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
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
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
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
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 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
>
>
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
>
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
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
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
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