date:20160621

[Freesurfer] aseg mask error

2016-06-21 Thread Jasmin Alves

FREESURFER_HOME: /home/rcf-proj/kap/shared/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

RedHat release: CentOS release 6.7 (Final)

Kernel info: Linux 2.6.32-573.22.1.el6.x86_64 x86_64


Hello Freesurfer,


For some strange reason, a participant's entire aseg is being mapped onto
one hemisphere. This is the case with two different mprage files.

I have attached a screenshot.

I am not quite sure how to fix this. Is it something I should fix using
TKMEDIT?

Thank you,

Jasmin

-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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[Freesurfer] Yeo 2011 Functional Cortical Parcellations

2016-06-21 Thread Bronwyn Overs


Hi Mailing List,

I am attempting to apply the Yeo 2011 7-network fucntional parcellations 
to a set of fs MRIs processed with v5.1.0. Below are listed the first 
three steps I plan to take and I am seeking advice as to:


A) Whether this approach is valid.
B) Steps to take next.

*
Steps 1-3:
*

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid 
Yeo2011_MNI152_FS

recon-all -all -subjid Yeo2011_MNI152_FS

*2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
mri_vol2vol --mov 
Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s 
Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z 
talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest


*3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ 
Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o 
Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph



When previously mapping the Choi 2012 straital parcellations, steps 4 
and 5 were:


4. *Creating a striatal mask in the native subject's space from 
freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens 
(26 & 58)*:
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 
26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz


*5. **Using this mask to mask the choi striatal parcellations*
fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz 
Yeo_atlas_subjID_mask.nii.gz



Do I need to do a similar thing for the Yeo cortical parcellations and 
if so what regions should I include in the cortical mask?


--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


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[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

2016-06-21 Thread Arkadiy Maksimovskiy

Hello,

Hello,

I am getting the following error:

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Command line:
mri_glmfit --y lh.BD_SD.thickness.10B.mgh --fsgd
FSGD_Collapsed_Across_Smokers_demeaned.fsgd dods --C BDvsSD1.mtx --surf
fsaverage lh --cortex --glmdir lh.BD_SD.glmdir

The FSGD file (if using one)

Design matrix:

Design matrix --
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -2.151   0.000   0.000   0.000   0.000   0.000   9.340   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -2.151   0.000   0.000   0.000   0.000   0.000  -2.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   1.849   0.000   0.000   0.000   0.000   0.000  -31.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -2.151   0.000   0.000   0.000   0.000   0.000  -37.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -2.151   0.000   0.000   0.000   0.000   0.000   26.340   0.000;
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000
0.000   0.000  -0.151   0.000   0.000   0.000   0.000   0.000  -20.660;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -1.151   0.000   0.000   0.000   0.000   0.000  -22.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   3.849   0.000   0.000   0.000   0.000   0.000  -16.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -1.151   0.000   0.000   0.000   0.000   0.000   14.340   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   2.849   0.000   0.000   0.000   0.000   0.000  -27.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   1.849   0.000   0.000   0.000   0.000   0.000   4.340   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -0.151   0.000   0.000   0.000   0.000   0.000  -30.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   0.849   0.000   0.000   0.000   0.000   0.000  -28.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   0.849   0.000   0.000   0.000   0.000   0.000  -23.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -2.151   0.000   0.000   0.000   0.000   0.000  -27.660   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000   2.849   0.000   0.000   0.000   0.000   0.000   13.340   0.000;
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000
0.000  -2.151   0.000   0.000   0.000   0.000   0.000   5.340   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -2.151   0.000   0.000
0.000   0.000   0.000   36.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -1.151   0.000   0.000
0.000   0.000   0.000  -0.660   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -2.151   0.000   0.000
0.000   0.000   0.000   54.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -1.151   0.000   0.000
0.000   0.000   0.000   45.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -2.151   0.000   0.000
0.000   0.000   0.000   22.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   1.849   0.000   0.000
0.000   0.000   0.000   38.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -1.151   0.000   0.000
0.000   0.000   0.000  -12.660   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.849   0.000   0.000
0.000   0.000   0.000  -12.660   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -0.151   0.000   0.000
0.000   0.000   0.000   16.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -0.151   0.000   0.000
0.000   0.000   0.000   50.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -2.151   0.000   0.000
0.000   0.000   0.000  -35.660   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -1.151   0.000   0.000
0.000   0.000   0.000   59.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -0.151   0.000   0.000
0.000   0.000   0.000   25.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -1.151   0.000   0.000
0.000   0.000   0.000   32.340   0.000   0.000   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000  -2.151   0.000   0.000
0.000   0.000   0.000   14.340   0.000   0.000   0.000   0.000   0.000;
 0.000

Re: [Freesurfer] cortical surface pattern matching

2016-06-21 Thread Bruce Fischl

Hi Greg

you could threshold then look at Hausdorff distance of the blobs. Or you 
could smooth before computing correlation as that will take spatial stuff 
into account.

