subject:"\[Freesurfer\] Recon\-all problem"

Re: [Freesurfer] FREESURFER Recon all problem

2021-11-28 Thread Douglas N. Greve

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 skip/ignore those 
seemingly blank files or should i delete them from the folder?


Thanks
error_message.png

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[Freesurfer] FREESURFER Recon all problem

2021-11-25 Thread Alison McDonnell

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 skip/ignore those seemingly blank files or should
i delete them from the folder?

Thanks
[image: error_message.png]
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Re: [Freesurfer] Recon-all problem

2016-02-28 Thread Mohamed Ali Bahri

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 installed 
> properly then recon-all works perfectly. Maybe make sure everything that was 
> required from installation has been done. Or try it again?
>
>> On 28 Feb 2016, at 11:17, Mohamed Ali Bahri  wrote:
>>
>> Can't locate MNI/Startup.pm in @INC (you may need to install the 
>> MNI::Startup module)
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University of Liège, Belgium
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Re: [Freesurfer] Recon-all problem

2016-02-28 Thread Maheen Siddiqui

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 again?

> On 28 Feb 2016, at 11:17, Mohamed Ali Bahri  wrote:
> 
> Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
> module)

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[Freesurfer] Recon-all problem

2016-02-28 Thread Mohamed Ali Bahri

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 CET 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.20504/nu0.mnc 
./tmp.mri_nu_correct.mni.20504/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.20504/0/ -iterations 1000 -distance 50
Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup 
module) (@INC contains: /usr/local/freesurfer/mni/share/perl5 /etc/perl 
/usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 
/usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 
/usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37.
BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct 
line 37.
ERROR: nu_correct

-- 
Dr. Mohamed Ali Bahri,
1er Logisticien de Recherche,
Cyclotron Research Centre,
University of Liège, Belgium
m.ba...@ulg.ac.be

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Re: [Freesurfer] recon all problem

2014-04-22 Thread Bruce Fischl


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 Miller wrote:


Hi Freesurfer Experts,

I seem to be having some difficulty with reconing a healthy young adult. I
have tried running this on multiple different computers and multiple
different versions (5.3 and 5.1) and all return the same weird recon (see
attached image). I have used the same sequence and commands on another
subject and the recon returned fine.

This participant did not have excess motion and the orig.mgz file looks
fine. Please let me know if there is any more information I could provide
that would be of use.

Commands used:

5.3:
recon-all -all -FLAIR (FLAIR image) -subjid (SUBJID) -FLAIRpial
-hippo-subfields
recon-all -all -subjid (SUBJID)

5.1:
recon-all -all -subjid (SUBJID) -hippo-subfields
recon-all -all -subjid (SUBJID)

Thanks,
Danielle Miller
--
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118


VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave  D11-103
Boston, MA 02130
OFFICE:(857) 364-2130


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Re: [Freesurfer] Recon-all problem

2013-11-19 Thread Z K

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 
Xubuntu (Linux) disk image with the freesurfer centOS4 build installed 
on top of it.

That said, if you upload your data I will attempt to recreate the issue 
you are experiencing. I can not promise a solution will be found but if 
something obvious jumps out at me I will provide the best advice I can 
on how to resolve the matter.

-Zeke

On 11/15/2013 05:02 PM, Devin Sodums wrote:
 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 after
 the mri_nu_correct.mni step, without any specific error message.  I
 have copied and pasted the error message from the unsuccessful, and
 successful run below, as well as the output from the bugr command.  I
 realize that tcsh is out of date, and I have tried updating it (which I
 am not sure if I was successful or not), but I got the same message with
 the successful run so I don't think that is the issue.  Any suggestions
 would be greatly appreciated.

 Best,
 Devin

 General info:

 fsuser@xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/b_s_20131018_124417$
 which freesurfer

 /usr/local/freesurfer/bin/freesurfer

 FREESURFER_HOME: /usr/local/freesurfer

 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 Debian version: wheezy/sid

 Kernel info: Linux 3.2.0-56-generic i686

 **

 *Unsuccessful Run:*

 xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/boucher_suzanne_20131018_12
 4417 recon-all -subjid b_s_20131018_fs -all

 WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0

 INFO: SUBJECTS_DIR is
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417

 Actual FREESURFER_HOME /usr/local/freesurfer

 Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux

 #

 #@# MotionCor Fri Nov 15 16:30:12 EST 2013

 Found 1 runs

 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz

 Checking for (invalid) multi-frame inputs...

