[Freesurfer] Job advertisement! - Germany

2011-06-01 Thread Loose, Daniel
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Schwerbehinderte Bewerber/innen werden bei ansonsten im Wesentlichen gleicher 
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Institut für Schlaganfall- und Demenzforschung
Herrn Frühauf, Geschäftsführer ISD
Heiglhofstr. 55
81377 München
E-Mail: i...@med.uni-muenchen.de
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[Freesurfer] display tessellation

2011-06-01 Thread Jose Luis Cantero Lorente
Dear Freesurfers,Is there a FS command to display tessellation on inflated cortical surfaces? Something similar to the attached file.Thanks in advance.Best regards,Jose---Jose L. Cantero, Ph.D.Laboratory of Functional NeuroscienceDepartment of Physiology, Anatomy and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Phone: +34 954 977433Fax: +34 954 349151Email: jlcan...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] display tessellation

2011-06-01 Thread Douglas N Greve

Hi Jose, you can just turn on the wireframe overlay. I think it is under 
the View menu.
doug

Jose Luis Cantero Lorente wrote:
> Dear Freesurfers,
>
> Is there a FS command to display tessellation on inflated cortical 
> surfaces? Something similar to the attached file.
>
> Thanks in advance.
>
> Best regards,
> Jose
>
> ---
> Jose L. Cantero, Ph.D.
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
> Phone: +34 954 977433
> Fax: +34 954 349151
> Email: jlcan...@upo.es
> http://www.upo.es/neuroaging/es/
>
> 
>
> 
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] freeview and wm-segmentation errors

2011-06-01 Thread Nick Schmansky
1. is your installation 64b?  is there a libXss.so in your /usr/lib64
dir? 

2. was this run from scratch or rerun?  if rerun, when was wm.mgz
created and by what release?  if created by a 5.1beta release late march
to early april, it could have a bug responsible for this.  if so, try
rerunning with the -clean flag.

n.


On Wed, 2011-06-01 at 01:06 +0200, von Polier, Georg Ferdinand Anto
wrote:
> Hi,
> 
> using FS 5.1 now, I encountered two problems: 
> 
> 1. when I try to start freeview on my personal laptop, this errors appears: 
> 
> [georg@localhost ~]$ freeview
> freeview.bin: error while loading shared libraries: libXss.so.1: cannot open 
> shared object file: No such file or directory
> 
> However,  libXss.so.1 is installed on my system running linux (Fedora 15). Do 
> you habe any idea?
> 
> 
> 2. Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the 
> stream finishes with errors repeatedly showing this message: 
> 
> #@# WM Segmentation Tue May 31 12:36:00 CEST 2011
> 
>  mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt 
> 
> znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes!
> 
> 
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
> cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri
> cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count 
> wm255.txt 
> sysname  Linux
> 
> input  wm.mgz
> frame  0
> nErode3d   0
> nErode2d   0
> output wm255.mgz
> Binarizing based on threshold
> min255
> max255
> binval1
> binvalnot 0
> Cannot allocate memory
> 
> recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011
> 
> 
> --
> | Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011
> | peak memory value: 2.386G
> | real time used: 04:58:38
> 
> I did allocate 4 GB of memory and did not face this error when using FS 5.0 
> or FS 5.1-beta-release with same settings. 
> 
> Any recommendations? 
> Thanks, Georg
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[Freesurfer] Extracting WMPARC stats

2011-06-01 Thread Alan Francis
Hi All:

I am trying to extract Volumes from the WMParc files into a txt file. Just
as you have the *asegstats2table* command for segmentation stats and the *
aparcstats2table* command for parcellation stats, is there a command you use
to extract data from the wmparc.stats file? I tried manipulating the
*aparcstats2table but
it only generates volumes from the lh.aparc files.*

thanks so much,

Alan Francis
Beth Israel Deaconess medical Center
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Re: [Freesurfer] Extracting WMPARC stats

