[Freesurfer] [Freesurfer/Freeview cutting]

[Dave Yas]

Hello,

Can we cut the surface (for flatting later) in freeview? if yes, how? I cant 
find a tutorial online for that.
tksurfer is not working, it crashes by it self. If i cant use freeview to cut, 
do you suggest another alternative?

thank you
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Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Kaushal, Mayank]

Your inputs have been very helpful.

Looking at the examples on LME webpage, the contrast for both univariate and 
mass-variate creates 3 rows with 14 columns for univariate and 17 for 
mass-variate analysis. My understanding is that 3 rows have been created 
because there are 4 groups being analyzed and applying that rationale to my 
data would mean that the contrast for my analysis would require 2 rows since I 
comparing 3 groups. Is my logic correct here?

So, for my analysis if I want to include two random effects, namely, intercept 
and time_from_base_scan, which are given in Column 1 and 2, respectively, the 
contrasts based on M having 6 columns would as follows:
CM.C = [1 1 ; 1 1] zeros(2,4)];
or
CM.C = [1 1 0 0 0 0; 1 1 0 0 0 0]

Mayank
On Mar 7, 2018, at 3:33 PM, Diers, Kersten /DZNE 
mailto:kersten.di...@dzne.de>> wrote:

ATTENTION: This email originated from a sender outside of MCW. Use caution when 
clicking on links or opening attachments.


Hi,

let me just mention that my previous comments were directed at the
design matrix X and not necessarily at the QDEC table. In that sense,
it is possible, but not necessary to modify the QDEC table prior to
loading it into Matlab. Alternatively, one might do these modifications
within Matlab, although this would require some additional manual
coding.

For the present analysis, however, the current qdec table looks fine.


About question 1:

If I understood correctly, you have so far loaded the (modified) QDEC
table and stored the extracted information within the matlab variable
'M'.

In addition to that you'd also need to sort the data within each
subject according to time, and load 'Y', 'lhcortex' and possibly
'lhsphere'. For a description of all of these steps please see the
"mass-univariate" section of the example data analysis on the tutorial
page.


About question 2:

Just to be precise, I assume that for this particular case the matlab
variable 'M' contains the following four columns: time-from-baseline,
age-at-baseline, group2, group3; where 'group2' and 'group3' indicate
memberships in groups 2 and 3, respectively.

Then, a design matrix can be created as follows:

X = [ones(length(M),1) M M(:,1).*M(:,3) M(:,1).*M(:,4)];

Then the order of the columns of X is: intercept, time-from-baseline,
age-at-baseline, group2, group3, time-from-baseline*group2, time-from-
baseline*group3.

Let's keep in mind that the order of columns in X is important for the
formulation of contrasts at a later stage (and is different from the
tutorial example).

Again, this procedure and the matrices M and X are specific for this
particular analysis scenario and cannot necessarily be generalized to
others.

Best regards,

Kersten


-Original Message-
From: "Kaushal, Mayank" mailto:mkaus...@mcw.edu>>
Reply-to: Freesurfer support list 
To: Freesurfer support list 
Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
Date: Wed, 7 Mar 2018 15:48:36 +0100

I have made the suggested edits and would appreciate if you could take
a look at the qdec.table.dat file attached to this conversation.

After going over the univariate example on the Freesurfer LME webpage,
I had a couple of questions.

1. How will data be loaded into Matlab? More specifically, what would
be the step(s) after the line M = Qdec2num(Qdec);?

2. Given that column named time_base_scan would be multiplied with
column named group2 as well as group3, what will be the equation for
creating the design matrix?
X = [ones(length(M),1) M M(:,).*M(:,)];


Mayank
On Mar 7, 2018, at 7:14 AM, Diers, Kersten /DZNE  wrote:

ATTENTION: This email originated from a sender outside of MCW. Use
caution when clicking on links or opening attachments.


Hi Mayank,

I may have a few more general considerations before commenting on the
number and kind of random effects.

In the current design matrix, column 2 (time from baseline) and
column
5 (visit) will be quite redundant. It is one of the advantages of the
LME model to be able to deal with unevenly spaced observation
intervals
and also with possibly missing visits. In that sense, all temporal
information is already contained within column 2, and I cannot see a
good reason to additionally include column 5. It may even complicate
things, due to the redundancy.

