Can you check the earlier volumes? And maybe post an image of the orig and/or
T1.mgz?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ???
Sent: Saturday, August 10, 2024 9:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error: GLOBAL region of the brain
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李志豪
2310117...@stu.pku.edu.cn
Hello , freesurfer developers,
I’m attempting to segment some brain mri data which is for training.But I
encounter the following error:
mri_watershed Error: GLOBAL region of the brain empty !
I have
External Email - Use Caution
Dear Freesurfer developers,
I am currently conducting a research project in which I am running 7T MP2RAGE
images in Freesurfer version 6.0.1 but have a run into an issue.
For 3 images I receive a watershed error stating “mri_watershed error: GLOBAL
%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Iman Kianian
Sent: Saturday, August 26, 2023 9:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error while running recon-all
External Email
transforms/talairach_with_skull.lta
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Iman Kianian
Sent: Saturday, August 26, 2023 9:52 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed Error while running recon-all
External Email - Use
External Email - Use Caution
Dear Freesurfer experts,
I am running recon all as part of the tractography pipeline on a group of
stroke patients.
This is are the first lines of my log file:
/opt/freesurfer/6.0/bin/recon-all -s sub-056 -i
/project/3015068.01/ilecam/Reolang/Dat
: freesurfer-boun...@nmr.mgh.harvard.edu
Date: Friday, 4 December 2020 at 4:54 am
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation
Make sure it looks reasonable (that there is a brain in there, and the
intensities look ok). You can send it to
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_wat
Have you looked at the T1.mgz?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation
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Hi
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It would be great if you can have a look at the nu.mgz and talairach.xmf but
unfortunately I´m not able to provide it in the mailing list.
Is there another way to send you the files?
Thanks,
Boris
> Am 11.10.2018 um 22:04 schrieb Bruce Fischl :
>
>
Hi Boris
the input to that watershed call is the T1.mgz, but it is already
problematic as you can see from the log. You should take a look at the
nu.mgz and make sure it is correct. You can also email me the nu.mgz and
the talairach.xfm (in the mri/transforms dir) if you want and I'll take a
External Email - Use Caution
Hi again,
sorry. Please find attached the recon-all.log. I´m not sure how to check the
input to watershed.
recon-all.log
Description: Binary data
Thanks,
Boris
> Am 11.10.2018 um 18:55 schrieb Bruce Fischl :
>
> Hi Boris
>
> can you check to m
Hi Boris
can you check to make sure that the input to the watershed looks ok? Also,
in general it is a lot easier for us to help if you send us the full
command line and screeen output and attach the recon-all.log
cheers
Bruce
On Thu, 11 Oct
2018, Boris Rauchmann wrote:
Externa
can you send the recon-all log file?
On 10/11/2018 11:22 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> When I run recon-all i get the follwing error message:
>
> mri_watershed Error:
> GLOBAL region of the brain empty !
> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1
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When I run recon-all i get the follwing error message:
mri_watershed Error:
GLOBAL region of the brain empty !
Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-X
I think so. Or apply it with mri_convert -at
On Fri, 27 Apr 2018, miracle
ozzoude wrote:
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Hello Bruce,
Thanks. Can I use tkregisterfv to visualize it?
Best,
Paul
On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl
wrote:
Hi Paul
that
External Email - Use Caution
Hello Bruce,
Thanks. Can I use tkregisterfv to visualize it?
Best,
Paul
On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl
wrote:
> Hi Paul
>
> that usually means something went wrong before the watershed. Check the
> input image to make sure that it
Hi Paul
that usually means something went wrong before the watershed. Check the
input image to make sure that it and the talairach_with_skull.lta are ok
cheers
Bruce
On Fri, 27 Apr 2018, miracle
ozzoude wrote:
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Hello FreeSurfer,
While runnin
External Email - Use Caution
Hello FreeSurfer,
While running recon-all on a subject, i got encountered an error during the
watershed step (mri_watershed). How do i fix this problem? I have attached
the recon-all.log and recon-all-status.log files. Thank you
Best,
Paul
recon-all
and found this thread:
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22\[Freesurfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22&o=newest&f=1
> My problem seems identical to the one described by initial poster.
> The suggestion was to try the f
rfer\]+mri_watershed+Error\%3A+indices+out+of+bounds%22&o=newest&f=1
My problem seems identical to the one described by initial poster.
The suggestion was to try the following command:
set mdir=$SUBJECTS_DIR/$subject/mri
mri_add_xform_to_header $mdir/transforms/talairach.xfm $mdir/nu.mgz
$mir/nu.mgz
Whe
Hello Edgar,
We think we were able to isolate the problem. Version 5.1 is failing to
apply the talairach transform to the nu.mgz. It gets computed and
applied to the orig.mgz but then not transferred during the next step.
When mri_normalize tries to run without this information, it fails, and
Hello Edgar,
I am going to be looking at your case and seeing if I can replicate the
error. I have your .nii file and will run it through our processing
stream here, but could you send me your subject folder so that I can
look through your files/logs to give me some more information?
