Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[zkaufman]

Current versions of the Mac freesurfer binaries are not compatible with
the v5.3 release. Too much has changed since then. If you wanted to use
the newest version on the code you will need to download the latest dev
version of freesurfer from this page (see "Development Version"):

  https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download

Hope this helps.

-Zeke

> There was an obscure error having to do with the ascii header when
> unpacking skyra data on the mac, that might be it. Zeke, can you get
> Ismail a version of mri_convert appropriate for his OS?
>
> doug
>
>
>
> On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:
>> Hi Doug,
>>
>> I tried it on the cluster and it worked, which is weird because it was
>> not working before … Any idea what might be the problem on my system ?
>> Thanks again.
>>
>> Ismail
>>
>>> On Jul 19, 2016, at 10:32 PM, Douglas Greve
>>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>
>>> I used the same version, but I used it on linux. Do you have a linux
>>> box with FS installed that you can try it on?
>>>
>>>
>>> On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
 I used the same command line as you did. And when I check with
 mri_probedicom I can see the ASCII header.

 Here is the version of FS I am using :
 freesurfer-i386-apple-darwin11.4.2-stable5-20130514

 Do you think it might be related ?

 Thanks again.

 Ismail

> On Jul 19, 2016, at 1:27 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> What is your exact command line?
>
> The version of the file that you gave me definitely has an ascii
> header,
> and I don't get that warning when I convert. What version of FS are
> you
> using on what platform? To check whether that file has an ascii
> header, run
>
> mri_probedicom --i
> MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
>
> There should be a line like below
>
> ### ASCCONV BEGIN
>
>
> On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
>> Hi Doug,
>>
>> That’s weird because I can’t convert it using only mri_convert, here
>> is the error I get :
>>
>> WARNING: file
>> /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
>> does not contain a Siemens ASCII header
>> has this file been anonymized?
>> ERROR: cannot unpack mosiacs without ASCII header
>>
>> Any idea why ?
>>
>> Best,
>>
>> Ismail
>>
>>> On Jul 19, 2016, at 1:11 PM, Douglas N Greve
>>> >> >
>>> wrote:
>>>
>>> I was able to convert it fine with
>>> mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
>>> output.nii.gz
>>> If I included -it dicom, the conversion did not have an error,
>>> but the
>>> output had only one slice. Since these are mosaics, they need the
>>> Siemens ascii header which is ignored with -it dicom. So ...
>>> don't use
>>> -it dicom
>>>
>>>
>>> On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
 Hi Doug,

 It is still an issue. I uploaded the DICOMs to you. Hope it could
 be
 useful.
 Thanks.

 Ismail

> On Jul 18, 2016, at 6:14 PM, Douglas N Greve
>  >
> wrote:
>
> Is this still a problem? If so, can you upload the dicom files
> to our
> file drop?
>
> On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
>> The file has not been anonymized.
>>
>> Thanks,
>>
>> Ismail
>>
>>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve
>>> >> >
>>> wrote:
>>>
>>> can you answer the question that it asks?
>>>
>>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
 Hi everyone,

 I’m having some issues converting my DICOMs (DWI) into NIFTI
 using
 mri_convert. I looked for other topics with people having
 the same
 kind of problem but couldn’t find an answer.

 Each time I run mri_convert on my DICOMs I get the following
 error :
 WARNING: file
 MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
 does not contain a Siemens ASCII header
 has this file been anonymized?
 ERROR: cannot unpack mosiacs without ASCII header

 Here are the following DICOMs informations :
 Identification
 NumarisVer   syngo MR D13
 ScannerModel Skyra
 PatientName

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[Douglas Greve]

There was an obscure error having to do with the ascii header when 
unpacking skyra data on the mac, that might be it. Zeke, can you get 
Ismail a version of mri_convert appropriate for his OS?


doug



On 7/20/16 10:34 AM, Koubiyr, Ismail wrote:

Hi Doug,

I tried it on the cluster and it worked, which is weird because it was 
not working before … Any idea what might be the problem on my system ?

Thanks again.

Ismail

On Jul 19, 2016, at 10:32 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I used the same version, but I used it on linux. Do you have a linux 
box with FS installed that you can try it on?



On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with 
mri_probedicom I can see the ASCII header.


Here is the version of FS I am using : 
freesurfer-i386-apple-darwin11.4.2-stable5-20130514


Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


What is your exact command line?

The version of the file that you gave me definitely has an ascii 
header,

and I don't get that warning when I convert. What version of FS are you
using on what platform? To check whether that file has an ascii 
header, run


mri_probedicom --i 
MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931


There should be a line like below

### ASCCONV BEGIN


On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:

Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here
is the error I get :

WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea why ?

Best,

Ismail


On Jul 19, 2016, at 1:11 PM, Douglas N Greve
> 
wrote:


I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error, 
but the

output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... 
don't use

-it dicom


On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:

Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be
useful.
Thanks.

Ismail


On Jul 18, 2016, at 6:14 PM, Douglas N Greve
> 
wrote:


Is this still a problem? If so, can you upload the dicom files 
to our

file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:

The file has not been anonymized.

Thanks,

Ismail


On Jul 5, 2016, at 11:20 AM, Douglas N Greve
> 
wrote:


can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:

Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI 
using
mri_convert. I looked for other topics with people having 
the same

kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following 
error :

WARNING: file
MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Here are the following DICOMs informations :
Identification
NumarisVer   syngo MR D13
ScannerModel Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime   123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo   1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime   4700
PhEncFOV 0
ReadoutFOV   0
Image information
RunNo 4
SeriesNo 5
ImageNo   1
NImageRows   990
NImageCols   990
NFrames   64
SliceArraylSize   0
IsMosaic 1
ImgPos   1075.1575 1069.8385 -48.6769
VolRes 2.1818   2.1818   2.
VolDim 000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs 0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1


Then I try using mri_convert -it dicom, it converts the files
but not
as it is expected, you could notice the difference when I run
mri_info
on my output :
Volume information for output.nii.gz
type: nii
  dimensions: 990 x 990 x 1 x 64
 voxel sizes: 2.1818, 2.1818, 2.
type: SHORT (4)
 fov: 2160.000
 dof: 0
  xstart: -1080.0, xend: 1080.0
  ystart: -1080.0, yend: 1080.0
  zstart: -1.0, zend: 1.0
  TR: 4700.00 msec, TE: 0.00 msec, TI: 0.0

[Freesurfer] Error with mri_glmfit_sim (dev version f)

[Nicola Toschi]

Hi List,

I am getting a couple of strange error when running a 3-group F-test.

WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
WARNING: 251446 NaNs found in volume 
analysis/Ftest/cache.th20.pos.sig.cluster.mgh...

And as a result, I consistently get huge clusters:

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ CWP
CWPLowCWPHi   NVtxsWghtVtx   Annot
1  inf   0  63247.45-38.8  -19.0   66.9 0.00010  
0.0  0.00020  98722 inf  precentral

However, this doesn't happen when running t-tests on the same data. 
Still, I think my F-contrast is correct (see below).

