it says finished without error
On 1/15/2025 5:13 PM, 박경일 wrote:
External Email - Use Caution
Dear FS Development Team,
I recently encountered an error while running the recon-all process.
This is the first time I’ve experienced an issue with this routine
process. Please refer to the
024 16:58:18
To: Freesurfer support list
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error
External Email - Use Caution
Dear FS experts,
I am encountering an error when running recon-all. I followed the FAQ
<https://se
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: 16 January 2024 13:41
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer recon-all qcache partial failure
The command should look like this ‘recon-all -s subjid -qcache -all -i
input-file
The command should look like this 'recon-all -s subjid -qcache -all -i
input-file'
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Asuka Toyofuku
Sent: Monday, January 15, 2024 9:45 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer recon-all qcache parti
nmr.mgh.harvard.edu
On Behalf Of Asuka Toyofuku
Sent: Friday, January 12, 2024 4:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer recon-all qcache partial failure
External Email - Use Caution
Dear Freesurfer researchers,
I have an issue with recon-all-qcashe
External Email - Use Caution
Dear Freesurfer researchers,
I have an issue with recon-all-qcashe results. (please find the recon-all.log
attached.)
The command created fsaverage mgh files (e.g., lh.thickness.fsaverage.mgh), but
it did not create fsaverage files with different s
: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error
Hi Krystal,
Can you try running recon-all without ‘-parallel’ flag?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To
Hi Krystal,
Can you try running recon-all without '-parallel' flag?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Krystal Xiwing Yau
Sent: Saturday, February 18, 2023 7:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] recon-all e
rom: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Krystal Xiwing Yau
Sent: Thursday, February 16, 2023 9:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] [FreeSurfer] recon-all exited with error
External Email - Use Caution
Dear FreeSurfer experts,
I ran the command &
If they are not part of the T1w series, then you can delete them (but
then they should not have caused the error). If they are part of the
series, then they are probably corrupted or perhaps the output of a very
aggressive anonymization.
On 11/25/2021 8:40 AM, Alison McDonnell wrote:
Just add -cw256 to the recon-all command line
On 11/23/2021 8:34 AM, Alison McDonnell wrote:
External Email - Use Caution
Hi Tim,
I looked at orig.mgz and it seemed fine and could see the whole head.
i dont know what is meant by the flag -cw256 error. I am taking over a
project from
External Email - Use Caution
Hi
I tried to running recon all on a large amount of data and got the below
error message. the listed files that say the tag image orientation can't be
found aer in the folder but seem to be blank. i was wondering is there a
way to run recon all and ski
External Email - Use Caution
Hi Tim,
I looked at orig.mgz and it seemed fine and could see the whole head. i
dont know what is meant by the flag -cw256 error. I am taking over a
project from someone else so used the same command line as them
Thanks,
Ali
On Tue, 23 Nov 2021 at 13
External Email - Use Caution
Dear Alison,
Did you already try what is suggested in the error message (include the flag
-cw256 with recon-all and inspect orig.mgz)? If so, what were the results?
Best,
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child
lf of Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, January 29, 2021 12:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer recon all
Hi Rahul
That typically
: [Freesurfer] Freesurfer recon all
Hi Rahul
That typically means that something has gone wrong, like too much skull being
left around. The timing of the defect correction is quadratic in the size of
the largest defect, so quite fast for small ones, but very very slow for big
ones (and less likely
Hi Rahul
That typically means that something has gone wrong, like too much skull being
left around. The timing of the defect correction is quadratic in the size of
the largest defect, so quite fast for small ones, but very very slow for big
ones (and less likely to be correct when done). Look
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 se
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 AM, Tim Schäfer wrote:
Ext
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
ut results?
>>
>> 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
u
>
> 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
...@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 will
...@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
downloading my orig.mgz:
> https://www.dropbox.com/s/crkndenx8ev957v/orig.mgz?dl=0
>
> Regards
>
> Frank
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Tim Schäfer
>
> Sent: 04 March 2020 23:27
> To:
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?
Best,
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 a
r. Try the
following: "recon-all -all -i 758251.dcm -s Subj14"
Best,
Falk
Von: freesurfer-boun...@nmr.mgh.harvard.edu
Im Auftrag von Jones, Kevin
Gesendet: Freitag, 1. Februar 2019 13:00
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Freesurfer Recon-all error
External Emai
External Email - Use Caution
Dear Freesurfer team
Thanks for you help. I am new to freesurfer, using a mac and getting an error with recon all when using my MRI data.
