date:20160909

[Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1

2016-09-09 Thread Seung Gul Kang

Hi,

I am new learner in freesurfer and analyzing the difference of the
thickness between two groups using qdec.

There is a error as below.
I don't know what is the reason.

ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y /mnt/hgfs/share/kang_fs/qdec/2/y.mgh --fsgd
/mnt/hgfs/share/kang_fs/qdec/2/qdec.fsgd dods --glmdir
/mnt/hgfs/share/kang_fs/qdec/2 --surf fsaverage lh --label
/mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Avg-Intercept-thickness.mat --C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-H-I-Intercept-thickness.mat
--C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-M-F-Intercept-thickness.mat
--C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-X-diagnosis-sex-Intercept-thickness.mat
  2. The FSGD file (if using one)
  3. And the design matrix above
Error in Analyze: command failed: mri_glmfit --y
/mnt/hgfs/share/kang_fs/qdec/2/y.mgh --fsgd
/mnt/hgfs/share/kang_fs/qdec/2/qdec.fsgd dods --glmdir
/mnt/hgfs/share/kang_fs/qdec/2 --surf fsaverage lh --label
/mnt/hgfs/share/kang_fs/fsaverage/label/lh.aparc.label --C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Avg-Intercept-thickness.mat --C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-H-I-Intercept-thickness.mat
--C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-Diff-M-F-Intercept-thickness.mat
--C
/mnt/hgfs/share/kang_fs/qdec/2/contrasts/lh-X-diagnosis-sex-Intercept-thickness.mat

matrix

Design matrix --
 1.000   0.000   0.000   0.000   27.000   0.000   0.000   0.000   3.000
0.000   0.000   0.000   2.600   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   28.000   0.000   0.000
0.000   4.000   0.000   0.000   0.000   2.440   0.000;
 1.000   0.000   0.000   0.000   25.000   0.000   0.000   0.000   1.000
0.000   0.000   0.000   2.510   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   26.000   0.000   0.000
0.000   7.000   0.000   0.000   0.000   2.500   0.000;
 1.000   0.000   0.000   0.000   35.000   0.000   0.000   0.000   1.000
0.000   0.000   0.000   2.450   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   30.000   0.000   0.000   0.000   0.000
0.000   0.000   0.000   2.380   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000   0.000
0.000   0.000   0.000   0.000   0.000   2.430   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000   0.000
0.000   1.000   0.000   0.000   0.000   2.390   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   28.000   0.000   0.000
0.000   0.000   0.000   0.000   0.000   2.350   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   33.000   0.000   0.000
0.000   2.000   0.000   0.000   0.000   2.400   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   45.000   0.000   0.000
0.000   0.000   0.000   0.000   0.000   2.300   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   38.000   0.000   0.000
0.000   0.000   0.000   0.000   0.000   2.300   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   24.000   0.000   0.000
0.000   0.000   0.000   0.000   0.000   2.480   0.000;
 1.000   0.000   0.000   0.000   28.000   0.000   0.000   0.000   0.000
0.000   0.000   0.000   2.310   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   30.000   0.000   0.000   0.000   0.000
0.000   0.000   0.000   2.460   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   39.000   0.000   0.000   0.000   3.000
0.000   0.000   0.000   2.230   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   48.000   0.000   0.000
0.000   4.000   0.000   0.000   0.000   2.410   0.000;
 1.000   0.000   0.000   0.000   32.000   0.000   0.000   0.000   3.000
0.000   0.000   0.000   2.370   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   32.000   0.000   0.000   0.000   4.000
0.000   0.000   0.000   2.510   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   31.000   0.000   0.000
0.000   2.000   0.000   0.000   0.000   2.380   0.000;
 1.000   0.000   0.000   0.000   33.000   0.000   0.000   0.000   1.000
0.000   0.000   0.000   2.390   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   33.000   0.000   0.000   0.000   1.000
0.000   0.000   0.000   2.540   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   44.000   0.000   0.000
0.000   4.000   0.000   0.000   0.000   2.290   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   41.000   0.000   0.000
0.000   2.000   0.000   0.000   0.000   2.420   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   41.000   0.000   0.000
0.000   1.000   0.000   0.000   0.000   2.400   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   43.000   0.000   0.000
0.000

[Freesurfer] Convert 4D volume time series to GIFTI surface time series

2016-09-09 Thread Prokopis Prokopiou

Dear all,

I am trying to convert 4D volume time series to GIFTI surface time series.
Following the instructions given in a previous post,  so far, I have tried
using mri_vol2surf and mris_convert, with no success (i.e. when I try to
open the surface file in freeview I get Failed to load Surface
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i). I would really appreciate if anyone could give me an advise on how to
make it work.  I give below the logs of each process.

