On Fri, Aug 2, 2013 at 12:22 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Amirhossein - The memory error doesn't occur when bbregister is running, but when dmri_train is running and loading the atlas data. You seem to have the snow leopard version of freesurfer installed, based on your build stamp (freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0). What version of the operating system do you have on your computer and how much memory?

Thanks,
a.y

On Mon, 29 Jul 2013, amirhossein manzouri wrote:

Hi,
Kindly find attched the trac-all.log !

On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Amirhossein - If your error happens when bbregister is run,
then it's not the error that the dmri_5.1_snow_leopard.tar.gz
fix was meant to address. In any case that fix is not relevant
to you b/c you're using 5.3 and not 5.1. Can you please send
your trac-all.log to establish where exactly the error is
happening?

Thanks,
a.y

On Thu, 25 Jul 2013, amirhossein manzouri wrote:

Hi ZeKe,
I am getting this error during Tracula procedure
somewhere between
bbregister!
BR

On Jul 24, 2013 5:42 PM, "Z K"
<zkaufman@nmr.mgh.harvard.edu> wrote:
Hello Amir,

According to the log file you've attached,
recon-all finished to
completion without any errors. Are you sure
you are encountering
a memory error? If so, why?

-Zeke

On 07/24/2013 11:28 AM, amirhossein manzouri
wrote:
Kindly find attached the recon-all.log

On Wed, Jul 24, 2013 at 4:50 PM, Z K
<zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu>>
wrote:

Hello Amir,

Thanks for that... could you also
please provide
the recon-all.log
file? It will be located in

$SUBJECT_DIR/subject_name/__scripts/recon-all.log

-Zeke

On 07/24/2013 03:01 AM, amirhossein
manzouri
wrote:

Hi,
The content is :

freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0
Can it help?

On Mon, Jul 22, 2013 at 10:31
PM, Z K
<zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu>

<mailto:zkaufman@nmr.mgh.__harvard.edu

<mailto:zkaufman@nmr.mgh.harvard.edu>>>
wrote:

Hello Amirhossein,

Can you please provide me
with the
contents of
build-stamp.txt in
the
/Applications/freesurfer directory?

-Zeke

On 07/22/2013 04:23 PM,
amirhossein
manzouri wrote:

Hi,
Yes I am getting the
memory error
with version 5.3,
exactly the
one that
is reported in this
link:
  https://mail.nmr.mgh.harvard.____edu/pipermail//freesurfer/____2011-July/0
1
9392.html

  <https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/0193
9
2.html
  <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.h
t
ml>>
Thanks,

On Mon, Jul 22, 2013 at
8:15 PM,
Anastasia Yendiki

<ayendiki@nmr.mgh.harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>

<mailto:ayendiki@nmr.mgh.

<mailto:ayendiki@nmr.mgh.>__har__vard.edu
<http://harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>>>
wrote:

Hi Amirhossein -
That fix
applied only to the 5.1
version. I'd
recommend using
the 5.3
version for tracula. Are
you getting a
memory error, and
if so with
which version?

Thanks,
a.y

On Mon, 22 Jul
2013,
amirhossein manzouri wrote:

Dear
Anastasia,
I am trying to
download
the

dmri_5.1_snow_leopard.tar.__gz from

FreeSurfer
website to
solve memory
problem but it is not
available. Would
you please
check the
source to the
link?

On Wed, Jul
17, 2013 at
5:51 PM, amirhossein
manzouri

<a.h.manzouri@gmail.com
<mailto:a.h.manzouri@gmail.com>
<mailto:a.h.manzouri@gmail.com

<mailto:a.h.manzouri@gmail.com>__>

<mailto:a.h.manzouri@gmail.com
<mailto:a.h.manzouri@gmail.com>

<mailto:a.h.manzouri@gmail.com

<mailto:a.h.manzouri@gmail.com>__>__>>
wrote:
The
format of my
bval file was wrong so
I edited
your
file and
tried
and it
worked, also bvec should be in
three columns
as you
have
mentioned
before.

On Wed, Jul
17, 2013 at
5:11 PM, Anastasia Yendiki

<ayendiki@nmr.mgh.harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>

<mailto:ayendiki@nmr.mgh.

<mailto:ayendiki@nmr.mgh.>__har__vard.edu
<http://harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>>>
wrote:

Good to
hear! Can
you please share with
all of
us what was
wrong
with your
original files? It may help
others who
have
the same
problem in the future.
Thanks!

On Wed,
17 Jul
2013, amirhossein
manzouri wrote:

Thanks
Anastasia,

IT HELPED!

On Tue, Jul
16, 2013 at 5:25 PM,
Anastasia

Yendiki
<ayendiki@nmr.mgh.harvard.edu
<mailto:ayendiki@nmr.mgh.harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>

<mailto:ayendiki@nmr.mgh.

<mailto:ayendiki@nmr.mgh.>__har__vard.edu
<http://harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>>>

wrote:

Hi
Amirhossein - I'm
attaching sample

files.

a.y

On Tue,
16 Jul 2013,
amirhossein

manzouri
wrote:

Hi Anastasia,

I
have tried both ,
3-row and

3-column
format and still

wrong bvecc and bval

from flip4fsl. Could
you please

send me a
sample of your

original files so I

can compare?

On Mon, Jul 15, 2013
at 7:44 PM,

Anastasia
Yendiki

<ayendiki@nmr.mgh.harvard.edu
<mailto:ayendiki@nmr.mgh.harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>

<mailto:ayendiki@nmr.mgh.

<mailto:ayendiki@nmr.mgh.>__har__vard.edu
<http://harvard.edu>

<mailto:ayendiki@nmr.mgh.__harvard.edu

<mailto:ayendiki@nmr.mgh.harvard.edu>>>>

wrote:

Hi Amirhossein
- Are your

original
bvecs/bvals in

3-row format

instead of
3-column format?

http://surfer.nmr.mgh.harvard.______edu/fswiki/FsTutorial/____Tracula

<http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula

<http://harvard.edu/fswiki/FsTutorial/__Tracula>

<http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula

<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula>>>

Thanks,

a.y

On Mon, 15 Jul
2013,

amirhossein
manzouri wrote:

Dear Experts,

I am
running trac-all

-prep -c
dmrirc on my

DWI

data.
After flip4fsl

step I get
the attached

bval

and bvec
file which

the bvec one
is wrong so

the

process exits

with
error in dtifit.
I
have also
attached

original

bvec and
bval.

--

Best regards,

Amirhossein Manzouri

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

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HelpLine at

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<http://www.partners.org/____complianceline>

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<http://www.partners.org/__complianceline

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--

Best regards,

Amirhossein Manzouri

--

Best regards,

Amirhossein
Manzouri

--
Best regards,
Amirhossein
Manzouri

--
Best regards,
Amirhossein
Manzouri

--
Best regards,
Amirhossein Manzouri

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--
Best regards,
Amirhossein Manzouri

--
Best regards,
Amirhossein Manzouri

--
Best regards,
Amirhossein Manzouri

Best regards,
Amirhossein Manzouri