If you have 3 groups, you will need two columns in the design matrix
to
indicate group membership (assuming that an intercept column is also
present). Choose one group (say, group 1) as the reference group,
which
will not explicitly be coded, and then use one of the two group
columns
to indicate if a person belongs to group 2 (1=yes, 0=no), and the
other
to indicate if a person belongs to group 3 (1=yes, 0=no).

Please don't code group membership numerically as 1, 2, 3 in a single
column, as this will impose a linear relation between group
membership
and outcome measure (similar to linear regression).

I am not sure about the current meaning o

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Diers, Kersten /DZNE]

Hi,

let me just mention that my previous comments were directed at the
design matrix X and not necessarily at the QDEC table. In that sense,
it is possible, but not necessary to modify the QDEC table prior to
loading it into Matlab. Alternatively, one might do these modifications
within Matlab, although this would require some additional manual
coding.

For the present analysis, however, the current qdec table looks fine.


About question 1:

If I understood correctly, you have so far loaded the (modified) QDEC
table and stored the extracted information within the matlab variable
'M'.

In addition to that you'd also need to sort the data within each
subject according to time, and load 'Y', 'lhcortex' and possibly
'lhsphere'. For a description of all of these steps please see the
"mass-univariate" section of the example data analysis on the tutorial
page.


About question 2:

Just to be precise, I assume that for this particular case the matlab
variable 'M' contains the following four columns: time-from-baseline,
age-at-baseline, group2, group3; where 'group2' and 'group3' indicate
memberships in groups 2 and 3, respectively.

Then, a design matrix can be created as follows:

X = [ones(length(M),1) M M(:,1).*M(:,3) M(:,1).*M(:,4)];

Then the order of the columns of X is: intercept, time-from-baseline,
age-at-baseline, group2, group3, time-from-baseline*group2, time-from-
baseline*group3.

Let's keep in mind that the order of columns in X is important for the
formulation of contrasts at a later stage (and is different from the
tutorial example).

Again, this procedure and the matrices M and X are specific for this
particular analysis scenario and cannot necessarily be generalized to
others.

Best regards,

Kersten


-Original Message-
From: "Kaushal, Mayank" 
Reply-to: Freesurfer support list 
To: Freesurfer support list 
Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
Date: Wed, 7 Mar 2018 15:48:36 +0100

I have made the suggested edits and would appreciate if you could take
a look at the qdec.table.dat file attached to this conversation.

After going over the univariate example on the Freesurfer LME webpage,
I had a couple of questions.

1. How will data be loaded into Matlab? More specifically, what would
be the step(s) after the line M = Qdec2num(Qdec);?

2. Given that column named time_base_scan would be multiplied with
column named group2 as well as group3, what will be the equation for
creating the design matrix?
X = [ones(length(M),1) M M(:,).*M(:,)];


Mayank
> On Mar 7, 2018, at 7:14 AM, Diers, Kersten /DZNE  de> wrote:
>
> ATTENTION: This email originated from a sender outside of MCW. Use
> caution when clicking on links or opening attachments.
> 
>
> Hi Mayank,
>
> I may have a few more general considerations before commenting on the
> number and kind of random effects.
>
> In the current design matrix, column 2 (time from baseline) and
> column
> 5 (visit) will be quite redundant. It is one of the advantages of the
> LME model to be able to deal with unevenly spaced observation
> intervals
> and also with possibly missing visits. In that sense, all temporal
> information is already contained within column 2, and I cannot see a
> good reason to additionally include column 5. It may even complicate
> things, due to the redundancy.
>
> If you have 3 groups, you will need two columns in the design matrix
> to
> indicate group membership (assuming that an intercept column is also
> present). Choose one group (say, group 1) as the reference group,
> which
> will not explicitly be coded, and then use one of the two group
> columns
> to indicate if a person belongs to group 2 (1=yes, 0=no), and the
> other
> to indicate if a person belongs to group 3 (1=yes, 0=no).
>
> Please don't code group membership numerically as 1, 2, 3 in a single
> column, as this will impose a linear relation between group
> membership
> and outcome measure (similar to linear regression).
>
> I am not sure about the current meaning of column 6, which multiplies
> age and time-from-baseline. It would be more important, in my eyes,
> to
> multiply time-from-baseline and group membership. Considering my
> second
> comment, this will also result in two colums. These will indicate
> whether or not the effect of time will differ between groups, and
> this
> (=different longitudinal trajectory) is often the primary interest in
> longitudinal studies.
>
> As far as I can see, your overall design is somewhat similar to the
> univariate example on the Freesurfer LME webpage, except that you
> have
> fewer groups and fewer covariates. As it does not matter for the
> design
> matrix whether or not the overall study is univariate or mass-
> univariate (as in your case), one suggestion would be that you
> construct your design in a similar way as in the given example.
>
> I hope that I have understood your design correctly, otherwise let me
> know.
>
> Best regards,
>
> Kersten
>
> 

