:
ERROR: Talairach QA check failed!
z-score = -6 = -6 = threshold
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check
Hi Annie,
The aparc+aseg has the aseg subcortical labels in the wm regions, and has
the parcellation labels along the cortex. This is overlaid on volumes in
tkmedit. A description and a snapshot is shown at the bottom of this
page:
Hello all,
Using the most updated version of freesurfer, I ran autorecon3 on a set of data
obtained with an old version of the software (the first version) and I obtained
the following error message:
Loading rh annotations from
Hi Annie,
I think what's happening is that it's failing in the aparc+aseg step, but
you can verify this by looking at the status log in your subjects
scripts/recon-all-status.log
This step uses some previously generated input to make a new segmentation.
The lh.ribbon.mgz is a newer addition
Chacko,
The error message 'mrisDefectAnalysis : defect xx overlap defect yy'
appears when running v3.0.1 of freesurfer. That bug was fixed in
v3.0.2. I suggest updating your version of freesurfer if possible.
Nick
On Mon, 2006-08-14 at 11:46 -0700, Chacko Cherian wrote:
Hello all,
One of
Hello all,
I was running recon-all for one of my images and this
happened to be the error that i got.Could someone
please clarify,
Thanks in advance
Chacko.
mri_watershed: error while loading shared libraries:
libstdc++.so.6: cannot
open shared object file: No such file or directory
Linux elmo
libstdc++ is the standard C++ library. if your Linux has libstdc+
+.so.5, then the rh9 build of freesurfer should be used. the centos
builds of freesurfer use libstdc++.so.6. or, libstd++.so.6 can be
downloaded from the web and installed (google 'libstdc++ rpm').
On Wed, 2006-07-26 at 14:38
Hi,
I came across an error in the third stage of reconstruction using
freesurfer. The images,scripts etc are at
space/megraid/42/ACE/PILOTDATA/DATA_PROCESS
The recon log says that recon-all exited with errors and stopped at Surf
Reg rh. I am a new user and was hoping that you could help me out
hmm, not sure what's going on here as your orig is newer than your
inflated, which it shouldn't be:
ls -lrt rh.*
-rw-rw-r-- 1 nandita nandita 3202384 Jun 29 15:53 rh.orig.nofix
-rw-rw-r-- 1 nandita nandita 3202704 Jun 29 15:53 rh.smoothwm.nofix
-rw-rw-r-- 1 nandita nandita 3203048 Jun 29
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