Thank you,
Prokopis

 

osboxes@osboxes:~$ mri_vol2surf --mov
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii --reg
$SUBJECTS_DIR/AL_subject/AL_registrations/AL.mat --hemi lh --o
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh --projfrac 0.5 --interp nearest

srcvol =
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii

srcreg =
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL_registratio
ns/AL.mat

srcregold = 0

srcwarp unspecified

surf = white

hemi = lh

ProjFrac = 0.5

thickness = thickness

reshape = 0

interp = nearest

float2int = round

GetProjMax = 0

INFO: float2int code = 0

Done loading volume

Reading surface
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL/surf/lh.whi
te

Done reading source surface

Reading thickness
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_test//AL_subject/AL/surf/lh.thi
ckness

Done

Mapping Source Volume onto Source Subject Surface

1 0.5 0.5 0.5

using old

Done mapping volume to surface

Number of source voxels hit = 11976

Writing to
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh

Dim: 139848 1 1

 

 

osboxes@osboxes:~$ mri_info
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh

Volume information for
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh

  type: MGH

dimensions: 139848 x 1 x 1 x 400

   voxel sizes: 1., 1., 1.

  type: FLOAT (3)

   fov: 139848.000

   dof: 0

xstart: -69924.0, xend: 69924.0

ystart: -0.5, yend: 0.5

zstart: -0.5, zend: 0.5

TR: 3000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees

   nframes: 400

   PhEncDir: UNKNOWN

ras xform present

xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
-3.2031

  : x_a =   0., y_a =   1., z_a =   0., c_a =
3.2031

  : x_s =   0., y_s =   0., z_s =   1., c_s =
72.

 

talairach xfm : 

Orientation   : LAS

Primary Slice Direction: axial

 

voxel to ras transform:

   -1.   0.   0. 69920.7969

0.   1.   0. 2.7031

0.   0.   1.71.5000

0.   0.   0. 1.

 

voxel-to-ras determinant -1

 

ras to voxel transform:

   -1.   0.   0. 69920.7969

   -0.   1.  -0.-2.7031

   -0.  -0.   1.   -71.5000

0.   0.   0. 1.

 

 

 

 

 

osboxes@osboxes:~$ mris_convert -f
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_surface_time_series_lh.
mgh   $SUBJECTS_DIR/AL_subject/AL/surf/lh.white
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i

 

 

 

freeview log: 

 

osboxes@osboxes:~$ mriseadGIFTIfile: mris is NULL! found when parsing file
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i

MRISread failed

mriseadGIFTIfile: mris is NULL! found when parsing file
/home/osboxes/Desktop/AL_subject/AL_registrations/AL_time_series_white_lh.gi
i

 

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Re: [Freesurfer] Parcelation a2009 as mask for SPM analysis

2016-09-09 Thread Douglas Greve

Did you verify that the result of mni152reg is accurate? It should have 
printed out a command line to check it


On 9/9/16 5:58 AM, Matyáš Kuhn wrote:
> Hi FreeSurfer experts,
>
> We would like to use Destrieux atlas for masking DLPFC in subjects, who
> uderwent fMRI and we used SPM to process the data. We want to find peaks
> in individuals according to some regions from the atlas (create
> individual mask). The problem I am facing is to get
> aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM
> and Freesurfer.
>
> I followed some discussions on mailing list and tried this:
>
> mni152reg --s $SUB
>
> mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \
>   --temp /.../spm/spmT_0001.nii \
>   --reg
> $SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \
>   --o aseg.$SUB.mni152.nii
>
> The process ended without errors, but while watching results in freeview
> - the results are not correctly aligned. Is FSL (which is part of
> mni152reg procedure) using some other MNI template than SPM?
> Any suggestions will be most appreciated.
>
> The freeview snapshot is here:
> https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a2009s_mni.PNG
>
>
> ___
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>
>