2011-06-01 Thread Martin Reuter
Hi Alan,

should work with asegstats2table:

asegstats2table --all-segs --subjects $ALL_TPN --segno $wmparcs \
 -t table.wmparc.txt -d space --stats wmparc.stats

where $ALL_TPN contains all subjects and $wmpars the segmentation ids 

Best, Martin

On Wed, 2011-06-01 at 12:44 -0400, Alan Francis wrote:
> Hi All:
>  
> I am trying to extract Volumes from the WMParc files into a txt file.
> Just as you have the asegstats2table command for segmentation stats
> and the aparcstats2table command for parcellation stats, is there a
> command you use to extract data from the wmparc.stats file? I tried
> manipulating the aparcstats2table but it only generates volumes from
> the lh.aparc files.
>  
> thanks so much,
>  
> Alan Francis 
> Beth Israel Deaconess medical Center
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[Freesurfer] reshape command

2011-06-01 Thread Jose Luis Cantero Lorente
Dear Freesurfers,

I am trying to reduce the number of vertices to display with the wireframe 
overlay on the inflated cortical surface. To this aim, I am using the following 
command line: 

mri_surf2surf --s Estudio_EHM_average --sval-xyz inflated --tval 
/root/trabajo/freesurfer/subjects/Estudio_EHM_average/surf/lh.reshaped.inflated 
--tval-xyz --hemi lh --reshape --reshape-factor 7

But when I load the reshaped surface in Matlab it contains the same number of 
vertices as originally. Why the reshape command (factor 7) is not decreasing 
the number of vertices on cortical surfaces?

Thanks in advance.

Best regards,
Jose
---
Jose L. Cantero, Ph.D.
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -
Phone: +34 954 977433
Fax: +34 954 349151
Email: jlcan...@upo.es
http://www.upo.es/neuroaging/es/


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Re: [Freesurfer] reshape command

2011-06-01 Thread Douglas N Greve
Hi Jose, that won't do it. You need to create a surface with fewer 
vertices. Try setting --trgicorder to 5 or 6 (your current value is 
effectively 7). Run with --help to get a list of orders and their number 
of vertices.

doug

Jose Luis Cantero Lorente wrote:
> Dear Freesurfers,
>
> I am trying to reduce the number of vertices to display with the 
> wireframe overlay on the inflated cortical surface. To this aim, I am 
> using the following command line:
>
> mri_surf2surf --s Estudio_EHM_average --sval-xyz inflated --tval 
> /root/trabajo/freesurfer/subjects/Estudio_EHM_average/surf/lh.reshaped.inflated
>  
> --tval-xyz --hemi lh --reshape --reshape-factor 7
>
> But when I load the reshaped surface in Matlab it contains the same 
> number of vertices as originally. Why the reshape command (factor 7) 
> is not decreasing the number of vertices on cortical surfaces?
>
> Thanks in advance.
>
> Best regards,
> Jose
> ---
> Jose L. Cantero, Ph.D.
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
> Phone: +34 954 977433
> Fax: +34 954 349151
> Email: jlcan...@upo.es
> http://www.upo.es/neuroaging/es/
> 
>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mri_ca_register error

2011-06-01 Thread Vanessa Lim
Hi,

I got freesurfer to run with this command:

mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T 
~/Desktop/freeSurfer/CG/mri/transforms/talairach.lta 
~/Desktop/freeSurfer/CG/mri/norm.mgz 
$FREESURFER_HOME/average/RB_all_2008-03-26.gca 
~/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z

but now have this error after some hours...
writing output transformation to 
/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z...
GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z):
 gzip encountered error.
mri_ca_register: 
GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z) 
failed

any ideas?  I can write to the folder and it has space...
Thanks,
Vanessa




Sent: Friday, 27 May 2011 11:44 a.m.
To: freesurfer@nmr.mgh.harvard.edu
Subject: mri_ca_register error


Hi,



I am getting the same error.  I did set the environment to an external drive 
with LOTS of space.  When I run it though I did notice it repeats the subject 
path which is the external drive but then says actual path 
~/apps/freesurfer/subjects - this doesn't have much space cause it's a 
virtualbox and I don't know how to make it bigger.  But the error below seems 
to be pointing to the right directory /home/...Desktop etc.