Or if you have a patch that you want to cross-correlate against the rest of 
the surface you could do it on the sphere, although that's a bit of a pain 
since you have to take the metric tensor into account

cheers
Bruce


On Tue, 21 Jun 2016, GREGORY 
R KIRK wrote:

> 
> Hi,
> 
> 
> has anyone created functionality to compare the spatial
> correlation/similarity
> 
> of two patterns in the form of cortical surface overlays. What I am looking
> at is a have
> 
> scalar at every point on the cortical surface. obviously this is just a list
> of vertices with
> 
> a scalar value associated with each. obviously I can map these both onto an
> average cortical surface and then simply compute the correlation of both of
> these.
> 
> 
> but of course pattern similarity is an inherently spatial problem and for
> cortical
> 
> surfaces a 2 dimensional spatial correlation or other similarity metric
> would be
> 
> what you want. Here the order of vertices in a vertex list maps somewhat
> like a
> 
> string around the cortex and so the next wrap around you have vertices which
> are
> 
> adjacent on the surface but distant by the metric of vertex count.
> 
> 
> is there any implementation of a similarity metric which takes this
> coordinate problem into account. In my measure every vertex across both hemi
> has a value and so i am not interested in something for a small localized
> patch.
> 
> 
> any thoughts appreciated
> 
> 
> Greg
> 
> 
>
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Re: [Freesurfer] XQuartz 2.7.9 update results in errors

2016-06-21 Thread Z K

Hello Kate,

Thanks for the information. We have seen similar behavior with previous 
XQuartz releases in the past as well. This tends to "freeze" certain 
vesion of OSX with certain versions of XQuartz. I will take a closer 
look but this is usually something that we have to deal with.

-Zeke

On 06/20/2016 08:34 PM, Kate Mills wrote:
> Hi All,
>
> My lab is having difficulty loading the freeview gui after updating to
> the latest version of XQuartz (2.7.9). We were wondering if others have
> experienced this issue? We have reverted by to XQuartz 2.7.8 on our
> machines for now. In case relevant, this errors seems to span Mac OS
> versions.
>
> Thank you!
>
> Kate
>
>
>
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Re: [Freesurfer] FSFAST- Cerebellum

2016-06-21 Thread Sabin Khadka

Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space.
I process my fmri data with

preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
-per-run -stc odd
and then to extract ROI time series values I did

mri_segstats --annot fsaverage rh aparc --i
rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
--excludeid 2004 --avgwf CorticalTimeSeries_rh.txt

and for cortical time series

mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
/opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
--i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
subCorticalTimeSeries.txt

Now I am not sure as how to extract cerebellum ROIs (time series as
described in Buckner et.al 2011)? If there are any other additional steps I
need to perform ? or if I have to use some other scripts commands (other
than mri_segstats).


Cheers,
Sabin Khadka

On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo  wrote:

> Hi Sabin,
>
> The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
> substructures of the cerebellum (e.g., Crus I, etc). Is that what you
> want? Or are you looking to use the functional parcels defined in
> Buckner 2011?
>
> In addition, I do not know how mri_segstats works, so I cannot verify
> how you call the command is correct. Maybe others can provide feedback
> here.
>
> However, the Buckner cerebellar parcellations in
> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
> space. From your command, I assume your data is in MNI305 space. So
> you might need to transform the parcellation from MNI152 to MNI305.
>
> Thanks,
> Thomas
>
> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka 
> wrote:
> > Hi all,
> >
> > I am trying to extract mean time series BOLD data using FSFAST from
> Cortical
> > ROIs + sub cortical ROIs and cerebellum.
> >
> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
> > -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> > mri_segstats --annot fsaverage rh aparc --i
> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >
> > and for cortical time series
> >
> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> --id
> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
> 58
> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> > subCorticalTimeSeries.txt
> >
> > But I am not sure on how exactly to extract time series from cerebellar
> > regions. So if I want to extract time series from regions as described in
> > Buckner et.al 2011. Could I just use mri_segstats for the labels
> 601-628 in
> > FreeSurferCololLUT.txt? If not could you please direct me to processes
> that
> > I can use.
> >
> > Cheers,
> > Sabin Khadka
> >
> > ___
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> >
> >
> > The information in this e-mail is intended only for the person to whom
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> > 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
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> 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] smoothing T1 images