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[Freesurfer] Viewing Retinotopy In Freeview

2016-09-09 Thread Taylor, Johnmark

Hello,

I am thinking of switching from Tksurfer to Freeview, but I want to make
sure that retinotopy visualization still works well. Is it straightforward
to view phase-encoded displays? There are a few options on tksurfer
(complex color wheel, ability to set number of cycles and angle offset for
phase encoded display, ability to smooth overlay) that I am not able to
immediately find on freeview. Currently, to visualize retinotopy data we
are using the strategy of loading both the real and complex parts of the
display on tksurfer. Are there analogous ways of doing all these steps on
freeview as of yet, or are they still waiting to be implemented?

Thank you very much,

JohnMark
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Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

2016-09-09 Thread Smaragdi A.

Hi,

that makes sense! I sent an old ascii file (that worked) to my mac, copied and 
pasted a design from there and sent back. Glad it was something simple.

 It is working now, thank you very much!

Areti

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 09 September 2016 16:41
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]


How did you create this file? It has "carriage returns" instead of "new lines" 
-- quite an obscure and annoying difference. It usually means that you created 
the file with something that is not a simple ascii text editor (or you created 
it under windows). If you 'less' the file in linux, you will see a bunch of 
"^M". You will need to change the file to used new lines instead of carriage 
returns

On 9/9/16 11:25 AM, Smaragdi A. wrote:

Hi,

do you mean the designfile? This is attached.

Thank you,

Areti

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 09 September 2016 16:20
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Is your matrix a simple ascii text file? If so, please send.


On 9/9/16 11:00 AM, Smaragdi A. wrote:


Dear mailinglist,

I get the following error when I run the mri_glmfit:

 MatrixReadTxT: could not scan value [8][360]
 WARNING: matlab elment type is 805908489, which is not a matrix.

It seems like problems such as this one are common, but I haven't found an 
answer in the archive for this specific one, and my design files have worked 
before (I have just taken out one continuous variable, so no extra rows or 
anything like that).

Many thanks,

Areti

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Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

2016-09-09 Thread Douglas Greve

How did you create this file? It has "carriage returns" instead of "new 
lines" -- quite an obscure and annoying difference. It usually means 
that you created the file with something that is not a simple ascii text 
editor (or you created it under windows). If you 'less' the file in 
linux, you will see a bunch of "^M". You will need to change the file to 
used new lines instead of carriage returns



On 9/9/16 11:25 AM, Smaragdi A. wrote:

Hi,

do you mean the designfile? This is attached.

Thank you,

Areti

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 09 September 2016 16:20
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Is your matrix a simple ascii text file? If so, please send.


On 9/9/16 11:00 AM, Smaragdi A. wrote:

Dear mailinglist,

I get the following error when I run the mri_glmfit:

  MatrixReadTxT: could not scan value [8][360]
  WARNING: matlab elment type is 805908489, which is not a matrix.

It seems like problems such as this one are common, but I haven't found an 
answer in the archive for this specific one, and my design files have worked 
before (I have just taken out one continuous variable, so no extra rows or 
anything like that).

Many thanks,

Areti

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Re: [Freesurfer] white and pial surface crossin in the lingual gyrus

2016-09-09 Thread Bruce Fischl


Hi Alain

I'm pretty sure that this is a bug in 5.3 that is fixed in dev and will 
not be an issue in 6.0. You can test this by downloading and trying out 
dev if you like.


cheers
Bruce
On Fri, 9 Sep 2016, Alain Imaging wrote:



Hello everybody,


I am gladly starting my freesurfer adventure after the awesome last course
in Copenhagen, but I have quickly realized that troubleshooting on your own
is not as easy as with experts going around in a room.


I was looking for errors after having run the recon all and I stumbled upon
this crossing between white and pial surface in the lingual gyrus (see
attached Figure1, green arrow).


It seems to me that the problem may arise from the fact that in the WM
volume (see attached Figure2) there are areas that have been categorized as
WM hypointensities, and in particular on the right, the problem could be
that the white matter surface, instead of going around these brighter
voxels, just goes straight down (I hope I have explained myself). Is the
fixing to this problem changing the value of those voxels (part of them, of
course) in the WM volume ?  If I look at the WM seg I see that indeed they
are left out from the mask. Or should I do something else ?