Thanks in advance for any advice!

Nicola

PS:

my F-contrast looks like this:

1   -1  0   0   0   0
1   0  -1   0   0   0

and my design matrix looks like this:

0   0   1   1   179 110
0   0   1   1   193 103
0   0   1   1   176 108
0   0   1   1   198 94
0   1   0   1   186 87
0   1   0   1   217 83
.

and my versions are

# $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
# $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $



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Re: [Freesurfer] Flattening the surface

[Younghoon Kim]

Hi Bruce,

I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to
generate a surface, but received an error message as below:

changing type of input volume to 8 bits/voxel...
$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
Cannot calloc()

Would this be because my input data is not compatible with the
mri_tessellate command?

Thanks,

Younghoon Kim

--
Younghoon Kim,
Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:

If you have a segmented volume, you can use mri_tessellate to create the
surface, then introduce the cut(s) and run mris_flatten -1 on the resulting
patch. You can check out our wiki

http://surfer.nmr.mgh.harvard.edu/fswiki

which has info on this process, although the flattening isn't terribly well
documented. You need the -1 flag to tell it to only use that one surface
that you are giving it, and not to assume that the entire FS directory
structure exists.

cheers
Bruce


On Wed, 20 Jul 2016, Younghoon Kim wrote:

> Hi Bruce,
>
> Great! I’m not an expert in FreeSurfer, so can you give me some advice
how to
> generate a surface of our volumetric data and flatten it?
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> Wellman Center, Massachusetts General Hospital
> Bouma’s Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
> On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:
>
> HI Younghoon
>
> I guess that could work. You will need to introduce at least one cut if
not
> more if you surface has substantial Gaussian curvature
>
> cheers
> Bruce
>
>
> On Wed,
> 20 Jul 2016, Younghoon Kim wrote:
>
> > Hi Bruce,
> >
> > We are only interested in the surface image of the volumetric data.
> >
> > For flattening, we do not care about the interior of the volume, so we
> would like
> > to remove the volume data inside.
> >
> > So what we want is to peel off the surface from the segmented brain
area
> and
> > flatten that surface.
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > Wellman Center, Massachusetts General Hospital
> > Bouma’s Lab
> > --
> > younghoon.h@gmail.com
> > aktivh...@kaist.ac.kr
> >
> > On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)

> wrote:
> >
> > Hi Younghoon
> >
> > what structure are you talking about? In general it doesn't make sense
to
> > flatten volumetric structures. We flatten the cortex, which is a folded
> > 2D sheet. What would you do with the interior of the volume?
> >
> > cheers
> > Bruce
> > On Wed, 20 Jul
> > 2016, Younghoon Kim wrote:
> >
> > > Hello,
> > >
> > > We have a volumetric data (mgz file) of a segmented brain region. We
want
> > to detect
> > > the surface of this segmented brain volume (i.e. deep brain region)
and
> > flatten it
> > > into a 2D image with its original surface texture.
> > >
> > > We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
> > data. We
> > > wonder if this could be adapted to our data set. Can anyone offer
some
> > advice on
> > > how to apply FreeSurfer to this more generic task?
> > >
> > > Thanks,
> > >
> > > Younghoon Kim
> > >
> > > --
> > > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > > OMICS Lab
> > > Wellman Center, Massachusetts General Hospital
> > > Bouma’s Lab
> > > --
> > > younghoon.h@gmail.com
> > > aktivh...@kaist.ac.kr
> > >
> > >___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
> >
> >
> >___
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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
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Re: [Freesurfer] Flattening the surface

[Bruce Fischl]

If you have a segmented volume, you can use mri_tessellate to create the 
surface, then introduce the cut(s) and run mris_flatten -1 on the resulting 
patch. You can check out our wiki


http://surfer.nmr.mgh.harvard.edu/fswiki

which has info on this process, although the flattening isn't terribly well 
documented. You need the -1 flag to tell it to only use that one surface 
that you are giving it, and not to assume that the entire FS directory 
structure exists.


cheers
Bruce


On Wed, 20 Jul 2016, Younghoon Kim wrote:


Hi Bruce,

Great! I’m not an expert in FreeSurfer, so can you give me some advice how to
generate a surface of our volumetric data and flatten it?

Thanks,

Younghoon Kim

--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote:

HI Younghoon

I guess that could work. You will need to introduce at least one cut if not
more if you surface has substantial Gaussian curvature

cheers
Bruce


On Wed,
20 Jul 2016, Younghoon Kim wrote:

> Hi Bruce,
>
> We are only interested in the surface image of the volumetric data.
>
> For flattening, we do not care about the interior of the volume, so we
would like
> to remove the volume data inside.
>
> So what we want is to peel off the surface from the segmented brain area
and
> flatten that surface.
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> Wellman Center, Massachusetts General Hospital
> Bouma’s Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
> On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:
>
> Hi Younghoon
>
> what structure are you talking about? In general it doesn't make sense to
> flatten volumetric structures. We flatten the cortex, which is a folded
> 2D sheet. What would you do with the interior of the volume?
>
> cheers
> Bruce
> On Wed, 20 Jul
> 2016, Younghoon Kim wrote:
>
> > Hello,
> >
> > We have a volumetric data (mgz file) of a segmented brain region. We want
> to detect
> > the surface of this segmented brain volume (i.e. deep brain region) and
> flatten it
> > into a 2D image with its original surface texture.
> >
> > We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
> data. We
> > wonder if this could be adapted to our data set. Can anyone offer some
> advice on
> > how to apply FreeSurfer to this more generic task?
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > Wellman Center, Massachusetts General Hospital
> > Bouma’s Lab
> > --
> > younghoon.h@gmail.com
> > aktivh...@kaist.ac.kr
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
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Re: [Freesurfer] Flattening the surface

[Younghoon Kim]

Hi Bruce,

Great! I’m not an expert in FreeSurfer, so can you give me some advice how
to generate a surface of our volumetric data and flatten it?

Thanks,

Younghoon Kim

--
Younghoon Kim,
Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:

HI Younghoon

I guess that could work. You will need to introduce at least one cut if not
more if you surface has substantial Gaussian curvature

cheers
Bruce


On Wed,
20 Jul 2016, Younghoon Kim wrote:

> Hi Bruce,
>
> We are only interested in the surface image of the volumetric data.
>
> For flattening, we do not care about the interior of the volume, so we
would like
> to remove the volume data inside.
>
> So what we want is to peel off the surface from the segmented brain area
and
> flatten that surface.
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> Wellman Center, Massachusetts General Hospital
> Bouma’s Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
> On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:
>
> Hi Younghoon
>
> what structure are you talking about? In general it doesn't make sense to
> flatten volumetric structures. We flatten the cortex, which is a folded
> 2D sheet. What would you do with the interior of the volume?
>
> cheers
> Bruce
> On Wed, 20 Jul
> 2016, Younghoon Kim wrote:
>
> > Hello,
> >
> > We have a volumetric data (mgz file) of a segmented brain region. We
want
> to detect
> > the surface of this segmented brain volume (i.e. deep brain region) and
> flatten it
> > into a 2D image with its original surface texture.
> >
> > We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
> data. We
> > wonder if this could be adapted to our data set. Can anyone offer some
> advice on
> > how to apply FreeSurfer to this more generic task?
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > Wellman Center, Massachusetts General Hospital
> > Bouma’s Lab
> > --
> > younghoon.h@gmail.com
> > aktivh...@kaist.ac.kr
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
is
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Re: [Freesurfer] Flattening the surface

[Bruce Fischl]

HI Younghoon

I guess that could work. You will need to introduce at least one cut if not 
more if you surface has substantial Gaussian curvature


cheers
Bruce


On Wed, 
20 Jul 2016, Younghoon Kim wrote:



Hi Bruce,

We are only interested in the surface image of the volumetric data.