Re: [Freesurfer] Installation problem

[Hoopes, Andrew]

Hi Neda,

What’s going on exactly? Is the source command hanging or is it repeatedly 
printing the freesurfer startup message?

best
Andrew



On March 7, 2018 at 3:03:38 AM, Neda Mohammadi 
(n55moham...@gmail.com) wrote:

Dear Expert,

I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:

1. Download and extract into the directory /usr/local
2.export FREESURFER_HOME=/usr/local/freesurfer

Its fine, but when I run this step

3.source $FREESURFER_HOME/SetUpFreeSurfer.sh

I receive this message n time

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Work/Processed_data/freesurfer
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0

and I must press Ctrl+C to stop.
What do I do now?

--
Best Regards,
Neda
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[Freesurfer] Jin, David S. wants to share the file alreadyexists_recon-all.log with you

[Jin, David S.]

To view alreadyexists_recon-all.log, sign 
in
 or create an account.
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Re: [Freesurfer] lh.BA_exvivo.annot Already Exists Error

[Jin, David S.]

Jin, David S. has shared a OneDrive for Business file with you. To view it, 
click the link below.



[https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]

alreadyexists_recon-all.log




Hi,

The command submitted was:


recon-all -autorecon2 -autorecon3 -subjid D31223 -openmp 4


The screen output was:


ERROR: /home/david/Desktop/JSS_FSnew/test_8core/D31223/label/lh.BA_exvivo.annot 
already exists

Linux locke 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 
2015 x86_64 x86_64 x86_64 GNU/Linux



I have attached recon-all.log as "alreadyexists_recon-all.log"



Many thanks,

David










From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Wednesday, March 7, 2018 2:09:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] lh.BA_exvivo.annot Already Exists Error

Hi David

can you send us the full command line, screen output and recon-all.log?

cheers
Bruce
On
Wed, 7 Mar 2018, Jin, David S. wrote:

>
> Hi,
>
> On our machine, with FS6, when we try to run recon-all, FS throws an error of 
> "lh.BA_exvivo.annot
> already exists" . However, upon deleting lh.BA_exvivo.annot, it still gives 
> the same error. Has
> anybody else encountered this?
>
>
>
>
>
> Many thanks,
>
> David
>
>
>
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Freesurfer Info Page - Harvard 
University
mail.nmr.mgh.harvard.edu
To see the collection of prior postings to the list, visit the Freesurfer 
Archives. A searchable archive which of messages PRIOR to March 2004 is at ...



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Re: [Freesurfer] Collecting 2 T1s Best?

[Bruce Fischl]

Hi Alessandra

it's really an empirical question. If 1 image has sufficient SNR/CNR, 
then adding a second doesn't always help (as it induces some 
blurring due to interpolation). But if your single image is noisy, which it 
might be at 0.8 iso, then a second will help. You might try it on one or 
two subjects and see what you think. An alternative, if you are not already 
getting them, would be a T2-space or FLAIR T2-space, which can help avoid 
dura and such


cheers
Bruce

On Wed, 7 Mar 2018, Alessandra Macbeth wrote:


Hi there,
I know in the past, it was recommended to acquire 2 T1 scans so that they could 
be averaged for
better SNR, etc. in order to improve cortical thickness and surface area 
measurements. Is this still
the recommendation? We have a few extra minutes in our scanning protocol and 
are debating whether to
include a 2nd T1.

Our parameters are: MPRAGE with .8mm^3 voxel size, slice thickness of .8, FA = 
8 degrees, TR =
2400ms, TE = 2.72ms, TI = 1060ms.

Best,
Alessandra

--
Alessandra Macbeth, M.A.
Doctoral Candidate - Department of PsychologyUniversity of California, Riverside

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Re: [Freesurfer] Collecting 2 T1s Best?

[Glasser, Matthew]

Are you getting a 0.8mm isotropic T2w or FLAIR?  You would probably get better 
mileage out of a different type of scan that can help exclude dura and blood 
vessels if you aren’t already getting one.  Also what coil are you using?  I 
might prefer a TI=1000ms simply because it spreads the CSF, GM, and WM 
histogram peaks out a little more evenly, whereas 1060 will have GM and WM 
closer together than GM and CSF.