I am working with freesurfer version Linux-centos6_x86_64-stable-pub-v5.3.0,
with Linux version 3.10.0-327.4.5.el7.x86_64 (Red Hat 4.8.3-9).


Thanks in advance for any suggestion


Alain 


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Re: [Freesurfer] Flattening the surface

2016-09-09 Thread Bruce Fischl


Hi Younghoon

yes, the vertex index is perserved across all the surface and patch 
representations, so you should always be able to go from a flattened 
vertex back to its white or pial location


cheers
Bruce
On Thu, 8 Sep 2016, Younghoon Kim 
wrote:



Hi Bruce,

I sent you a message a while ago but have’t received your reply.

I generated a mgh file using mri_vol2surf, and thus mapped the texture that
I want to project onto both the inflated and the flattened surfaces.

I wonder whether it is possible to reversely map the vertices on the
vectorized surface (such as, ‘lh.orig’ or ‘lh.inflate') back to the voxels
in the volumetric file (mgz file), i.e. find the xyz coordinate of each
vertex in the frame of reference of the volumetric file (mgz file) used to
generate the vectorized surface.

Also, I’ve noticed that the number of the columns in the texture mapping
file (i.e. ‘lh.sig.mgh’, the output of mri_vol2surf command), is equal to
the number of the vertices on the vectorized surface. I assume that the
texture mapping file and the vectorized surface has a one-to-one
vertex/column correspondence. If so, I wonder how the texture intensity of
each vertex is stored in the texture mapping file and eventually mapped onto
the vectorized surface.

Thanks,

Younghoon Kim

--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr


켜짐 2016년 7월 27일 에서 06:51:01, Bruce Fischl
(fis...@nmr.mgh.harvard.edu) 작성됨:

sure, you can do that with mri_vol2surf. Basically the initial surface
and the final (inflated) surface have the same number of vertices, so
the
vertex identity is preserved and mri_vol2surf samples values from the
volume onto the surface which can then be displayed on any surface
configuration (like inflated)

On Tue, 26 Jul 2016, Younghoon Kim wrote:

> Hi Bruce,
>
> Thanks to your advice, I was able to obtain the surface of the
segmented
> brain area and its inflated surface using FreeSurfer.
>
> The generated surface however does not contain any texture, which is
needed
> for further steps in my project.
>
> I am considering to project the texture of the segmented brain area
(the
> pixel intensity on the surface of the volumetric data) to the
generated
> surface (vectorized surface). I wonder whether this can be done in a
similar
> way to the way you project fMRI signal to the 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 21, 2016 at 11:15:43 AM, Bruce Fischl
(fis...@nmr.mgh.harvard.edu)
> wrote:
>
> and 255 is the label that you want to cover? 16G may not be enough.
Do
> you
> have any machines with more RAM?
>
> On Thu, 21 Jul 2016, Younghoon
> Kim wrote:
>
> > Hi Bruce,
> >
> > Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
> the size is about 3000x2000x140. (We obtained this brain image using
> different imaging methods)
> >
> > Our machine has 16GB RAM.
> >
> > Thanks,
> >
> > Younghoon Kim
> >
> > --
> > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
> > OMICS Lab
> > --
> > younghoon.h@gmail.com
> > aktivh...@kaist.ac.kr
> >
> >
> > On July 21, 2016 at 10:35:18 AM, Bruce Fischl
> (fis...@nmr.mgh.harvard.edu) wrote:
> >
> > is Brain_FS.mgz a segmented volume? How much memory do you have on
> that
> > machine?
> >
> > On Wed, 20 Jul 2016, Younghoon Kim wrote:
> >
> > > 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
>

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

2016-09-09 Thread Smaragdi A.

Hi,

do you mean the designfile? This is attached. 

Thank you,

Areti

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: 09 September 2016 16:20
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Is your matrix a simple ascii text file? If so, please send.