For flattening, we do not care about the interior of the volume, so we would 
like
to remove the volume data inside.

So what we want is to peel off the surface from the segmented brain area and
flatten that surface.

Thanks,

Younghoon Kim

--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote:

Hi Younghoon

what structure are you talking about? In general it doesn't make sense to
flatten volumetric structures. We flatten the cortex, which is a folded
2D sheet. What would you do with the interior of the volume?

cheers
Bruce
On Wed, 20 Jul
2016, Younghoon Kim wrote:

> Hello,
>
> We have a volumetric data (mgz file) of a segmented brain region. We want
to detect
> the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
> into a 2D image with its original surface texture.
>
> We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
data. We
> wonder if this could be adapted to our data set. Can anyone offer some
advice on
> how to apply FreeSurfer to this more generic task?
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> Wellman Center, Massachusetts General Hospital
> Bouma’s Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
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Re: [Freesurfer] Flattening the surface

[Younghoon Kim]

Hi Bruce,

We are only interested in the surface image of the volumetric data.

For flattening, we do not care about the interior of the volume, so we
would like to remove the volume data inside.

So what we want is to peel off the surface from the segmented brain area
and flatten that surface.

Thanks,

Younghoon Kim

--
Younghoon Kim,
Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu)
wrote:

Hi Younghoon

what structure are you talking about? In general it doesn't make sense to
flatten volumetric structures. We flatten the cortex, which is a folded
2D sheet. What would you do with the interior of the volume?

cheers
Bruce
On Wed, 20 Jul
2016, Younghoon Kim wrote:

> Hello,
>
> We have a volumetric data (mgz file) of a segmented brain region. We want
to detect
> the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
> into a 2D image with its original surface texture.
>
> We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
data. We
> wonder if this could be adapted to our data set. Can anyone offer some
advice on
> how to apply FreeSurfer to this more generic task?
>
> Thanks,
>
> Younghoon Kim
>
> --
> Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> OMICS Lab
> Wellman Center, Massachusetts General Hospital
> Bouma’s Lab
> --
> younghoon.h@gmail.com
> aktivh...@kaist.ac.kr
>
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Re: [Freesurfer] tkmedit issue - image too bright in tkmedit after running gcut

[Bruce Fischl]

Hi Fred

that just means that you need to change the window levels.

Note that we have deprecated the use of tksurfer and tkmedit and don't 
really support them any longer

cheers
Bruce
On Wed, 20 Jul 
2016, Uquillas, Federico D'Oleire wrote:

> Hi fellow FreeSurfer users,
>
> I just did a gcut procedure and now that I'm opening it up again to check out 
> how it went the brain is so bright I can't see white matter and gray matter 
> contrast.
>
> Anybody ever experience this before?
> I tried exiting the terminal, and opening it again, but that doesn't do the 
> trick.
>
> I'm opening up the image in tkmedit. If I use Freeview, the image looks fine 
> and is not super bright as when I open it up in tkmedit. Not sure what is 
> going on.
>
> Any thoughts?
>
> Best,
>
> Fred
>
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Re: [Freesurfer] Flattening the surface

[Bruce Fischl]

Hi Younghoon

what structure are you talking about? In general it doesn't make sense to 
flatten volumetric structures. We flatten the cortex, which is a folded 
2D sheet. What would you do with the interior of the volume?


cheers
Bruce
On Wed, 20 Jul 
2016, Younghoon Kim wrote:



Hello,

We have a volumetric data (mgz file) of a segmented brain region. We want to 
detect
the surface of this segmented brain volume (i.e. deep brain region) and flatten 
it
into a 2D image with its original surface texture.

We’ve noticed that Freesurfer supports an algorithm to flatten volumetric data. 
We
wonder if this could be adapted to our data set. Can anyone offer some advice on
how to apply FreeSurfer to this more generic task?

Thanks,

Younghoon Kim

--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr

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[Freesurfer] Flattening the surface

[Younghoon Kim]

Hello,

We have a volumetric data (mgz file) of a segmented brain region. We want
to detect the surface of this segmented brain volume (i.e. deep brain
region) and flatten it into a 2D image with its original surface texture.

We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
data. We wonder if this could be adapted to our data set. Can anyone offer
some advice on how to apply FreeSurfer to this more generic task?

Thanks,

Younghoon Kim

--
Younghoon Kim,
Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr
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Re: [Freesurfer] Beta-Zero Correction - No Phase File

[Afzal, Afsana]

Hi Doug, 

Thanks for getting back to me. I've tried mri_convert $Input_file --split 
$Output_file to split up the fieldmaps but I'm getting 6 to 12 different 
outputs (depending on the fieldmap) rather than just the mag and phase files 
which is what I was expecting. 

Have you encountered this before and is there another way to unpack the 
fieldmaps into just the mag and phase components? 

Thanks so much for you time, 

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2016 12:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Beta-Zero Correction - No Phase File

You can extract frames from a multi frame file with
mri_convert input.nii.gz --frame 0 output.frame0.nii.gz


On 07/12/2016 02:29 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm working with a dataset that outputs only one file (not two
> separate mag and phase files) for the fieldmap. The data was also
> collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx
> (not sure if this is the reason the fieldmaps are unpacking
> differently). I've attached the .dat file for one of the fieldmaps in
> this email.
>
> If there a way to separate out the mag and phase from the single
> fieldmap file so I can use epidewarp.fsl?
>
> Thanks,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream

[Harms, Michael]

Hi Anastasia,


I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html


It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal TRACULA stream, but Janosch’s last post seemed to indicate that her issue wasn’t resolved even with the new build of dmri_paths
 that you generated.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






 



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Re: [Freesurfer] error during longitudinal -long stream

[Jinsong Tang]

Hi Martin,

We run all cross, base and long with 5.3. I guess the problem maybe we run
cross on  a computer and then copy the results to another computer to run
the cross and long. the "*fsaverage" is not copied. Does this matter？*

Best，

Jinsong

On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter  wrote:

> Hi Jinsong,
>
> I have never seen this. Stable 5.3 is very stable and I doubt it is a bug.
> How did you process base and cross sectionals? Also with 5.3 ?
>
> I would recommend to process cross and base with 5.3, then re-run the long
> and see if you can replicate this problem. Let me know what happens.
>
> Best, Martin
>
>
> > On Jul 20, 2016, at 12:48 AM, Jinsong Tang 
> wrote:
> >
> > Hi all,
> >
> > I found an error during the longitudinal -long stream:
> >
> > recon-all -long P1001-2 P1001 -all
> > ..
> >
> > FREESURFER_HOME /space/raid/fmri/freesurfer
> > Actual FREESURFER_HOME /space/raid/fmri/freesurfer
> > build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC
> 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
> > ..
> >
> > mris_spherical_average -erode 1 -orig white -t 0.4 -o P1001-2.long.P1001
> label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
> >
> > painting output onto subject P1001-2.long.P1001.
> > processing subject lh.EC_average...
> >
> MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):
> could not open file
> > eroding label 1 times before writing
> > thresholding label stat at 0.400 before writing
> > Not a directory
> > mris_spherical_average: could not read surface file
> /space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
> > Not a directory
> > Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC
> 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux
> >
> > recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul  8
> 21:33:02 PDT 2016
> >
> >
> > Please help me fix this error!
> >
> > Thanks and best regards,
> >
> > Jinsong
> >
> >
> > ___
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Re: [Freesurfer] Fwd: question about voxel size

[Bruce Fischl]

Hi Dorsa

I don't see any holes in the thalamus in your aseg, nor separated pieces. 
What voxel coords do you mean? Remember to look at the data in other 
orientations. Things  that look like islands in one view may be peninsulas

in anothers

cheers

Bruce

On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote:


I mean the holes in the thalamus and also some parts that are labeled as 
thalamus
but not attached to the rest of thalamus volume. 

On Wed, Jul 20, 2016 at 10:49 AM, Bruce Fischl  
wrote:
  what missing parts do you mean? The segmentation seemed pretty
  reasonable, but the contrast wasn't good enough to say how accurate it
  was in some places
  On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote:

Yes it is taken at 3T. I have asked our team to provide
these information about the
MRIs and will let you know when I hear back. I also wanted
to ask if you know a
good way to refine the thalamus and fill out the missing
parts within the volume?
Thank you 
Dorsa

On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl
 wrote:
      what is a "3TS" image? Do you mean it was acquired at
3T? What sequence
      and what parameters (TE/TR/TI/TD/flip angle)?

      cheers
      Bruce
      On Tue, 19 Jul 2016, Dorsa
      Haji Ghaffari wrote:

      > Hi Bruce,
      > that is a 3TS T1 weighted image and is taken after
the patients have
      taken
      > the contrast medium. I have played with the
intensities in Analyze
      and this
      > is the best I could get. Do you have any
suggestions for getting
      better
      > contrast?
      >
      > Thank you
      >
      > Dorsa
      >
      > On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl
      
      > wrote:
      >       also, please post to the list so that others
can answer!
      >       thanks
      >       Bruce
      >       On Tue, 19 Jul 2016, Dorsa Haji Ghaffari
wrote:
      >
      >             Here it is. Also can you explain why
the algorithm
      >             works best with 1mm^3
      >             voxel size?
      >
      >             Thank you!
      >
      >
      >
      >
      >
      >
      >
      >
      > 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
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      the
      > e-mail
      > contains patient information, please contact the
Partners Compliance
      > HelpLine at
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      you
      > in error
      > but does not contain patient information, please
contact the sender
      > and properly
      > dispose of the e-mail.
      >
      >
      >
      >
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[Freesurfer] Fwd: Connectome Research Coordinator (Senior), University of Pennsylvania

[Jeff Phillips]

Dear colleagues,

The Penn Frontotemporal Degeneration Center at the University of
Pennsylvania (http://ftd.med.upenn.edu/) is seeking a research coordinator
for the multi-site FTD Connectome study. Please see the details below;
applications should be directed to http://jobs.hr.upenn.edu/postings/18756.

Thanks,

Jeff Phillips
Postdoctoral Fellow
Penn FTD Center
University of Pennsylvania

Duties:

The primary responsibility of the successful candidate will be the
coordination of a multi-site consortium using a novel approach to
neuroimaging of neurodegenerative diseases. The lead site is Penn, and
participating sites include Mayo Clinic, UCSF, MGH and Northwestern. All
sites have specialized neuroimaging equipment, and we will be using
advanced neuroimaging tools developed locally and in collaboration with the
Human Connectome Project (HCP) to analyze the acquired data. The successful
candidate also will be responsible for managing the Penn site.

This project is coordinated with two other multi-site registries involving
these same sites that are recruiting participants for this neuroimaging
project (and other studies). Participants will include: 1. healthy control
subjects; 2. individuals who have a frontotemporal degeneration (FTD)
spectrum disorder such as primary progressive aphasia, progressive
supranuclear palsy, or FTD with amyotrophic lateral sclerosis; and 3.
individuals who are carrying a mutation that has resulted in an FTD
spectrum disorder or are at risk for developing a FTD-spectrum disorder.

Coordination will include weekly meetings with project coordinators at the
other participating sites, developing reports for monthly meetings with NIH
and principal investigators at other sites, monitoring imaging data flow to
our coordinating site, monitoring the database that tracks participants,
monitoring data flow from Penn to the HCP coordinating center, and managing
requests for data from investigators. Other administrative responsibilities
will include help managing the consortium budget. Local site
responsibilities will include assistance with on-going recruitment
processes, helping to collect imaging data, managing the local budget,
supervising local technical and research staff, and participating in
imaging analyses. Also included are implementation of Connectome imaging
analysis and operation of the Prisma MRI scanner.

Position is contingent on continued funding.

Qualifications:

A Bachelor’s degree and to 3 to 5 years of experience, or equivalent
combination of education and experience, are required. Masters degree or
PhD in neuroscience, psychology, linguistics, biology, biomedical
engineering or related fields and 2 years to 3 years of experience strongly
preferred. Past research and project coordination experience working in a
similar lab setting is highly desirable. Experience with the following is
preferred: Linux/Unix, brain imaging data analysis, MATLAB, computer
programming, statistical analysis, research project management, or
neuropsychological assessment. The candidate must be able to work
independently and have strong organizational and interpersonal skills.

Apply at http://jobs.hr.upenn.edu/postings/18756
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Re: [Freesurfer] Fwd: question about voxel size

[Dorsa Haji Ghaffari]

I mean the holes in the thalamus and also some parts that are labeled as
thalamus but not attached to the rest of thalamus volume.