I ran your tutorial recon all and the tutorial data worked fine. My burned CD T1 MRI files did not have the
Hi Bruce,
This is the sequence details:
- Axial FLAIR: Plane=AXIAL; Acquisition Type=2D; Coil=8HRBRAIN; Field
Strength=3.0 tesla; Flip Angle=90.0 degree; Manufacturer=GE MEDICAL
SYSTEMS; Matrix X=256.0 pixels; Matrix Y=256.0 pixels; Matrix Z=42.0 ; Mfg
Model=Signa HDxt; Pixel Spacing X=0.8593999
and can you give us details of your FLAIR acquisition? What are the voxel
sizes? What sequence?
On Tue, 20 Feb 2018, Shim Hee Youn wrote:
> Hi Bruce,
>
> Thanks for your email. I am using Freesurfer version 6 and the command I
> used to run is this:
>
> qsub -m n -o o -e e -V recon-all -subjid ${
Hi Bruce,
Thanks for your email. I am using Freesurfer version 6 and the command I
used to run is this:
qsub -m n -o o -e e -V recon-all -subjid ${Z}_${Image}_fs -i
${step1LocalDir}/$T1 -FLAIR ${step1LocalDir}/${FLAIR} -FLAIRpial -all
Best Regards,
Shim Hee Youn
Research Assistant
Multimodal N
Hi Shim Hee
we need to know what commands you ran, the full screen output from them,
and what version of FS you are using (at least!)
cheers
Bruce
On Mon, 19 Feb 2018, Shim Hee Youn wrote:
Hi Freesurfer team,
I am currently using ADNI dataset to run Freesurfer Recon all for MPRAGE, SPGR
Dear Antonin,
Thank you for your reply and clarification at
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055331.html
. I was changing the recon-all file in the subject folder rather than the one
in the freesurfer/bin folder. The command recon-all now runs to completion
Dear Shadia,
please check, that you really edited your recon.all, as I suggested in my
previous mail. Your recon-all file is located here:
/home/s1163658/freesurferv60/bin/recon-all
According to your recon-all.log, there is still an ln -s command invoked (which
should be replaced by cp command)
Dear Shadia,
There are 2 spots in recon-all where symbolic link is created.
The first you can overcome by:
find following line in your recon-all:
set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)
and replace it by
set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix
Hello Albert,
The centos4 vs centos6 output you are seeing is not the problem. Log
files get appended to (unless you use the -noappend option), so you'll
actually see the proper FREESURFER_HOME value your expecting later in
the file.
The issue is that the version of the MNI tools shipped with
Hi Bhavani
those files don't list the error. Please see:
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?highlight=%28reporting%29%7C%28error%29
for the information we need in order to be able to help you.
cheers
Bruce
On Thu, 12 Feb 2015, Selvaraj, Bhavani
wrote:
> Hi
> I tried runni
Hi
I tried running recon all command for two case study and it ended with error.
I am attaching the document.
Please could you help me solve this issue?
Thanks,
Bhavani
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] o
I have sent the attachment mentioned in the mail below via mail drop.
On Thu, Feb 28, 2013 at 4:28 PM, Blessy M wrote:
> The skull stripped image using FS did not look very good, I am not sure if
> this was the result of skullt stripping or the fact that the volume was
> more than 256^3 (and use
have you checked the skull stripping? It looked like it might be cutting
off some brain. If you upload the subject I'll take a look (although we
will need the volume before skull stripping). Why are you not stripping
within FS? That might make life easier for you
cheers
Bruce
p.s. I think thi
The process is still running but nothing new written in the last 24 hrs.
Excerpts from recon-all.log
..
77 defects to be corrected
0 vertices coincident
reading input surface /home/#/subjects/./surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from
1. It is not contrast enhanced.
2. I am rerunning recon-all after giving it a manually skull stripped
image. Hopefully this will work.
So basically did this:
recon-all -subjid . -autorecon1 -noskullstrip -notal-check
cp T1.mgz brainmask.auto.mgz
ln -s brainmask.auto.mgz brainmask.mgz
recon-all -
thanks. I actually meant a tksurfer image, but this might do. Two
questions:
1. Is this a contrast-enhanced acquisition? That will make things more
difficult, although we have processed them in the past.
2. I think the skull stripping removed some brain tissue, which may be the
source of you
I should have send it with an extension. But it is tiff, just as you asked.
On Tue, Feb 26, 2013 at 3:03 PM, Bruce Fischl wrote:
> Hi Blessy
>
> what format is this? If you don't send it with an extension there is no
> way to know
> Bruce
>
> On Tue, 26 Feb 2013, Blessy M wrote:
>
> Forgot t
Hi Blessy
what format is this? If you don't send it with an extension there is no
way to know
Bruce
On Tue, 26 Feb 2013, Blessy M wrote:
Forgot the image. please find attached.
