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:
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
I will try to reinstall it again.
Many thanks for your kind answer,
Best regards,
Mohamed
On 28/02/16 12:44, Maheen Siddiqui wrote:
> Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup
> module)
>
> Maybe there was a step missed of the installation? If everything is in
Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup
module)
Maybe there was a step missed of the installation? If everything is installed
properly then recon-all works perfectly. Maybe make sure everything that was
required from installation has been done. Or try it ag
Dear Experts,
I have the following error with recon-all (freesurfer v 5.3). Anybody have an
idea about this problem?
Many thanks in advance,
Mohamed
orig_nu.log
file--
Iteration 1 Fri Feb 26 14:13:20
Hi Danielle
what does it look like withouth the FLAIR postprocessing? And what FLAIR
sequence are you using? We have only ever used the T2-space FLAIR and have
been told that it works great with that, but not as well with other FLAIR
variants.
cheers
Bruce
On Tue, 22 Apr 2014, Danielle Mil
Devin,
The VirtualBox install of freesurfer is an unsupported version that has
been provided as a convenience to Windows users or other users that wish
to use the freesurfer software but do not have immediate access to Mac
or Linux platform. The Virtual box installation is literally just an
Xu
Dear Freesurfer experts,
I have recently installed Freesurfer onto a VirtualBox Linux environment, and
had no problems running the supplied practice subject, 'Bert', all the way
through reconstruction. However, when I started trying to analyze my own
subject's, recon-all keeps exiting just aft
why are you putting a dot in front of the path? There's no dot in the
dcmunpack output
doug
On 09/14/2012 01:35 PM, Eiran Vadim Harel wrote:
> It still does not find the file.
>
>
> [shimshon:TrioTim-35101-20120912-135155-195000] (nmr-stable5.0-env)
> recon-all -i
> ./cluster/archive/301/siemens/
It still does not find the file.
[shimshon:TrioTim-35101-20120912-135155-195000] (nmr-stable5.0-env)
recon-all -i
./cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358
-i
./cluster/archive/301/siemens/TrioTim-35101-20120912-1
/cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358
On 09/14/2012 01:01 PM, Eiran Vadim Harel wrote:
> Hi,
>
> 3 T1_MPRAGE_sag_short 3.39 2430 7 unknown ROW 190
> /cluster/archive/301/siemens/TrioTim-35101-20120912-135155-1
Hi,
3 T1_MPRAGE_sag_short 3.39 2430 7 unknown ROW 190
/cluster/archive/301/siemens/TrioTim-35101-20120912-135155-195000/MR.1.3.12.2.1107.5.2.32.35101.3.2012091214284986179598358
This is what it gives me when i do dcmunpack. What shall i use as the file
indicator in the recon-all -i ./
Thank
You'll need to run dcmunpack without the -martinos flag. This will
(eventually) give you a list of runs and corresponding file names. Find
the one that is the MPRAGE you want to recon, and pass that as -i to
recon-all. Unfortunately the name change makes it harder/slower to
unpack data here.
do
Hi all,
Is there a change in the unpacking of the MPRAGE and DICOM files?
The names of the files have changed.
what file name should be put in the command:
recon-all -i./file name -s subjectname
Thanks,
Eiran
___
Freesurfer mailing list
Freesurfer@nmr.mgh
hi everyone
thank you very much for your help; i've sent the link to the
Administrator of the grid and wil have the answer tomorow
thank you again
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard
Laouchedi,
The log says the file name is too long perhaps because of the tmp dir file
names.
Allison
On Mon, 2 Jan 2012, LAOUCHEDI MAKHLOUF wrote:
hi everyone
i run recon-all on 200 subjects on a cloud system and i
had the following message :
mp
hi everyone
i run recon-all on 200 subjects on a cloud system and i had
the following message :
mpr2mni305 failed, see transforms/talairach_avi.log
so i attached the corresponding log to this message. does anyone have an idea
of the error
thanks
i looked in the .bashrc file and it is written :
FREESURFER_HOME=/home/amesse/software/freesurfer5.1 ;
but freesurfer is installed in another account to which i have no
access for the moment. i'll see it on monday
thank you michael
___
Freesu
what does the file transforms/talairach_avi.log say?
and are those pathnames real? or something the email added?
n.
