Also, are you running it with a T1 input or a T2? The file name looks
like it might be a T2.
On 4/10/2020 10:12 AM, Bruce Fischl wrote:
Hi David
did you check the skull stripping as suggested? Seems like the input
volume given to the CC finder was empty. Work backwards and find the
earliest
Hi David
did you check the skull stripping as suggested? Seems like the input
volume given to the CC finder was empty. Work backwards and find the
earliest volume where something is wrong
cheers
Bruce
On Fri, 10 Apr 2020, David
Schwantner wrote:
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External Email - Use Caution
Thank you in advance for the assistance!
I am running the following command:
recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all
The log is at
https://github.com/dschwant/mri_to_3d/blob/master/202004090853_error_recon-all.log,
and the nii file
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Thank you in advance for the assistance!
I am running the following command:
recon-all -i 1131_T2_raw.nii.gz -s DS_T2 -all
I have attached the log file. Here is the tail. As you can see, I am
running it in Ubuntu 18.04.4 under the Window
Hi Vin
are you sure you have space on that disk? Can you run:
mri_info /home/Downloads/reorient/test.nii
mri_info /media/results/mri/orig/001.mgz
ls -l /media/results/mri/orig/001.mgz /media/results/mri/rawavg.mgz
and send us the results?
cheers
Bruce
On Thu, 25 Jul 2019,
vin rasa wrote:
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Please also find recon-all.log file.
Thanks!
On Thu, Jul 25, 2019 at 6:50 AM vin rasa wrote:
> Dear Freesurfer experts,
> Greetings!
>
>
> In the first minute of recon-all, we are getting following error:
>
> mghRead(/media/results/mri/rawavg.mgz):
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Dear Freesurfer experts,
Greetings!
In the first minute of recon-all, we are getting following error:
mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at
slice 0
T1 data type is int16, data type 4 (looked using fslinfo)
Looking
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Hi. I am getting the following error trying to run recon-all (with Version
6.0), it is failing while running the routine mri_nu_correct.mni:
Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5
/usr/local/share/perl5 /usr/lib64
ure out
why they're not saving on our own.
Thanks for your help!
Phil
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Marie Schaer
Sent: Wednesday, August 26, 2015 2:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error running recon
paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);
}
>>
ERROR: make_roi_paths did not complete successfully!
Linux KOENIGS-PC1 2.6.32-5-amd64 #1 SMP Wed Jun 17 16:09:06 UTC 2015 x86_64
GNU/Linux
recon-all -s M87100094 exited with ERRORS
total, A, mesh_outer, perim,
verticeslist, step);
}
>>
ERROR: make_roi_paths did not complete successfully!
Linux KOENIGS-PC1 2.6.32-5-amd64 #1 SMP Wed Jun 17 16:09:06 UTC 2015 x86_64
GNU/Linux
recon-all -s M87100094 exited with ERRORS at Wed Aug 26 09:56:37 CDT 2015
To report a p
Hi Philip,
Can you send me the full recon-all.log for this subject so that I can see also
matlab version and whether other vertices ran or if it crashed on the first one.
Thanks,
Marie
On Aug 26, 2015, at 8:00 AM, Philip Deming
mailto:pdem...@wisc.edu>> wrote:
Hi Freesurfer Support,
I pos
Hi Freesurfer Support,
I posted this question about a month ago, and I still haven't found a solution.
Any help would be greatly appreciated.
When running the recon-all -localGI command, I get the following errors, which
result in the message: make_roi_paths did not complete successfully!
Er
Hi all,
I'm trying to run recon-all on some data using one of the hpc clusters at
my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem
but I'm trying to rerun the data with the new version.
I keep getting this error (FreeSurfer's log file is attached here)
regarding the mni
Hi Antonella
we usually view the ?h.white and ?h.pial surfaces over the norm.mgz and
the aseg.mgz and check them all for accuracy. If things are not where you
think they should be, then you need to take one of the interventions
documented on the wiki.
cheers
Bruce
On Wed, 22 Jun 2011, Antone
Dear experts of the Freesurfer,
I am just learning freesurfer software and I was running recon-all for a
subject in my directory. I can view the volumes and surfaces and I would
be very grateful if you can list the next steps to be followed.
Do I need to make a data correction(check my data)
Hi there,
I am using the SuSE Itanium release and when running "recon-all", I am
getting the following error:
"mri_convert: cannot execute binary file"
Any clue?
Thanks in advance,
Regards,
Amir
Amir M. Tahmasebi, Ph.D.
Medical Image Analysis Lab.
School of Computing,
Queen's University,
Ki
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