On Wed, Jul 20, 2016 at 10:49 AM, Bruce Fischl 
wrote:

> what missing parts do you mean? The segmentation seemed pretty reasonable,
> but the contrast wasn't good enough to say how accurate it was in some
> places
>
> On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote:
>
> Yes it is taken at 3T. I have asked our team to provide these information
>> about the
>> MRIs and will let you know when I hear back. I also wanted to ask if you
>> know a
>> good way to refine the thalamus and fill out the missing parts within the
>> volume?
>> Thank you
>> Dorsa
>>
>> On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl 
>> wrote:
>>   what is a "3TS" image? Do you mean it was acquired at 3T? What
>> sequence
>>   and what parameters (TE/TR/TI/TD/flip angle)?
>>
>>   cheers
>>   Bruce
>>   On Tue, 19 Jul 2016, Dorsa
>>   Haji Ghaffari wrote:
>>
>>   > Hi Bruce,
>>   > that is a 3TS T1 weighted image and is taken after the patients
>> have
>>   taken
>>   > the contrast medium. I have played with the intensities in Analyze
>>   and this
>>   > is the best I could get. Do you have any suggestions for getting
>>   better
>>   > contrast?
>>   >
>>   > Thank you
>>   >
>>   > Dorsa
>>   >
>>   > On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl
>>   
>>   > wrote:
>>   >   also, please post to the list so that others can answer!
>>   >   thanks
>>   >   Bruce
>>   >   On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
>>   >
>>   > Here it is. Also can you explain why the algorithm
>>   > works best with 1mm^3
>>   > voxel size?
>>   >
>>   > Thank you!
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>>   > 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.
>>   >
>>   >
>>   >
>>   >
>> ___
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>>
>>
>>
>>
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Fwd: question about voxel size

[Bruce Fischl]

what missing parts do you mean? The segmentation seemed pretty 
reasonable, but the contrast wasn't good enough to say how accurate it 
was in some places

On Wed, 20 Jul 2016, Dorsa Haji Ghaffari wrote:


Yes it is taken at 3T. I have asked our team to provide these information about 
the
MRIs and will let you know when I hear back. I also wanted to ask if you know a
good way to refine the thalamus and fill out the missing parts within the 
volume?
Thank you 
Dorsa

On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl  
wrote:
  what is a "3TS" image? Do you mean it was acquired at 3T? What sequence
  and what parameters (TE/TR/TI/TD/flip angle)?

  cheers
  Bruce
  On Tue, 19 Jul 2016, Dorsa
  Haji Ghaffari wrote:

  > Hi Bruce,
  > that is a 3TS T1 weighted image and is taken after the patients have
  taken
  > the contrast medium. I have played with the intensities in Analyze
  and this
  > is the best I could get. Do you have any suggestions for getting
  better
  > contrast?
  >
  > Thank you
  >
  > Dorsa
  >
  > On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl
  
  > wrote:
  >       also, please post to the list so that others can answer!
  >       thanks
  >       Bruce
  >       On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
  >
  >             Here it is. Also can you explain why the algorithm
  >             works best with 1mm^3
  >             voxel size?
  >
  >             Thank you!
  >
  >
  >
  >
  >
  >
  >
  >
  > 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.
  >
  >
  >
  >
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Re: [Freesurfer] Fwd: question about voxel size

[Dorsa Haji Ghaffari]

Yes it is taken at 3T. I have asked our team to provide these information
about the MRIs and will let you know when I hear back. I also wanted to ask
if you know a good way to refine the thalamus and fill out the missing
parts within the volume?

Thank you
Dorsa

On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl 
wrote:

> what is a "3TS" image? Do you mean it was acquired at 3T? What sequence
> and what parameters (TE/TR/TI/TD/flip angle)?
>
> cheers
> Bruce
> On Tue, 19 Jul 2016, Dorsa
> Haji Ghaffari wrote:
>
> > Hi Bruce,
> > that is a 3TS T1 weighted image and is taken after the patients have
> taken
> > the contrast medium. I have played with the intensities in Analyze and
> this
> > is the best I could get. Do you have any suggestions for getting better
> > contrast?
> >
> > Thank you
> >
> > Dorsa
> >
> > On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   also, please post to the list so that others can answer!
> >   thanks
> >   Bruce
> >   On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
> >
> > Here it is. Also can you explain why the algorithm
> > works best with 1mm^3
> > voxel size?
> >
> > Thank you!
> >
> >
> >
> >
> >
> >
> >
> >
> > 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.
> >
> >
> >
> >
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[Freesurfer] R: problems by running longitudinal mass univariate analysis

[Valsasina Paola]

Dear Martin

to follow-up mu previous question, I was finally able to run the 
lme_mass_fit_vw script till the end. Unfortunately, it came out that converge 
of the algorithm was failed in 99% of the locations.
I have only one study group (with a variable number of follow-up , and I used 
as design matrix exactly the same proposed in the online guide:
X=[ones(length(M),1) M M(:,1).*M(:,2)]

so, I don’t see any specific region of failure associated with the design matrix

Therefore, I suppose that this is due to the fact that input images are wrong 
(empty or with some problems?).
How can I investigate further the correctness of my input data? The 
longitudinal pipeline was performed correctly, and mris_preproc command to 
generate the mass univariate file seems to work without errors. Can I 
eventually load somewhere my image file (i.e., the concatenated 
lh.thickness.mgh including all scans), so that someone chan check that input 
images for lme estimation are OK?
Thank you so much in advance
Kind regards
Paola


Da: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Per conto di Martin Reuter
Inviato: 14 July 2016 12:12
A: Freesurfer support list
Oggetto: Re: [Freesurfer] problems by running longitudinal mass univariate 
analysis


Hi Paola,

1 . It really takes a long time, though I think you probably are missing the 
parallel toolbox, and running this sequentially will be really slow.

2. You need to wait till the end and look at the percent of places where it did 
not converge. It is normal that it does not converge in some places. Also make 
sure the design matrix is not (close to) singular, which can happen if you have 
nearly collinear columns.

Best Martin
On Jul 14, 2016 10:43 AM, Valsasina Paola  wrote:

Dear FS experts



I am trying to run the commands for performing the longitudinal mixed effect 
statistics with the LME Matlab toolbox.

I am following the instructions on the web page; however, I have two questions:



1) when I run the command lme_mass_fit_vw, the script is running for a very 
long time, after 3 hours the estimation was just at 10% (unfortunately, my 
laptop is equipped with Windows and is not particularly powerful). I had to 
stop the script at that point; before restarting it again I would like to be 
sure: is this behavior normal?  Is it correct that lme_mass_fit_vw is running 
for such a long time?



2) when the script was running, there were several warnings on the Matlab 
screen, saying that the algorithm was not converging (at most of locations). Is 
it also normal? How can I check the correctness of my input image? When I open 
with freeview the “lh.thickness_sm10.mgh” volume, I just see a black screen 
with valid timeseries values in the minority of voxels (I imagine that these 
timeseries are concatenated thickness values of my study subjects). Is there 
another way to better visualize and check a concatenated 4d mgh file? Failure 
of convergence is referring to empty/zero voxels of this image?



Thank you for any advice on these two topics

Kind regards

Paola






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Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi Doug,

I tried it on the cluster and it worked, which is weird because it was not 
working before … Any idea what might be the problem on my system ?
Thanks again.

Ismail

On Jul 19, 2016, at 10:32 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I used the same version, but I used it on linux. Do you have a linux box with 
FS installed that you can try it on?

On 7/19/16 1:57 PM, Koubiyr, Ismail wrote:
I used the same command line as you did. And when I check with mri_probedicom I 
can see the ASCII header.