Peace,

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Alessandra Macbeth 
mailto:alessandramacb...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, March 7, 2018 at 1:29 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Collecting 2 T1s Best?

Hi there,

I know in the past, it was recommended to acquire 2 T1 scans so that they could 
be averaged for better SNR, etc. in order to improve cortical thickness and 
surface area measurements. Is this still the recommendation? We have a few 
extra minutes in our scanning protocol and are debating whether to include a 
2nd T1.

Our parameters are: MPRAGE with .8mm^3 voxel size, slice thickness of .8, FA = 
8 degrees, TR = 2400ms, TE = 2.72ms, TI = 1060ms.

Best,
Alessandra

--
Alessandra Macbeth, M.A.
Doctoral Candidate - Department of Psychology
University of California, Riverside
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Collecting 2 T1s Best?

[Alessandra Macbeth]

Hi there,

I know in the past, it was recommended to acquire 2 T1 scans so that they
could be averaged for better SNR, etc. in order to improve cortical
thickness and surface area measurements. Is this still the recommendation?
We have a few extra minutes in our scanning protocol and are debating
whether to include a 2nd T1.

Our parameters are: MPRAGE with .8mm^3 voxel size, slice thickness of .8,
FA = 8 degrees, TR = 2400ms, TE = 2.72ms, TI = 1060ms.

Best,
Alessandra

-- 
Alessandra Macbeth, M.A.
Doctoral Candidate - Department of Psychology
University of California, Riverside
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Re: [Freesurfer] lh.BA_exvivo.annot Already Exists Error

[Bruce Fischl]

Hi David

can you send us the full command line, screen output and recon-all.log?

cheers
Bruce
On 
Wed, 7 Mar 2018, Jin, David S. wrote:

> 
> Hi,
> 
> On our machine, with FS6, when we try to run recon-all, FS throws an error of 
> "lh.BA_exvivo.annot
> already exists" . However, upon deleting lh.BA_exvivo.annot, it still gives 
> the same error. Has
> anybody else encountered this?
> 
> 
> 
> 
> 
> Many thanks,
> 
> David
> 
> 
>
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[Freesurfer] -qcache error

[Krishna Patel]

Hi - I would like to do group analysis on freesurfer data that is processed
with verson 6. However when I try to run

recon-all -s subjid -qcache

I get following error after it runs for some time and generates some of the
files.

 ERROR: cannot find surf/lh.white.K

When I look at the log file - I see that this file was deleted. See
following.


total integrated curvature = -1.022*4pi (-12.846) --> 2 handles
ICI = 169.4, FI = 1785.3, variation=28139.036
writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K


Does anyone have any idea of what might be the issue here?

Thanks,
-Krishna
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[Freesurfer] lh.BA_exvivo.annot Already Exists Error

[Jin, David S.]

Hi,

On our machine, with FS6, when we try to run recon-all, FS throws an error of 
"lh.BA_exvivo.annot already exists" . However, upon deleting 
lh.BA_exvivo.annot, it still gives the same error. Has anybody else encountered 
this?





Many thanks,

David
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Re: [Freesurfer] FSdev compilation error

[Hoopes, Andrew]

Hi Victor,

Can you send over the config.log? Also, it’s probably worth noting that the 
cuda dev builds are currently failing due to recent mrisurf.c changes (working 
on fixing this now), so if you’re trying to resolve this as soon as possible, 
it might make sense to checkout and build an older version.

best
Andrew



On March 7, 2018 at 12:13:12 PM, Victor Hansen 
(victor.han...@nru.dk) wrote:

Hello Bruce

I am the one inputting the commands - thanks for your tip about MNI libraries, 
I managed to point it towards the right location for them.
However, the "make" step is now complaining about the PetSC libraries: 
https://paste.ubuntu.com/p/68G4sBB7DK/
I have tried to point it towards the local libraries with --with-petsc= but 
then ./configure complains that it can't find them at all.
Thank you for your help.
--
Best regards
Victor Hansen
IT support
Neurological Research Unit, Rigshospitalet
nru.dk

On Wed, 2018-03-07 at 10:24 -0500, Bruce Fischl wrote:

Hi Mel (and Victor?)

the missing functions are all from the MNI lib. Not sure what you are
missing. Maybe Andrew (ccd)  knows?

cheers
Bruce


On Wed, 7 Mar 2018, Melanie Ganz wrote:



Dear list,   In order to use a brandnew Nvidia GPU we downloaded FSdev and are 
trying to compile it locally with a new CUDA version. We get all the way to the 
configure command described on 
http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page  
which is:   ./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1 
--with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages 
--enable-fermi-gpu --libdir=/usr/lib64   Then there are no errors about any 
libraries, but instead errors about "undefined reference" in the files 
utils/mri.c and utils/mriio.c (see error below). I searched in the archives and 
couldn’t find anything about this. Any ideas?   Cheers, Mel   make[2]: Entering 
directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm' /bin/sh ../libtool 
 --tag=CC   --mode=link g++ -I../include  -fdata-sections -ffunction-sections 
-Wl,--gc-sections 
-L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib 
-L/usr/lib64 -L/usr/X11R6/lib64  -fopenmp -fdata-sections -ffunction-sections 
-Wl,--gc-sections -Wl,-Map,ld_map.txt-Wl,--no-demangle
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib  
-L/data2/Ganz/FSdev/freesurfer/ce 
ntos6-x86_64-packages/itk/current/lib/InsightToolkit  -o mri_gdfglm 
mri_gdfglm.o fsgdf.o ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a 
../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a 
../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a 
../expat/libexpat.a ../minc_1_5_1/libminc_1_5_1.a 
../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a
   /data2/Ganz/FSdev/freesurfer/ 
centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packa 
ges/itk/current/lib/InsightToolkit/libITKCommon.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insi 
ghtToolkit/libITKNumerics.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaI
 O.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a
   /data2/Ganz/FSdev 
/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a
   /data2/Ganz/FSdev/freesurfer/centos6-x86_ 
64-packages/itk/current/lib/InsightToolkit/libitkpng.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib 
/InsightToolkit/libitksys.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.
 a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a
   /data2/Ganz/FSde 
v/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a
   /data2/Ganz/FSdev/freesurfer/centos6-x86_6 
4-packages/itk/current/lib/InsightToolkit/libitkgdcm.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib 
/InsightToolkit/libitkopenjpeg.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitk
 jpeg8.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a
   /data2/Ganz/FS 
dev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a
   /data2/Ganz/FSdev/freesurfer/centos6-x 
86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a 
/usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl -lpthread  -lvnl_algo -lvnl 
-lvcl -lnetlib -lv3p_netlib  libtool: link: g++ -I../include -fdata-sections 
-ffunction-sections -Wl,--gc-sections -fopenmp -fdata-sections 
-ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle 
-o mri_gdfglm mri_gdfglm.o fsgdf.o /u

Re: [Freesurfer] FSdev compilation error

[Bruce Fischl]

Hi Mel (and Victor?)

the missing functions are all from the MNI lib. Not sure what you are 
missing. Maybe Andrew (ccd)  knows?


cheers
Bruce


On Wed, 7 Mar 2018, Melanie Ganz wrote:



Dear list,

 

In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to 
compile it locally with a new CUDA version. We get
all the way to the configure command described on 
http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
 which is:

 

./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1
--with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages 
--enable-fermi-gpu --libdir=/usr/lib64

 

Then there are no errors about any libraries, but instead errors about "undefined 
reference" in the files utils/mri.c and
utils/mriio.c (see error below). I searched in the archives and couldn’t find 
anything about this. Any ideas?

 

Cheers,

Mel

 

make[2]: Entering directory '/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm'

/bin/sh ../libtool  --tag=CC   --mode=link g++ -I../include  -fdata-sections 
-ffunction-sections -Wl,--gc-sections
-L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib 
-L/usr/lib64 -L/usr/X11R6/lib64  -fopenmp
-fdata-sections -ffunction-sections -Wl,--gc-sections 
-Wl,-Map,ld_map.txt-Wl,--no-demangle
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib  
-L/data2/Ganz/FSdev/freesurfer/ce
ntos6-x86_64-packages/itk/current/lib/InsightToolkit  -o mri_gdfglm 
mri_gdfglm.o fsgdf.o ../utils/libutils.a
../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a 
../hipsstubs/libhipsstubs.a ../log/liblog.a
../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a 
../minc_1_5_1/libminc_1_5_1.a
../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a
   /data2/Ganz/FSdev/freesurfer/
centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packa
ges/itk/current/lib/InsightToolkit/libITKCommon.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insi
ghtToolkit/libITKNumerics.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKMetaI
O.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKniftiio.a
   /data2/Ganz/FSdev
/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNrrdIO.a
   /data2/Ganz/FSdev/freesurfer/centos6-x86_
64-packages/itk/current/lib/InsightToolkit/libitkpng.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib
/InsightToolkit/libitksys.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitktiff.
a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkv3p_netlib.a
   /data2/Ganz/FSde
v/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkzlib.a
   /data2/Ganz/FSdev/freesurfer/centos6-x86_6
4-packages/itk/current/lib/InsightToolkit/libitkgdcm.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib
/InsightToolkit/libitkopenjpeg.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitk
jpeg8.a   
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg12.a
   /data2/Ganz/FS
dev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libitkjpeg16.a
   /data2/Ganz/FSdev/freesurfer/centos6-x
86_64-packages/itk/current/lib/InsightToolkit/libITKDICOMParser.a 
/usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl
-lpthread  -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib 