On Tue, Feb 26, 2013 at 2:45 PM, Blessy M wrote:
I ran this command, and got the attached image
t
I ran this command, and got the attached image
tkmedit ./ brainmask.mgz lh.inflated.nofix
For some reason tksurfer is not looking good/complete
tksurfer ./ lh inflated
On Tue, Feb 26, 2013 at 11:53 AM, Bruce Fischl
wrote:
> you can save a tif of it and post it to the list
>
> On Tue, 26 Feb 201
you can save a tif of it and post it to the list
On Tue, 26 Feb 2013, Blessy
M wrote:
Yes it is still at defect 32.
The tail of the recon-all.log is as follows:
CORRECTING DEFECT 30 (vertices=18, convex hull=22)
After retessellation of defect 30, euler #=-7 (59491,172395,112897) :
differenc
Yes it is still at defect 32.
The tail of the recon-all.log is as follows:
CORRECTING DEFECT 30 (vertices=18, convex hull=22)
After retessellation of defect 30, euler #=-7 (59491,172395,112897) :
difference with theory (-28) = -21
CORRECTING DEFECT 31 (vertices=244, convex hull=142)
After retess
is it still on defect 32? What does the tail of the recon-all.log say? And
can you send us an image of the lh.inflated.nofix (if it is the lh that is
running)?
On
Tue, 26 Feb 2013, Blessy M wrote:
I verified lh.orig.nofix, and it looks fine. But, there has been no new files
created since S
I verified lh.orig.nofix, and it looks fine. But, there has been no new
files created since Saturday (2/23/2013).
I am considering stopping the process.
I was thinking, I had created a skull stripped image, and was giving that
as input to recon-all in the command below:
recon-all -subjid . -nosku
try looking at the lh.inflated.nofix or lh.orig.nofix (or rh, whichever
one is running) and see if something is dramatically wrong (like skull
attached to brain, or hemis connected, etc)
On Mon, 25 Feb 2013, Blessy
M wrote:
Recon is still running. I started the process on 2/21/2013. Its b
Recon is still running. I started the process on 2/21/2013. Its been 4 days.
I ran this command, and viewed the aseg file, and that looks reasonable
tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg
Currently it is at this stage:
Correction of the Topology
Finding true center and radius of Spher
I don't think either one of these are errors, just warnings that occur
pretty frequently and I don't think should impact the results. Does the
recon finish? Do the results look ok?
On Fri, 22 Feb 2013, Blessy M wrote:
I am getting the bottom two sets of errors while doing a simple recon-all.
I am getting the bottom two sets of errors while doing a simple recon-all.
More specifically while running this command:
recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2
-autorecon3
Has someone encountered this kind of errors? Is there a fix?
1)
Computing MAP estimate using
Thanks. It's working now. J
>-Original Message-
>From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>Sent: 13 May 2010 15:12
>To: Jason Connolly
>Cc: 'freesurfer@nmr.mgh.harvard.edu'
>Subject: Re: [Freesurfer] freesurfer recon-all running in a
Hi Jason,
you have to tell it do do something (e.g. -autorecon2, -all, etc...)
cheers
Bruce
On Thu,
13 May 2010, Jason Connolly wrote:
> Dear freesurfer experts:
>
> Recon-all is running in a few seconds (obvious error).
>
> I am getting the following screen output on Linux, when I run recon-a
Dear freesurfer experts:
Recon-all is running in a few seconds (obvious error).
I am getting the following screen output on Linux, when I run recon-all:
recon-all -i /usr/local/freesurfer/subjects/arlene/mri/orig/AC_3Danat.img -s
arlene -force
INFO: /usr/local/freesurfer/subjects/arlene exists
Check the skull strip. Sometimes this happens when some structure is not
removed. Also check whether the brain stem and cerebellum have been
properly cut away and that the hemispheres have been properly separated
(look at the wm.mgz for this).
David Qixiang Chen wrote:
> Hi,
> We are having one
where is it getting stuck? that is, look at the recon-all.log (and
recon-all.cmd file). often times recon-all gets stuck in the topology
fixer, because of some horrible wm.mgz file, which itself could be due
to other problems. also, i assume the first thing performed before
starting recon-all was
Hi David,
usually this means the topology fixing has encountered a very large
defect, typically caused by the cerebellum or skull being attached to one
of the cortical hemispheres. Try looking at the orig.nofix in tksurfer or
the filled.mgz in tkmedit and do a sanity check on them.
cheers,
Bru
Hi,
We are having one scan going through recon-all that is taking way
longer than ordinary. Other scans took about 20-30 hours to calculate,
while this particular scan is taking 3+ days and has still not being
completed.
Just wondering how often something like this happens, and if there's
any known
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