2016-06-21 Thread Bruce Fischl


Hi John

you can try mri_nlfilter if you like. It implement a nonlocal means/medians 
algorithm that I wrote in 1995 or so:


Bruce Fischl and Eric L. Schwartz. 
1999. Adaptive Nonlocal Filtering: A Fast Alternative to Anisotropic 
Diffusion for Image Enhancement. IEEE Trans. Pattern Anal. Mach. Intell. 
21, 1 (January 1999), 42-48. DOI=http://dx.doi.org/10.1109/34.745732


I'm not sure I would trust thickness estimates after nonlinear filtering, 
but it might help getting surface reconstructions and parcellations and 
such.


cheers
Bruce


On Tue, 21 Jun 2016, John Anderson wrote:



Hi FS experts,
I have T1 images with low quality (noise and artifacts). I am wondering if
smoothing these images, before runing the command "Recon-all", can help to
improve the segmentation and parcellation process for these images.
Thanks for any advice!
Bests,
John

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[Freesurfer] smoothing T1 images

2016-06-21 Thread John Anderson


Hi FS experts,

I have T1 images with low quality (noise and artifacts). I am wondering if smoothing these images, before runing the command "Recon-all", can help to improve the segmentation and parcellation process for these images.

Thanks for any advice!

Bests,
John
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Re: [Freesurfer] Error loading a constructed annotation file

2016-06-21 Thread Bittner, Nora

Thanks for your quick answer.
Yes, I have read permissions for that file. I can also load the rh.orig into 
freeview without any error message appearing in the terminal. Looks quite nice.
I tried using mris_fix_topology by taking the exact command from the 
recon-all.log of the particular subject.  And that indeed gives me an error 
message:

My command:
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 995005 rh > 
$SUBJECTS_DIR/995005/scripts/mris_fix_topology 2> 
$SUBJECTS_DIR/995005/scripts/mris_fix_topology

Full terminal output:
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading input surface 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
0
number of generations :10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient :  10.0
normal dot loglikelihood coefficient :  1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search :  1
initial patch selection :   1
select all defect vertices :0
ordering dependant retessellation:  0
use precomputed edge table :0
smooth retessellated patch :2
match retessellated patch : 1
verbose mode :  0

*
before topology correction, eno=-30 (nv=140324, nf=280708, ne=421062, g=16)
mrisReadTriangleFile(/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.orig):
 surface doesn't match 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.qsphere.nofix

Invalid argument
mrisReadTriangleFile failed.

Invalid argument
MRISreadOriginalProperties: could not read surface file orig
Invalid argument
mris_fix_topology: could not read original surface orig
Invalid argument

Seems like there is a mismatch between rh.orig and rh.qsphere.nofix. I never 
modified rh.orig. Do you have any idea, how this can happen?

Thank you very much!
Nora

Arbeitsgruppe Konnektivität
   Institut für Neurowissenschaften und Medizin (INM-1)
   Forschungszentrum Jülich GmbH
   52425 Jülich
   Tel.: 02461-612412
   Email: n.bitt...@fz-juelich.de

und

Arbeitsgruppe Konnektivität im menschlichen Gehirn
   C. und O. Vogt Institut für Hirnforschung
   Heinrich-Heine-Universität Düsseldorf
   Universitätsklinikum Düsseldorf
   40225 Düsseldorf
   Tel.: 0211-8106109
   Email: n.bitt...@fz-juelich.de

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
Gesendet: Dienstag, 21. Juni 2016 10:22
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Error loading a constructed annotation file

It does look like the problem is the rh.orig. Do you have read permissions for 
that file? It may be that the file is corrupt. Can you load just that file in 
freeview or tksurfer? If not, you can try to regenerate it by running 
mris_fix_topology (look in the subject/scripts/recon-all.log file for command).
On 6/20/16 8:47 PM, Bittner, Nora wrote:

Hi Bruce,



thanks, I will have a closer look to my annotation / label files I used, maybe 
something is wrong with them. I am happy to get an answer anyway.

I already attached the full commandline and the full terminal ouptput - didn´t 
you get the attached files? Is there another way to send you the files?