>
> GCAMwrite(transforms/talairach.m3z): gzip encountered error.
> writing output transformation to transforms/talairach.m3z...
> mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed
> ERROR: mri_ca_register with non-zero status 252
> but continuing despite the error
> #--
> #@# CA Reg Inv Thu May 26 12:42:11 EDT 2011
> /home/virtualuser/Desktop/freeSurfer/CG2/mri
>
> mri_ca_register -invert-and-save transforms/talairach.m3z
>
> Loading, Inverting, Saving, Exiting ...
> Reading transforms/talairach.m3z
> ERROR: cannot find or read transforms/talairach.m3z
> ERROR: mri_ca_register with non-zero status 0
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 
> 2009 i686 GNU/Linux
>
> Cheers,
> Vanessa
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Re: [Freesurfer] mri_ca_register error

2011-06-01 Thread Bruce Fischl
how much RAM do you have on your machine? For some reason gzip needs tons 
of it
On Wed, 1 Jun 2011, Vanessa Lim wrote:

> Hi,
>
> I got freesurfer to run with this command:
>
> mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T 
> ~/Desktop/freeSurfer/CG/mri/transforms/talairach.lta 
> ~/Desktop/freeSurfer/CG/mri/norm.mgz 
> $FREESURFER_HOME/average/RB_all_2008-03-26.gca 
> ~/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z
>
> but now have this error after some hours...
> writing output transformation to 
> /home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z...
> GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z):
>  gzip encountered error.
> mri_ca_register: 
> GCAMwrite(/home/virtualuser/Desktop/freeSurfer/CG/mri/transforms/talairach.m3z)
>  failed
>
> any ideas?  I can write to the folder and it has space...
> Thanks,
> Vanessa
>
>
> 
>
> Sent: Friday, 27 May 2011 11:44 a.m.
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: mri_ca_register error
>
>
> Hi,
>
>
>
> I am getting the same error.  I did set the environment to an external drive 
> with LOTS of space.  When I run it though I did notice it repeats the subject 
> path which is the external drive but then says actual path 
> ~/apps/freesurfer/subjects - this doesn't have much space cause it's a 
> virtualbox and I don't know how to make it bigger.  But the error below seems 
> to be pointing to the right directory /home/...Desktop etc.
>
>
>>
>> GCAMwrite(transforms/talairach.m3z): gzip encountered error.
>> writing output transformation to transforms/talairach.m3z...
>> mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed
>> ERROR: mri_ca_register with non-zero status 252
>> but continuing despite the error
>> #--
>> #@# CA Reg Inv Thu May 26 12:42:11 EDT 2011
>> /home/virtualuser/Desktop/freeSurfer/CG2/mri
>>
>> mri_ca_register -invert-and-save transforms/talairach.m3z
>>
>> Loading, Inverting, Saving, Exiting ...
>> Reading transforms/talairach.m3z
>> ERROR: cannot find or read transforms/talairach.m3z
>> ERROR: mri_ca_register with non-zero status 0
>> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 
>> 2009 i686 GNU/Linux
>>
>> Cheers,
>> Vanessa
>
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[Freesurfer] mri_convert and timeseries data

2011-06-01 Thread Jennifer Bramen

Dear Freesurfer Users

I am trying to use mri_convert to reorient a nifti file. The file is a  
bold sequence, but for some reason, mri_convert is only outputting the  
first volume. I get this error as well:


WARNING: niiRead(): unknown time units 0 in 2010_10_20_21_bold_gp2.nii

Any idea regarding what I am doing wrong? Here is the command I used:

mri_convert --in_orientation SLP --out_orientation LPI   
2010_10_20_21_bold_gp2.nii 2010_10_20_21_bold_gp_RPI2.nii


Any help would be greatly appreciated!

Best regards

Jen


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[Freesurfer] Problem in func2roi-sess

2011-06-01 Thread John Richey
Dear freesurfer experts, 

I am having a problem in extracting ROI data using func2roi-sess, and any
help would be most appreciated. I wish to evaluate functional data in two
ROIs that I created using mri_cor2label (left and right amygdala). Here is
the command line:

func2roi-sess -roidef 54 -analysis autreg_analysis_vol -anatlabel 54 -s
20110519_12925 -maskthresh 1.3

 Below, I pasted the relevant portion of the logfile produced by
func2roi-sess. To the best of my understanding, at least part of the problem
seems to be due to the fact that a file called COR-.info can't be found, nor
can a file called "bold/001//../transforms/talairach.xfm". I've also tried
it with the flag -labelspace tal (and native), but no luck. 

Should these have been produced by selxavg3-sess , or perhaps I am missing a
step somewhere along the way? 