You can
Hello Bruce,
I just wanted to touch base regarding the "Indices_oob.nii" subject I had
sent to MGH. Were you by any chance able to detect the issue with running
recon-all on this subject. Thanks in advance for taking a look at this.
Best regards,
Edgar Busovaca
_
Hello Edgar,
Could you upload the whole subject folder? I could try to run it through
recon all here and see if I can reproduce the error. It would also allow
me to look through your log files to see if I can spot anything that
could be causing this issue.
You can use FileDrop2.0 if the dire
Hello Bruce,
I took a look at the file with freeview and I can't identify anything
peculiar about the data. The file is named Indices_oob.nii and has been
uploaded to /transfer/incoming on the FTP file exchange server. Thank you
for your swift reply and in advance for your time.
Best regards,
E
Hi Edgar
the LINE SEARCH thing is not a real problem. I've never seen "indices out
of bounds" before though. Is there anything strange about your dataset?
Does freeview display it properly (that is, are what freeview thinks the
RAS dirs the correct anatomical ones)? If you upload the dataset w
Dear Freesurfer users,
I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early (
during the skullstrip).
During skullstripping the following warning appears twice:
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTAT
Dear Freesurfer users,
I have attempted to process a subject (.nii type input) through recon-all
-all, but for some reason the processing gambit is terminated early (
during the skullstrip).
During skullstripping the following warning appears twice:
IFLAG= -1 LINE
__
Hi Bruce, True, I am trying to use Freesurfer skullstripping as a first step to
create an input for Brain extraction tool of FSL so as to get in general
acceptable extracted brains without changing BET options a lot for different
brain.
So, what I am doing is as following:
I Deoblique anatomica
Dear experts,
I have a encountered an Error while doing skull-stripping using freesurfer on
my T1 weighted images, using mri_watershed
I am using the following command:
mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz
and here is the error:
mri_watershed Error:
w=White Matter =Inte
you could also try adding the -no-wsgcaatlas flag to the end of
recon-all. but also make sure that the T1.mgz is not junk.
n.
On Thu, 2010-09-23 at 12:06 -0400, Bruce Fischl wrote:
> can you check the talairach xform and see if it's ok?
> On Thu, 23 Sep 2010,
> Shugao Xia wrote:
>
> > Hi,
> >
can you check the talairach xform and see if it's ok?
On Thu, 23 Sep 2010,
Shugao Xia wrote:
> Hi,
>
> I ran recon-all on one subject, and exited with errors:
>
> mri_watershed Error: GLOBAL region of the brain empty!
>
> what is the reason which caused this error? Thank you in advance
>
> Best
Hi,
I ran recon-all on one subject, and exited with errors:
mri_watershed Error: GLOBAL region of the brain empty!
what is the reason which caused this error? Thank you in advance
Best
Shugao
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.e
Hi Toh,
did you check the talairach transform? If it's ok, try either running the
watershed skull stripping with a different preflooding height or without
the atlas.
cheers
Bruce
On Sat, 17 Jul 2010, Toh Hock Wong wrote:
> Dear freesurfer experts,
>I need your help on recon. I tried to p
Dear freesurfer experts,
I need your help on recon. I tried to perform recon-all on my
anonymized control subjects (chunk of face/eyes removed on T1.mgz) and
run autorecon1.
It ran smoothly till the end of workflow of autorecon1 and came up
with the following:
mri_watershed Error:
Hi ,
I encountered an error during the watershed and I tried to check the
disk space running : zcat
/usr/local/freesurfer/subjects/s2/mri/T1.mgz>
/usr/local/freesurfer/subjects/s2/mri/T1.mgh
An image file appeared but it is impossible to open it because it has
a width of zero .
what does i
Kathy,
Can you send me the 001.mgz file for one of these subjects? Send it via
the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The 001.mgz file is in the /mri/orig directory (and you might have
a 002.mgz file as well, if you had two structurals for this subject).
Nic
Hello all,
I've been working with a set of about 200 brains, and in 19 of these I'm
getting the error "mri_watershed Error: GLOBAL region of the brain empty
!". I've checked the talairach transformation with tkregister2, and in 17
of those cases, the transformations look fine (the two other cases
Dear FS experts,
When I run recon-all, one of my subjects get this error in mri_watershed
process:
*WATERSHED**
Sorting...
first estimation of the COG coord: x=121 y=125 z=133 r=78
first estimation of the main basin volume: 2032411 voxel
Hi Ozlem,
if it's the talairach_with_skull.lta as described previously. I have a fix
for it that will be in the upcoming stable. In the interim you could try
running watershed without the talaiarch_with_skull.lta
cheers,
Bruce
Hello,
I have the same error (mri_watershed Error: GLOBAL regi
Hello,
I have the same error (mri_watershed Error: GLOBAL region of the brain empty
!) as described Micheal Harms' mail (below) which left I guessed as
unanswered. Any help would be appreciated.
Thanks,
Ozlem OZMEN-OKUR
Bogazici Univ. Biomedical Engineering
Istanbul-TURKEY
[Freesurfer] autoreco
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