My command line was:



mris_label2annot --h rh --subject 995005 --ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a 
fronparnetwork --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.cortex.label 
--l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label
 --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label
 --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label
 --nhits nhits.mgh



And the terminal output (the full output is too big to simply copy it here - so 
I will attach the file again):



reading ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt

Number of ctab entries 5



$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $

cwd /data/Team_Caspers/Bittner/Skripte_Freesurfer

cmdline mris_label2annot --h rh --subject 995005 --ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a 
fronparnetwork --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.cortex.label 
--l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label
 --l

Re: [Freesurfer] Error loading a constructed annotation file

2016-06-21 Thread Douglas Greve

It does look like the problem is the rh.orig. Do you have read 
permissions for that file? It may be that the file is corrupt. Can you 
load just that file in freeview or tksurfer? If not, you can try to 
regenerate it by running mris_fix_topology (look in the 
subject/scripts/recon-all.log file for command).


On 6/20/16 8:47 PM, Bittner, Nora wrote:

Hi Bruce,

thanks, I will have a closer look to my annotation / label files I used, maybe 
something is wrong with them. I am happy to get an answer anyway.
I already attached the full commandline and the full terminal ouptput - didn´t 
you get the attached files? Is there another way to send you the files?

My command line was:

mris_label2annot --h rh --subject 995005 --ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a 
fronparnetwork --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.cortex.label 
--l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label
 --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label
 --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label
 --nhits nhits.mgh

And the terminal output (the full output is too big to simply copy it here - so 
I will attach the file again):

reading ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt
Number of ctab entries 5

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /data/Team_Caspers/Bittner/Skripte_Freesurfer
cmdline mris_label2annot --h rh --subject 995005 --ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a 
fronparnetwork --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.cortex.label 
--l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label
 --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label
 --l 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label
 --nhits nhits.mgh
sysname  Linux
hostname imecas08
machine  x86_64
user cjockwitz

subject 995005
hemirh
SUBJECTS_DIR /data/Team_Caspers/1000Brains-Projects/Freesurfer
ColorTable 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt
AnnotName  fronparnetwork
NHitsFile nhits.mgh
nlables 4
LabelThresh 0 0.00
Loading /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.orig
  1 -1 NOT_FOUND
  2 255 $SUBJECTS_DIR/995005/label/mask_Blob1_nonlinear.label
WARNING: vertex 77969 maps to multiple labels! (overwriting)
 (Warning message for many vertices) ...
WARNING: vertex 68151 maps to multiple labels! (overwriting)
Mapping unhit to unknown
Found 8016 unhit vertices
Writing annot to 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.fronparnetwork.annot

Thank you for helping me!
Best regards,
Nora


Arbeitsgruppe Konnektivität
Institut für Neurowissenschaften und Medizin (INM-1)
Forschungszentrum Jülich GmbH
52425 Jülich
Tel.: 02461-612412
Email: n.bitt...@fz-juelich.de

und

Arbeitsgruppe Konnektivität im menschlichen Gehirn
C. und O. Vogt Institut für Hirnforschung
Heinrich-Heine-Universität Düsseldorf
Universitätsklinikum Düsseldorf
40225 Düsseldorf
Tel.: 0211-8106109
Email: n.bitt...@fz-juelich.de

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Montag, 20. Juni 2016 18:28
An: Freesurfer support list
Betreff: Re: [Freesurfer] Error loading a constructed annotation file

Hi Nora

sorry for the long response time. Doug is on vacation and that slows everything down! Can 
you send the full command line and full terminal output? I think the "1 -1 NOT_FOUND 
..." error refers to not being able to find an annotation/parcellation NOT to the 
orig surface.

cheers
Bruce

On Fri, 17 Jun 2016,
Bittner, Nora wrote:


Dear Bruce,

thank you for your quick reply.
Attached I send you the command line, the color table I used, the terminal 
output from mris_label2annot and the error message that appears when loading my 
annotation file into freeview.
In the terminal output of mris_label2annot I recognized an error message in 
line 21. It seems that the rh.orig surface can´t be found, although it actual 
is in the subject´s folder ( I controlled this twice). I don´t understand this. 
I will put the first lines here, but the complete terminal output of 
mris_label2annot is attached.

Terminal Output:
"Reading ctab 
/data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt
Number of ctab entries 5

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /data/Team_Caspers/Bittner/Skripte_Freesurfer
cmdline mris_label2annot --h rh --subject 995005 --ctab

[Freesurfer] aseg mask error

[Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Re: [Freesurfer] cortical surface pattern matching

Re: [Freesurfer] XQuartz 2.7.9 update results in errors

Re: [Freesurfer] FSFAST- Cerebellum

Re: [Freesurfer] smoothing T1 images

[Freesurfer] smoothing T1 images

Re: [Freesurfer] Error loading a constructed annotation file

Re: [Freesurfer] Error loading a constructed annotation file

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