libtool: link: g++ -I../include -fdata-sections -ffunction-sections 
-Wl,--gc-sections -fopenmp -fdata-sections
-ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle 
-o mri_gdfglm mri_gdfglm.o fsgdf.o
/usr/lib64/libuuid.so  
-L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/lib 
-L/usr/lib64
-L/usr/X11R6/lib64 
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit
 ../utils/libutils.a ../fsgdf/libfsgdf.a
../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a 
../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a
../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a 
../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKAlgorithms.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKCommon.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/InsightToolkit/libITKNumerics.a
/data2/Ganz/FSdev/freesurfer/centos6-x8

[Freesurfer] FSdev compilation error

[Melanie Ganz]

Dear list,

 

In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to
compile it locally with a new CUDA version. We get all the way to the
configure command described on
http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
which is: 

 

./configure --disable-Werror --with-cuda=/usr/local/cuda-9.1
--with-pkgs-dir=/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages
--enable-fermi-gpu --libdir=/usr/lib64

 

Then there are no errors about any libraries, but instead errors about
"undefined reference" in the files utils/mri.c and utils/mriio.c (see error
below). I searched in the archives and couldn't find anything about this.
Any ideas?

 

Cheers,

Mel

 

make[2]: Entering directory
'/indirect/data2/Ganz/FSdev/freesurfer/mri_gdfglm'

/bin/sh ../libtool  --tag=CC   --mode=link g++ -I../include  -fdata-sections
-ffunction-sections -Wl,--gc-sections
-L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/l
ib -L/usr/lib64 -L/usr/X11R6/lib64  -fopenmp -fdata-sections
-ffunction-sections -Wl,--gc-sections -Wl,-Map,ld_map.txt -Wl,--no-demangle
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insig
htToolkit  -o mri_gdfglm mri_gdfglm.o fsgdf.o ../utils/libutils.a
../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a
../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a
../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a
../minc_1_5_1/libminc_1_5_1.a ../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKAlgorithms.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKCommon.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKNumerics.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKMetaIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKniftiio.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKNrrdIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkpng.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitksys.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitktiff.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkv3p_netlib.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkzlib.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkgdcm.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkopenjpeg.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkjpeg8.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkjpeg12.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libitkjpeg16.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKDICOMParser.a /usr/lib64/libuuid.so -lrt -lz -lm -lcrypt -ldl
-lpthread  -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib 

libtool: link: g++ -I../include -fdata-sections -ffunction-sections
-Wl,--gc-sections -fopenmp -fdata-sections -ffunction-sections
-Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mri_gdfglm
mri_gdfglm.o fsgdf.o /usr/lib64/libuuid.so
-L/indirect/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/qt/current/l
ib -L/usr/lib64 -L/usr/X11R6/lib64
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/vxl/current/lib
-L/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insig
htToolkit ../utils/libutils.a ../fsgdf/libfsgdf.a ../rgb/librgb.a
../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a
../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a
../expat/libexpat.a ../minc_1_5_1/libminc_1_5_1.a
../netcdf_3_6_0_p1/libnetcdf_3_6_0_p1.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKAlgorithms.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKCommon.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKNumerics.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKMetaIO.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKniftiio.a
/data2/Ganz/FSdev/freesurfer/centos6-x86_64-packages/itk/current/lib/Insight
Toolkit/libITKNr

Re: [Freesurfer] Compatibility of subcortical and cortical segmentations between Version 5.3 and 6.0

[Bruce Fischl]

Hi Nils

no, in general we don't recommend this. It adds unneeded variance (and 
maybe bias).