Here is the version of FS I am using : 
freesurfer-i386-apple-darwin11.4.2-stable5-20130514

Do you think it might be related ?

Thanks again.

Ismail

On Jul 19, 2016, at 1:27 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

What is your exact command line?

The version of the file that you gave me definitely has an ascii header,
and I don't get that warning when I convert. What version of FS are you
using on what platform? To check whether that file has an ascii header, run

mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931

There should be a line like below

### ASCCONV BEGIN


On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote:
Hi Doug,

That’s weird because I can’t convert it using only mri_convert, here
is the error I get :

WARNING: file
/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Any idea why ?

Best,

Ismail

On Jul 19, 2016, at 1:11 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu> 
> wrote:

I was able to convert it fine with
mri_convert MR.1.3.12.2.1107.5.2.19.45306.2014091812372179441003292
output.nii.gz
If I included -it dicom, the conversion did not have an error, but the
output had only one slice. Since these are mosaics, they need the
Siemens ascii header which is ignored with -it dicom. So ... don't use
-it dicom


On 07/19/2016 11:06 AM, Koubiyr, Ismail wrote:
Hi Doug,

It is still an issue. I uploaded the DICOMs to you. Hope it could be
useful.
Thanks.

Ismail

On Jul 18, 2016, at 6:14 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu> 
> wrote:

Is this still a problem? If so, can you upload the dicom files to our
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
The file has not been anonymized.

Thanks,

Ismail

On Jul 5, 2016, at 11:20 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu> 
> wrote:

can you answer the question that it asks?

On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
Hi everyone,

I’m having some issues converting my DICOMs (DWI) into NIFTI using
mri_convert. I looked for other topics with people having the same
kind of problem but couldn’t find an answer.

Each time I run mri_convert on my DICOMs I get the following error :
WARNING: file
MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

Here are the following DICOMs informations :
Identification
NumarisVer   syngo MR D13
ScannerModel Skyra
PatientName   x
Date and time
StudyDate 20140918
StudyTime 121037.203000
SeriesTime   123450.60
AcqTime   123257.367500
Acquisition parameters
PulseSeq ep_b0
Protocol AX DTI no angle MS NEX 4 2
PhEncDir COL
EchoNo   1
FlipAngle 90
EchoTime 96
InversionTime -1
RepetitionTime   4700
PhEncFOV 0
ReadoutFOV   0
Image information
RunNo 4
SeriesNo 5
ImageNo   1
NImageRows   990
NImageCols   990
NFrames   64
SliceArraylSize   0
IsMosaic 1
ImgPos   1075.1575 1069.8385 -48.6769
VolRes 2.1818   2.1818   2.
VolDim 000
Vc -1.  -0.   0.
Vr -0.  -1.   0.
Vs 0.   0.   0.
VolCenter   0.   0.   0.
TransferSyntaxUID 1.2.840.10008.1.2.1


Then I try using mri_convert -it dicom, it converts the files
but not
as it is expected, you could notice the difference when I run
mri_info
on my output :
Volume information for output.nii.gz
type: nii
  dimensions: 990 x 990 x 1 x 64
 voxel sizes: 2.1818, 2.1818, 2.
type: SHORT (4)
 fov: 2160.000
 dof: 0
  xstart: -1080.0, xend: 1080.0
  ystart: -1080.0, yend: 1080.0
  zstart: -1.0, zend: 1.0
  TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
 nframes: 64
 PhEncDir: UNKNOWN
ras xform present
  xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
-4.8425
: x_a =  -0., y_a =  -1., z_a = -0., c_a =
-10.1615
: x_s =   0., y_s =   0.

Re: [Freesurfer] ExploreDTI Workshop!

[Szabolcs David]

FYI - we're holding the next ExploreDTI Workshop!
When: 28-30 November, 2016
Where: Utrecht
Details: http://www.exploredti.com/workshop

Cheers,
Szabolcs

On Sat, Feb 27, 2016 at 8:00 PM, Szabolcs David 
wrote:

> Thrilled to announce that we are going to hold an ExploreDTI workshop in
> Utrecht (July 4-6)! More details can be found here:
> http://www.exploredti.com/workshop.
>
> We hope to see you there!
>
> Cheers,
> Szabolcs
>
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Re: [Freesurfer] reading lh.BA1_exvivo.label recon-all error

[Z K]

Hello Renata,

Their was a brief period of time in the Dev version of freesurfer when 
certain labels didnt exist in the fsaverage subject. You just happen to 
download and install that version. I believe if you download the latest 
version from this page (see "Development Version") that error will go away:

   https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Download

-Zeke

On 07/20/2016 03:35 AM, Vaz pandolfo, Renata wrote:
> Dear FreeSurfer developers,
>
> I am running recon-all on a healthy subject and I am also trying to get
> the hippocampal subfields segmentation.
> On the mri directory there is no hippocampus output, and the recon-all
> exited with errors.
>
> Command:
>
> recon-all -all \
> -i
> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz
> -s no_T2_20110815 \
> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
> -hippocampal-subfields-T1
>
> Error:
>
> SUBJECTS_DIR
> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
> FREESURFER_HOME /usr/local/freesurfer
> Loading source label.
> Invalid argument
> ERROR reading
> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label
> Linux lundb2 4.4.0-28-generic #47-Ubuntu SMP Fri Jun 24 10:09:13 UTC
> 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s no_T2_20110815 exited with ERRORS at Do 7. Jul 22:26:35
> CEST 2016
>
> Extra info:
>
> Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611
> uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8
> 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> logs: recon-all and hippocampal-subfields-T1T2 attached
>
>
> Thank you!
>
>
>
>
> ___
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[Freesurfer] Factors affect cortical thickness in normal population

[shi yao wang]

Dear FS experts,
We have few dataset of normal patients. They will be arranges as controls.
I am wondering the factors affecting normal patients cortical thickness:
Age,
Sex
Native Language
Hand prefer
IQ

Any others?

thanks
Lawrence
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Re: [Freesurfer] PVE correction tool on Freesurfer 6

[Lee Subin Kristine]

Hi Doug,


Thanks for your help!

For your response to question #1 from my previous email(copied below), then if 
all PET images were smoothed so that they all have a uniform resolution of 8mm 
FWHM, would I put 8 for the psf flag?


> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the
> point-spread function of the scanner or would a default value of 6
> work for all? I am using PET images from multiple centers and thus
> each image are from different scanners, and I'm not sure how I would
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change
depending upon recon method and parameters and even the ligand used. If
you get it about right, probably it will be close enough.


Also, for the second question (copied below), then does setting it to .01 mean 
maximum sensitivity to gray matter in each PET voxel, and thus this is the 
recommended threshold for the most accurate resutls?


> (b) For the mgx flag, is the GM threshold .01 an optimal threshold
> referring to the p-value?(am new to PVEcorrection and asking out of
> curiosity) What is the difference if I enter .01 versus I don't enter it?
>
You must enter a threshold. When Muller-Gartner is implemented, there
are two stages: (1) orthogonalization (subtracting out non-GM) and (2)
rescaling. In the rescaling step, each voxel is divided by the fraction
of GM in that voxel. If that fraction is 0, then you will get an error.
If it is close to 0, you can get extreme noise amplification in that
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be
rescaled, otherwise the voxel is set to 0.