 WARNING: only one run found. This is OK, but motion

 correction cannot be performed on one run, so I'll

 copy the run to rawavg and continue.

   cp
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz


 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs

   mri_convert
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
 --conform

 mri_convert
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
 --conform

 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

 reading from
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz...

 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

 i_ras = (0.0156845, -0.970744, 0.239606)

 j_ras = (0.0185749, 0.239877, 0.970626)

 k_ras = (0.999704, 0.0107731, -0.0217938)

 Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.

 Data is conformed to 1 mm size and 256 voxels for all directions

 changing data type from float to uchar (noscale = 0)...

 MRIchangeType: Building histogram

 Reslicing using trilinear interpolation

 writing to
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz...

   mri_add_xform_to_header -c
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/transforms/talairach.xfm
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz


 INFO: extension is mgz

 #

 #@# Talairach Fri Nov 15 16:30:45 EST 2013

 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri

   mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
 --i orig.mgz --o orig_nu.mgz

 Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
 17:31:43 UTC 2013 i686 i686 i386

[Freesurfer] Recon-all problem

2013-11-15 Thread Devin Sodums

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 after the mri_nu_correct.mni step, 
without any specific error message.  I have copied and pasted the error message 
from the unsuccessful, and successful run below, as well as the output from the 
bugr command.  I realize that tcsh is out of date, and I have tried updating 
it (which I am not sure if I was successful or not), but I got the same message 
with the successful run so I don't think that is the issue.  Any suggestions 
would be greatly appreciated.

Best,
Devin

General info:
fsuser@xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/b_s_20131018_124417$
 which freesurfer
/usr/local/freesurfer/bin/freesurfer
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Debian version: wheezy/sid
Kernel info: Linux 3.2.0-56-generic i686

Unsuccessful Run:
xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/boucher_suzanne_20131018_12
 4417 recon-all -subjid b_s_20131018_fs -all
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 
UTC 2013 i686 i686 i386 GNU/Linux
#
#@# MotionCor Fri Nov 15 16:30:12 EST 2013
Found 1 runs
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
 cp 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz
 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs
 mri_convert 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz
 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
 --conform

mri_convert 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz
 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
 --conform
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.0156845, -0.970744, 0.239606)
j_ras = (0.0185749, 0.239877, 0.970626)
k_ras = (0.999704, 0.0107731, -0.0217938)
Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz...

 mri_add_xform_to_header -c 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/transforms/talairach.xfm
 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz
 
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz

INFO: extension is mgz
#
#@# Talairach Fri Nov 15 16:30:45 EST 2013
/home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 
UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s b_s_20131018_fs exited with ERRORS at Fri Nov 15 16:30:58 EST 2013

SUCCESSFUL RUN:

INFO: extension is mgz
#
#@# Talairach Fri Nov 15 15:53:35 EST 2013
/usr/local/freesurfer/subjects/bert/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz
 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
INFO: transforms/talairach.xfm already exists!
The new transforms/talairach.auto.xfm will not be copied to 
transforms/talairach.xfm
This is done to retain any edits made to transforms/talairach.xfm
Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
#
#@# Talairach Failure Detection Fri Nov

[Freesurfer] recon-all problem

2012-09-14 Thread Eiran Vadim Harel

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
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Re: [Freesurfer] recon-all problem

2012-09-14 Thread Douglas N Greve

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.
doug

On 09/14/2012 11:06 AM, Eiran Vadim Harel wrote:
 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
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] recon-all problem

2012-09-14 Thread Eiran Vadim Harel

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 ./
Thanks!
eiran

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.
doug

On 09/14/2012 11:06 AM, Eiran Vadim Harel wrote:
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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] recon-all problem

2012-09-14 Thread Douglas N Greve

/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,