On 9/9/16 11:00 AM, Smaragdi A. wrote:
> Dear mailinglist,
>
> I get the following error when I run the mri_glmfit:
>
>  MatrixReadTxT: could not scan value [8][360]
>  WARNING: matlab elment type is 805908489, which is not a matrix.
>
> It seems like problems such as this one are common, but I haven't found an 
> answer in the archive for this specific one, and my design files have worked 
> before (I have just taken out one continuous variable, so no extra rows or 
> anything like that).
>
> Many thanks,
>
> Areti
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  105
1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   15  112.5
1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   16  97.5
1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  102.5
1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   15  112.5
1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   15  95
1   0   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  90
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   18  90
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  97.5
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   16  102.5
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   16  110
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   15  82.5
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   16  80
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  115
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  88
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   17  95
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   16  103
0   1   0   0   0   0   0   0   0   0   
0   0   0   0   0   0   16  110
0   0   1   0   0   0   0   0   0   0   
0   0   0   0   0   0   17  71
0   0   1   0   0   0   0   0   0   0   
0   0   0   0   0   0   18  70
0   0   1   0   0   0   0   0   0   0   
0   0   0   0   0   0   18  85
0   0   1   0   0   0   0   0   0   0   
0   0   0   0   0   0   17  95
0   0   1   0   0   0   0   0   0   0   
0   0   0   0   0   0   14  80
0

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

2016-09-09 Thread Douglas Greve

Is your matrix a simple ascii text file? If so, please send.

On 9/9/16 11:00 AM, Smaragdi A. wrote:
> Dear mailinglist,
>
> I get the following error when I run the mri_glmfit:
>
>  MatrixReadTxT: could not scan value [8][360]
>  WARNING: matlab elment type is 805908489, which is not a matrix.
>
> It seems like problems such as this one are common, but I haven't found an 
> answer in the archive for this specific one, and my design files have worked 
> before (I have just taken out one continuous variable, so no extra rows or 
> anything like that).
>
> Many thanks,
>
> Areti
>
> ___
> 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
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[Freesurfer] MatrixReadTxT: could not scan value [8][360]

2016-09-09 Thread Smaragdi A.

Dear mailinglist,

I get the following error when I run the mri_glmfit:

MatrixReadTxT: could not scan value [8][360]
WARNING: matlab elment type is 805908489, which is not a matrix.

It seems like problems such as this one are common, but I haven't found an 
answer in the archive for this specific one, and my design files have worked 
before (I have just taken out one continuous variable, so no extra rows or 
anything like that).

Many thanks,

Areti

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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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dispose of the e-mail.

[Freesurfer] Parcelation a2009 as mask for SPM analysis

2016-09-09 Thread Matyáš Kuhn

Hi FreeSurfer experts,

We would like to use Destrieux atlas for masking DLPFC in subjects, who 
uderwent fMRI and we used SPM to process the data. We want to find peaks 
in individuals according to some regions from the atlas (create 
individual mask). The problem I am facing is to get 
aparc.a2009s+aseg.mgz to MNI space so I could overlay results from SPM 
and Freesurfer.

I followed some discussions on mailing list and tried this:

mni152reg --s $SUB

mri_label2vol --seg $SUBJECTS_DIR/$SUB/mri/aparc.a2009s+aseg.mgz \
 --temp /.../spm/spmT_0001.nii \
 --reg 
$SUBJECTS_DIR/$SUB/mri/transforms/reg.mni152.2mm.dat \
 --o aseg.$SUB.mni152.nii

The process ended without errors, but while watching results in freeview 
- the results are not correctly aligned. Is FSL (which is part of 
mni152reg procedure) using some other MNI template than SPM?
Any suggestions will be most appreciated.

The freeview snapshot is here: 
https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question/freeview_a2009s_mni.PNG


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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] ERROR: matrix is ill-conditioned or badly scaled, condno = 22801.1

[Freesurfer] Convert 4D volume time series to GIFTI surface time series

Re: [Freesurfer] Parcelation a2009 as mask for SPM analysis

[Freesurfer] Viewing Retinotopy In Freeview

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Re: [Freesurfer] white and pial surface crossin in the lingual gyrus

Re: [Freesurfer] Flattening the surface

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

Re: [Freesurfer] MatrixReadTxT: could not scan value [8][360]

[Freesurfer] MatrixReadTxT: could not scan value [8][360]

[Freesurfer] Parcelation a2009 as mask for SPM analysis

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