cheers
Bruce


On Wed, 7 Mar 2018, Nils Opel wrote:

> Hi Freesurfer Developers,
>
> i am currently collecting structural imaging data from several large cohorts 
> that have been processed using different freesurfer versions (5.3 and 6.0).
>
> I would be interested on your experiences regarding compatibility between 
> both versions for subcortical and cortical segmentations.
>
> More specifically: would it be appropriate to include subcortical and 
> cortical measures derived from both freesurfer versions (5.3 and 6.0) in the 
> same analysis?
>
> Thanks a lot in advance and best regards,
> Nils
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trouble shooting: pial surface & wm hypointensities

[Bruce Fischl]

Hi Marie

hmmm, it's hard to see without seeing why it is happening. Maybe you can 
attach some images? Alternatively you can upload a  subject dir and give 
us the coordinates of the regions that are not as accurate as you would 
wish, and we will take a look.

cheers
Bruce
On Wed, 7 Mar 2018, Marie Sigmund wrote:

> 
> Hello FreeSurfer Developers,
> 
> I am trouble-shooting some FreeSurfer Data and there are two errors which 
> occur frequently.
> 
> 1. The pial surface does not include all of the graymatter. I read that you 
> should in this case corr
> ect the WM so it adjusts the GM automatically. I tried this out a couple of 
> times and there is still
>  some GM left over which is not included. 
> 
> 2. Gyri or sulci are sometimes labeled as wm-hypointensities. I thought about 
> correcting it on the a
> seg.presurf volume (on the website it is stated that using a FreeSurfer 
> version of 6.0 or higher you
>  should make corrections to the ASEG there). The problem is that on this 
> volume the segmentation is 
> different to the final one and not necessarily wrong. 
> 
> I've searched the list and no similar errors have been reported. Does anyone 
> have any thoughts on ho
> w to trouble-shoot this one? Thanks a lot!
> 
> 1) FreeSurfer version: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 2) uname -a: Linux R0223 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 
> 17:43:14 UTC 2015 x86_6
> 4 x86_64 x86_64 GNU/Linux
> 
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Diers, Kersten /DZNE]

Hi Mayank,

I may have a few more general considerations before commenting on the
number and kind of random effects.

In the current design matrix, column 2 (time from baseline) and column
5 (visit) will be quite redundant. It is one of the advantages of the
LME model to be able to deal with unevenly spaced observation intervals
and also with possibly missing visits. In that sense, all temporal
information is already contained within column 2, and I cannot see a
good reason to additionally include column 5. It may even complicate
things, due to the redundancy.

If you have 3 groups, you will need two columns in the design matrix to
indicate group membership (assuming that an intercept column is also
present). Choose one group (say, group 1) as the reference group, which
will not explicitly be coded, and then use one of the two group columns
to indicate if a person belongs to group 2 (1=yes, 0=no), and the other
to indicate if a person belongs to group 3 (1=yes, 0=no).

Please don't code group membership numerically as 1, 2, 3 in a single
column, as this will impose a linear relation between group membership
and outcome measure (similar to linear regression).

I am not sure about the current meaning of column 6, which multiplies
age and time-from-baseline. It would be more important, in my eyes, to
multiply time-from-baseline and group membership. Considering my second
comment, this will also result in two colums. These will indicate
whether or not the effect of time will differ between groups, and this
(=different longitudinal trajectory) is often the primary interest in
longitudinal studies.

As far as I can see, your overall design is somewhat similar to the
univariate example on the Freesurfer LME webpage, except that you have
fewer groups and fewer covariates. As it does not matter for the design
matrix whether or not the overall study is univariate or mass-
univariate (as in your case), one suggestion would be that you
construct your design in a similar way as in the given example.

I hope that I have understood your design correctly, otherwise let me
know.

Best regards,

Kersten

-Original Message-
From: "Kaushal, Mayank" 
Reply-to: Freesurfer support list 
To: Freesurfer support list 
Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
Date: Tue, 6 Mar 2018 19:22:57 +0100

I have tabulated the columns for easier comprehension.

Column 1

Column 2

Column 3

Column 4

Column 5

Column 6

intercept

time of each scan from base scan for a given subject

age at first scan for a given subject

group (1, 2, or 3)

visit (1,2 3, or 4)

Column 2 * Column 3


Thanks again.

Mayank
On Mar 6, 2018, at 12:05 PM, Kaushal, Mayank > wrote:

Changing the Matlab directory worked.
Thanks for all your inputs, Kersten.