Best,

Subin


보낸 사람: Douglas Greve  대신 
freesurfer-boun...@nmr.mgh.harvard.edu 
보낸 날짜: 2016년 7월 19일 화요일 오전 10:28:42
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6


the response is in the body f the mail

On 7/18/16 9:27 PM, Lee Subin Kristine wrote:

Hi Doug,

It seems that the email reply you just sent to me was empty. Could you please 
check your email message again?


Thank you as always,

Subin



보낸 사람: Douglas N Greve 
 대신 
freesurfer-boun...@nmr.mgh.harvard.edu
 

보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6



On 07/12/2016 11:03 PM, Lee Subin Kristine wrote:
>
> Hi Doug,
>
>
> Thanks a lot for the page! It was very helpful.
>
>
> I have a few questions about one of the commands and a question for
> one of the output files.
>
>
> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the
> point-spread function of the scanner or would a default value of 6
> work for all? I am using PET images from multiple centers and thus
> each image are from different scanners, and I'm not sure how I would
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change
depending upon recon method and parameters and even the ligand used. If
you get it about right, probably it will be close enough.
>
> (b) For the mgx flag, is the GM threshold .01 an optimal threshold
> referring to the p-value?(am new to PVEcorrection and asking out of
> curiosity) What is the difference if I enter .01 versus I don't enter it?
>
You must enter a threshold. When Muller-Gartner is implemented, there
are two stages: (1) orthogonalization (subtracting out non-GM) and (2)
rescaling. In the rescaling step, each voxel is divided by the fraction
of GM in that voxel. If that fraction is 0, then you will get an error.
If it is close to 0, you can get extreme noise amplification in that
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be
rescaled, otherwise the voxel is set to 0.
>
>
> 2) From the *gtm.stats.dat *output file, the 5th column(number of PET
> voxels in the ROI) of, for example, the ctx-lh-precuneus and
> ctx-rh-precuneus are 1744 and 1805 respectively. However, in the
> *?h.aparc.stats* files from recon-all, the 4th column(gray matter
> volume) of lh-precuneus and rh-precuneus are 5928 and 6125
> respectively. I am confused because I thought the number of PET voxels
> should be equal to the number of GM voxels in the ROI?
>
You need to scale by the size of the PET voxel.
>
> Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what
> programs can I open them with? It doesn't seem it is openned with
> mricron or gedit.
>
They are nifti files, though you probably don't want

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

[pierre deman]

ok thanks a lot for the quick answer.

let me know when it works.
our mri voxel size is 1 mm isotropic.
(if it changes anything, I am working on ubuntu 14.04).

Cheers,
Pierre

On Wed, Jul 20, 2016 at 11:15 AM, Iglesias, Eugenio 
wrote:

> Thanks a lot, Pierre.
> I’ll get this sorted out as soon as possible.  I’m in the process of
> modifying the module so it supports data with resolution >1mm, and also
> incorporating the longitudinal segmentation method described in
> https://doi.org/10.1016/j.neuroimage.2016.07.020
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 20 Jul 2016, at 09:57, pierre deman  wrote:
>
> Hi,
>
> I downloaded the new freesurfer development version and I still have the
> same problem when running the hippocampal-subfields
>
> "Invalid MEX-file 
> '/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64':
> libkvlGEMSCommon.so: cannot open shared object file: No such file or
> directory
> Error in kvlClear (line 11)
>
> Error in segmentSubjectT1_autoEstimateAlveusML (line 133)
>
> MATLAB:invalidMEXFile".
>
> Does anyone have any idea about a solution ?
>
> Cheers,
> Pierre
>
>
> On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio 
> wrote:
>
>> And thanks to Zeke, of course ;-)
>>
>>
>> Juan Eugenio Iglesias
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 13 Jul 2016, at 11:19, Iglesias, Eugenio  wrote:
>>
>> Dear all,
>> our expert developer Zeke Kaufman figured out what the problem was. We
>> have now fixed the Linux version; the MAC version will hopefully be ready
>> as well in a couple of days. I have also fixed other bugs (including the
>> problem that caused the code to get stuck every once in a while).
>> You can downloaded the latest development version from our website.
>> Thanks everyone for your feedback.
>> Cheers,
>> Eugenio
>>
>>
>>
>> Juan Eugenio Iglesias
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 8 Jul 2016, at 12:14, Iglesias, Eugenio  wrote:
>>
>> I think I identified the problem; hopefully this will be sorted out very
>> soon.
>> Cheers,
>> Eugenio
>>
>> Juan Eugenio Iglesias
>> Translational Imaging Group
>> University College London
>> http://www.jeiglesias.com
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>> On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis <
>> rpereacama...@mgh.harvard.edu> wrote:
>>
>> *Warning: This message has had one or more attachments removed
>> (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s)
>> for more information.*
>> Hi all,
>> I am currently trying to run hippocampal subfields in a couple of my
>> participants using FreeSurfer6.0 (located at
>> *nmr*:/usr/local/freesurfer/stable6).
>>
>> It did run successfully for many of my subjects earlier in the year but
>> some of them only had a let hemisphere segmentation. So I decided to re-run
>> them using launchpad and also my local nmr computer.
>>
>> Now, none of the hippocampal sufields segmentations appear (no
>> rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at
>> /scripts/scripts/hippocampal-subfields-T1T2.log and the error I
>> get is:
>>
>> Error:Cannot find CTF archive
>> /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
>>
>>
>> Could a missing *.ctf  cause the error? (btw, the re-run happened after
>> the major hardware crash).
>>
>> Thanks in advance for your help,
>> Rodrigo
>>
>> PS: I am attaching the *log files as suggested in the bug reporting page.
>>
>>
>> ---
>> Rodrigo Dennis Perea
>> Research Fellow
>> Department of Radiology
>> Athinoula A. Martinos Center
>> Massachusetts General Hospital
>> rpereacama...@mgh.harvard.edu
>>
>>
>>
>>
>>
>>
>> This is a message from the E-Mail Virus Protection System at UCL
>> --
>>
>> The original e-mail attachment (recon-all.cmd) is on the list of
>> unacceptable attachments for UCL and has been replaced by this
>> warning message.  This constraint is in place to protect users
>> from viruses and other malware.
>>
>> If you think this attachment is a legitimate file and you wish to
>> receive it, please ask the sender to rename the file extension (eg
>> rename file.exe to file.ex_) and resend it to avoid this constraint.
>> On receiving the file you will have to save it and rename it back to
>> its original extension.
>>
>>
>> Reference: 1bLDxs-0003ZW-3F
>>
>> --
>> UCL E-mail Virus Protection System
>> serviced...@ucl.ac.uk
>> Internal phone: 25000
>>
>>
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The info

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

[Iglesias, Eugenio]

Thanks a lot, Pierre.
I’ll get this sorted out as soon as possible.  I’m in the process of modifying 
the module so it supports data with resolution >1mm, and also incorporating the 
longitudinal segmentation method described in 
https://doi.org/10.1016/j.neuroimage.2016.07.020
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 20 Jul 2016, at 09:57, pierre deman 
mailto:deman.pie...@gmail.com>> wrote:

Hi,

I downloaded the new freesurfer development version and I still have the same 
problem when running the hippocampal-subfields

"Invalid MEX-file 
'/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64':
 libkvlGEMSCommon.so: cannot open shared object file: No such file or directory
Error in kvlClear (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 133)

MATLAB:invalidMEXFile".