Many thanks,
J Richey


...
INFO: label2mask_linear: there were 2141 label hits
voxsize = 60.8, rszthresh = 1e-07, thresh = 6.08e-06
INFO: label2mask_linear: there were 75 hits in final mask
label2mask_linear: done
Averging over ROI
INFO: vol2maskavg: nhits = 75
Done averging over ROI (nhits = 75)
---
/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105
19_12925
mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001
--srcreg bold/register.dat --label
/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105
19_12925/label/54.label --talxfm talairach.xfm --finalmskvol
bold/autreg_analysis_vol/54/mask --roiavgtxt
bold/autreg_analysis_vol/54/-001.txt
---
corRead(): can't open file bold/001/COR-.info

/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105
19_12925
mri_vol2roi
 --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg
bold/register.dat --label
/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105
19_12925/label/54.label --talxfm talairach.xfm --finalmskvol
bold/autreg_analysis_vol/54/mask --roiavgtxt
bold/autreg_analysis_vol/54/-001.txt
version $Id: mri_vol2roi.c,v 1.32 2011/03/02 00:04:25 nicks Exp $

roifile = bold/autreg_analysis_vol/54/-001
roitxtfile = bold/autreg_analysis_vol/54/-001.txt
oldtxtstyle = 0
srcvol = bold/001/
srcfmt = bvolume
srcreg = bold/register.dat
srcregold = 0
srcwarp unspecified
label file =
/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105
19_12925/label/54.label
labelreg unspecified
label fill thresh = 1e-07
mskvol unspecified
Loading volume bold/001/ ...can't find talairach file
'bold/001//../transforms/talairach.xfm'
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Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label

2011-06-01 Thread Esther Walton

Thanks so much for your input.

Could somebody please answer the second part of the question? 
That is, ignoring the fact that the label looks a bit weird as it is, is the 
overlay between the label and the volume okay, as seen in the second file I 
attached in my first email? If not, any idea what could have gone wrong?

Thanks for all your help,

Esther

Date: Tue, 31 May 2011 10:36:06 +0200
From: christophe.destri...@univ-tours.fr
To: estherkil...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label



Hi Esther

I had a look to the 2005 aparc for fsaverage and the intraparietal sulcus is 
indeed weird. 

Why don't you use the 2009 version of the atlas that includes major 
improvements ; this parcellation is fully described in 

Automatic parcellation of human cortical gyri and sulci using standard 
anatomical nomenclature. ; Destrieux C, Fischl B, Dale A, Halgren E. ; 
Neuroimage. 2010 Oct 15;53(1):1-15

I let Bruce or Doug answer the second part of your question ; cheers

PS I attached a snapshot of the 2009 parcellation for the same hemi

-- 
Christophe Destrieux,

Directeur du Département 
Communication et Multimedia
http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612

Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université 
François Rabelais de Tours
http://www.u930.tours.inserm.fr/

Laboratoire
 d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé
37032 Tours - 
France
tel (33) 2 47 36 61 36  - fax (33) 2 47 36 62 07


De: "Esther Walton" 
À: freesurfer@nmr.mgh.harvard.edu
Envoyé: Lundi 30 Mai 2011 23:41:24
Objet: [Freesurfer] S_intraparietal-and_Parietal_transverse.label










Dear list,
 
I am interested in the S_intraparietal-and_Parietal_transverse label from
the Desitreux atlas using aparc.a2005s.annot.
 
If I load this into fsaverage, it has three regions to it (see dark purple
label in the attached screenshot): two big ones, very close to each other,
connected by two narrow bridges, and another much smaller region more
dorsally.
 
Does this look fine to you?!
 
Secondly, assuming this is ok, I created labels for each subject using
mri_annotation2label and turned those labels into ROIs in standard space
using
 
mri_label2vol --label
xx/label/lh.S_intraparietal-and_Parietal_transverse.label --temp
xx/reg_standard/example_func.nii.gz --reg
xx/reg/freesurfer/anat2std.register.dat --o
xx/reg_standard/stats/lh.S_intraparietal-and_Parietal_transverse.nii.gz
 
However, when I load this volume with:
 
tksurfer fsaverage lh inflated -overlay
lh.S_intraparietal-and_Parietal_transverse.nii.gz -mni152reg -fthresh 0.1
-fmax 1
 
it looks a bit off (see yellow label and red ROI in second screenshot).
 
Would you think that's still ok taking into account the individual anatomy
or did something go wrong somewhere?
 
Thanks for your help,
 
Esther
 
  
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