On Wed, 2011-12-28 at 17:08 +, LAOUCHEDI MAKHLOUF wrote:
>
> Hi everyone
>
> I run freesurfer recon-all command with the flag -all and I have this
> error
>
>
> ERROR:mpr
Hi everyone
I run freesurfer recon-all command with the flag -all and I have this error
ERROR:mpr2mni305 failed, see transforms/talairach_avi.log
Some one have any idea?
Thanks
this is the whole process:
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK
Hi Vanessa,
Is sparseg a directory? Try pointing it at one of the dcm files from that set .
Best Martin
On May 12, 2011, at 8:21 PM, Vanessa Lim wrote:
> Hi,
>
>
>
> I have files from Siemen's Skyra which I have used MRI_Convert to nii
>
> I have tried using just the dicom files as well as
can you send us the command line you are using?
Bruce
On Fri, 13 May 2011, Vanessa
Lim wrote:
> Hi,
>
>
>
> I have files from Siemen's Skyra which I have used MRI_Convert to nii
>
> I have tried using just the dicom files as well as changing the files to
> *.nii.gz but I still get the error
>
>
Hi,
I have files from Siemen's Skyra which I have used MRI_Convert to nii
I have tried using just the dicom files as well as changing the files to
*.nii.gz but I still get the error
corRead(): can't open file
/home/virtualuser/apps/freesurfer/subjects/SPARSEG/COR-.info
$Id: mri_convert.c,v 1
Janani,
For the Failure Detection error, please take a look here:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F
and
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07958.html
For your other ques
I'm looking through it and also looking at tkregister2 help, and I have some
questions
1)Does Recon only work on fully structural data? If you have funtional
information on it will recon fail?
2)Also- Does it matter what the files are named... for ex- if the first 50
are named JohnSmith_001_01_01.i
Hi Jan,
the place to look at is
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Best,
Martin
On Tuesday 30 March 2010 12:30:35 Janani Dhinakaran wrote:
> Hello everyone,
> I wanted to know what I can do to fix this error- it occurs when I'm
> running recon-all -all -s Subject
>
Hello everyone,
I wanted to know what I can do to fix this error- it occurs when I'm running
recon-all -all -s Subject
Tue Mar 30 11:27:20 BST 2010
talairach_avi done
#
#...@# Talairach Failure Detection Tue Mar 30 11:27:20 BST 2010
/home/s0964091/Deskto
n-all? is there any way to put the background to zero?
Best
Gabriel
Date: Tue, 22 Dec 2009 10:51:16 -0500
From: fis...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Subject: RE: [Freesurfer] recon-all problem
Hi Gabriel,
can you post this type of question to the list so others can answe
check the talairach and the intensity normalization (T1.mgz) to make sure
they both succeeded. One or the other may need to be corrected.
cheers,
Bruce
On Tue, 22 Dec
2009, Gabriel Go.Es. wrote:
Dear Fs experts
I'm trying to run a recon-all on one subject but FS gives me the followin
Dear Fs experts
I'm trying to run a recon-all on one subject but FS gives me the following
error message:
#...@# Skull Stripping Mon Dec 21 17:25:55 CET 2009
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006
x86_64 x86_64 x86_64 GNU/Linux
recon-all exite
what version are you running? What was your recon-all command line?
On Thu,
6 Apr 2006, Nguyen, Thang Q wrote:
Hello all,
I'm not sure if this is a problem with the incorporation of the mgz
format or not but when I run recon-all, the skull stripping step
requests for COR-.info files. The onl
Hello all,
I'm not sure if this is a problem with the incorporation of the mgz
format or not but when I run recon-all, the skull stripping step
requests for COR-.info files. The only format that I have in the mri
folder is the mgz format. Is there an override option that tells
recon-all that I am
Paul,
Which machine did this run on?
Nick
On Tue, 2005-09-06 at 13:55 -0400, Paul Aparicio wrote:
> Hello all,
>
> I run recon-all and get this problem:
>
> -
> Nu Intensity Correction Tue Sep 6 13:04:59 EDT 2005
> mri_convert orig nu0.mnc
> mri_co
Hello all,
I run recon-all and get this problem:
-
Nu Intensity Correction Tue Sep 6 13:04:59 EDT 2005
mri_convert orig nu0.mnc
mri_convert orig nu0.mnc
reading from orig...
TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00
i_ras = (-1, -0, 0)
j_ras =
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