Does anyone have any idea about a solution ?

Cheers,
Pierre


On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
And thanks to Zeke, of course ;-)


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 13 Jul 2016, at 11:19, Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Dear all,
our expert developer Zeke Kaufman figured out what the problem was. We have now 
fixed the Linux version; the MAC version will hopefully be ready as well in a 
couple of days. I have also fixed other bugs (including the problem that caused 
the code to get stuck every once in a while).
You can downloaded the latest development version from our website.
Thanks everyone for your feedback.
Cheers,
Eugenio



Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 8 Jul 2016, at 12:14, Iglesias, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

I think I identified the problem; hopefully this will be sorted out very soon.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis 
mailto:rpereacama...@mgh.harvard.edu>> wrote:


Warning: This message has had one or more attachments removed (recon-all.cmd). 
Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.

Hi all,
I am currently trying to run hippocampal subfields in a couple of my 
participants using FreeSurfer6.0 (located at 
*nmr*:/usr/local/freesurfer/stable6).

It did run successfully for many of my subjects earlier in the year but some of 
them only had a let hemisphere segmentation. So I decided to re-run them using 
launchpad and also my local nmr computer.

Now, none of the hippocampal sufields segmentations appear (no 
rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at 
/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get 
is:

Error:Cannot find CTF archive 
/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf


Could a missing *.ctf  cause the error? (btw, the re-run happened after the 
major hardware crash).

Thanks in advance for your help,
Rodrigo

PS: I am attaching the *log files as suggested in the bug reporting page.


---
Rodrigo Dennis Perea
Research Fellow
Department of Radiology
Athinoula A. Martinos Center
Massachusetts General Hospital
rpereacama...@mgh.harvard.edu






This is a message from the E-Mail Virus Protection System at UCL
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Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

[pierre deman]

Hi,

I downloaded the new freesurfer development version and I still have the
same problem when running the hippocampal-subfields

"Invalid MEX-file
'/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64':
libkvlGEMSCommon.so: cannot open shared object file: No such file or
directory
Error in kvlClear (line 11)

Error in segmentSubjectT1_autoEstimateAlveusML (line 133)

MATLAB:invalidMEXFile".

Does anyone have any idea about a solution ?

Cheers,
Pierre


On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio 
wrote:

> And thanks to Zeke, of course ;-)
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 13 Jul 2016, at 11:19, Iglesias, Eugenio  wrote:
>
> Dear all,
> our expert developer Zeke Kaufman figured out what the problem was. We
> have now fixed the Linux version; the MAC version will hopefully be ready
> as well in a couple of days. I have also fixed other bugs (including the
> problem that caused the code to get stuck every once in a while).
> You can downloaded the latest development version from our website.
> Thanks everyone for your feedback.
> Cheers,
> Eugenio
>
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 8 Jul 2016, at 12:14, Iglesias, Eugenio  wrote:
>
> I think I identified the problem; hopefully this will be sorted out very
> soon.
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis <
> rpereacama...@mgh.harvard.edu> wrote:
>
> *Warning: This message has had one or more attachments removed
> (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s)
> for more information.*
> Hi all,
> I am currently trying to run hippocampal subfields in a couple of my
> participants using FreeSurfer6.0 (located at
> *nmr*:/usr/local/freesurfer/stable6).
>
> It did run successfully for many of my subjects earlier in the year but
> some of them only had a let hemisphere segmentation. So I decided to re-run
> them using launchpad and also my local nmr computer.
>
> Now, none of the hippocampal sufields segmentations appear (no
> rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at
> /scripts/scripts/hippocampal-subfields-T1T2.log and the error I
> get is:
>
> Error:Cannot find CTF archive
> /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf
>
>
> Could a missing *.ctf  cause the error? (btw, the re-run happened after
> the major hardware crash).
>
> Thanks in advance for your help,
> Rodrigo
>
> PS: I am attaching the *log files as suggested in the bug reporting page.
>
>
> ---
> Rodrigo Dennis Perea
> Research Fellow
> Department of Radiology
> Athinoula A. Martinos Center
> Massachusetts General Hospital
> rpereacama...@mgh.harvard.edu
>
>
>
>
>
>
> This is a message from the E-Mail Virus Protection System at UCL
> --
>
> The original e-mail attachment (recon-all.cmd) is on the list of
> unacceptable attachments for UCL and has been replaced by this
> warning message.  This constraint is in place to protect users
> from viruses and other malware.
>
> If you think this attachment is a legitimate file and you wish to
> receive it, please ask the sender to rename the file extension (eg
> rename file.exe to file.ex_) and resend it to avoid this constraint.
> On receiving the file you will have to save it and rename it back to
> its original extension.
>
>
> Reference: 1bLDxs-0003ZW-3F
>
> --
> UCL E-mail Virus Protection System
> serviced...@ucl.ac.uk
> Internal phone: 25000
>
>
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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.
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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 . I

Re: [Freesurfer] error during longitudinal -long stream

[Martin Reuter]

Hi Jinsong, 

I have never seen this. Stable 5.3 is very stable and I doubt it is a bug. How 
did you process base and cross sectionals? Also with 5.3 ?

I would recommend to process cross and base with 5.3, then re-run the long and 
see if you can replicate this problem. Let me know what happens.

Best, Martin


> On Jul 20, 2016, at 12:48 AM, Jinsong Tang  wrote:
> 
> Hi all,
> 
> I found an error during the longitudinal -long stream:
> 
> recon-all -long P1001-2 P1001 -all
> ..
> 
> FREESURFER_HOME /space/raid/fmri/freesurfer
> Actual FREESURFER_HOME /space/raid/fmri/freesurfer
> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC 2016 
> (832c776) x86_64 x86_64 x86_64 GNU/Linux
> ..
> 
> mris_spherical_average -erode 1 -orig white -t 0.4 -o P1001-2.long.P1001 
> label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 
> 
> painting output onto subject P1001-2.long.P1001.
> processing subject lh.EC_average...
> MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):
>  could not open file
> eroding label 1 times before writing
> thresholding label stat at 0.400 before writing
> Not a directory
> mris_spherical_average: could not read surface file 
> /space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg
> Not a directory
> Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC 2016 
> (832c776) x86_64 x86_64 x86_64 GNU/Linux
> 
> recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul  8 21:33:02 PDT 
> 2016
> 
> 
> Please help me fix this error!
> 
> Thanks and best regards,
> 
> Jinsong
> 
> 
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