Sorry to prolong the conversation but if possible, I would appreciate
input on whether my thought process regarding the LME analysis is on
the right track.

I am looking to compare cortical thickness between 3 groups over
multiple visits.

The design matrix created by me X = [ones(length(M),1) M
M(:,1).*M(:,2)];
Column 1 Column 2 Column 3 Column 4 Column 5 Column 6
intercept time of each scan from base scan age at first scan group (1,
2, or 3) visit (1,2 3, or 4)  Column 2 * Column 3

Presently, I am running lhstats = lme_mass_fit_vw(X,[1
2],Y,ni,lhcortex,[],1) as a test run.

However, I would like to include Columns 1, 4, and 5 as random effects
for LME analysis and if possible even include Column 2 as a random
effect to have 4 random effects.lhstats = lme_mass_fit_vw(X,[1
4 5],Y,ni,lhcortex,[],1) or  lhstats = lme_mass_fit_vw(X,[1 2 4
5],Y,ni,lhcortex,[],1)

Now, I would like to know if having 3 or possibly 4 random effects
would be too many random effects.

Mayank
On Mar 6, 2018, at 8:57 AM, Diers, Kersten /DZNE mailto:kersten.di...@dzne.de>> wrote:

ATTENTION: This email originated from a sender outside of MCW. Use
caution when clicking on links or opening attachments.


The LME toolbox will create a text file ('parfor_progress1.txt') in
Matlab's present working directory to indicate its progress in
processing each vertex.

To create this file it needs to have write permissions in Matlab's
present working directory.

I speculate that your present working directory in Matlab is the root
directory '/' where the toolbox cannot create a file.

The solution would be to not run the scripts from '/', but to set the
Matlab working directory to another directory where you have write
permissions.

Best regards

Kersten


-Original Message-
From: "Kaushal, Mayank" mailto:mkaus...@mcw.edu>>
Reply-to: Freesurfer support list >
To: Freesurfer support list mailto:free
sur...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Running Linear Mixed Effects (LME) Model
Date: Tue, 6 Mar 2018 15:17:31 +0100

After downloading version 6.0. and running lhstats =
lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1), I received the fol

[Freesurfer] ASEG and APARCSTATS2TABLE on longitudinal data

[Lisa Delalande]

 Hi FreeSurfer experts,

I would like to use the asegstats2table and the aparcstats2table commands
on my longitudinal data, which have been processing following the
longitudinal pipeline (recon-all -cross, - base and finally -long). And I
have two questions :

1) Am I obliged to do the ''long_stats_slopes --qdec
./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas volume
--do-avg --do-rate --do-pc1 --time months'' command before using the
aseg/aparc commands ?

2) And I would like to know which subjectsID I have to choose for the
command line, example :
asegstats2table --subjects *001_tp1 002_tp1*...etc. (cross)? OR *template_001
template_002*...etc (base)? OR *001_tp1.long.template_001
002_tp1.long.template_002*...etc (long)?
Knowing that it's for a comparison test-retest (microlongitudinal : 1
month).


Thanks you in advance for your precious help,
Best regards,

Lisa
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[Freesurfer] trouble shooting: pial surface & wm hypointensities

[Marie Sigmund]

Hello FreeSurfer Developers,

I am trouble-shooting some FreeSurfer Data and there are two errors which occur frequently.

1. The pial surface does not include all of the graymatter. I read that you should in this case correct the WM so it adjusts the GM automatically. I tried this out a couple of times and there is still some GM left over which is not included. 

2. Gyri or sulci are sometimes labeled as wm-hypointensities. I thought about correcting it on the aseg.presurf volume (on the website it is stated that using a FreeSurfer version of 6.0 or higher you should make corrections to the ASEG there). The problem is that on this volume the segmentation is different to the final one and not necessarily wrong. 

I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Thanks a lot!

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) uname -a: Linux R0223 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux


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[Freesurfer] Installation problem

[Neda Mohammadi]

Dear Expert,

I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps:

1. Download and extract into the directory /usr/local
2.export FREESURFER_HOME=/usr/local/freesurfer

Its fine, but when I run this step

3.source $FREESURFER_HOME/SetUpFreeSurfer.sh

I receive this message n time

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Work/Processed_data/freesurfer
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0

and I must press Ctrl+C to stop.
What do I do now?

-- 
*Best Regards,*
*Neda*
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