I think you can load overlays into freeview. After that it is a matter of setting the thresholds right. I think we have a fix for the "sliver" problem.
doug
On 7/14/11 10:26 PM, Babak wrote:
Thanks Doug, I fixed that problem and completed the analysis process, but tksurfer doesn't work on my system. It seems to be the Sliver problem, and I used the freeview to look at my surfaces and volumes. I'm not sure however if I can use freeview for retinotopic mapping. Could you kindly give me some insight on that?
Thanks Again, Babak
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, July 08, 2011 3:57 PM To: Babak Subject: Re: [Freesurfer] retinotopy manual?
does /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.haluk.lh.n ii.gz exist? If not, then you need to run the preprocessing (or exclude -no-preproc)
Babak wrote:
Hi Doug,
Another freeSurfer newbie question . I followed your steps for retinotopic mapping in freesurfer
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16562.html),
and got as far as selxavg3. I have attached the error and log file that I got, if you could kindly have a look.
Thanks a lot,
Babak
---------------------------------------------------- Log File
[bnooryme@Vision-1 data-parent]$ selxavg3-sess -a rtopy.haluk.lh -sf /data/fMRIdata/1/users/babak/data-parent/haluk/subjectname -d /data/fMRIdata/1/users/babak/data-parent -no-preproc
Surface data haluk lh
selxavg3-sess logfile is
/data/fMRIdata/1/users/babak/data-parent/log/selxavg3-sess-bold-rtopy.haluk. lh-110708131238.log
/data/fMRIdata/1/users/babak/data-parent/haluk
Fri Jul 8 13:12:38 CDT 2011
anadir = /data/fMRIdata/1/users/babak/data-parent/haluk/bold/rtopy.haluk.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------- matlab output --------------------
Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R)>
Copyright 1984-2009 The MathWorks, Inc.
Version 7.9.0.529 (R2009b) 64-bit (glnxa64)
August 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
/home/programs/freesurfer/fsfast/toolbox/fast_selxavg3.m
#@# haluk ###############################
/data/fMRIdata/1/users/babak/data-parent/haluk
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/home/programs/freesurfer/fsfast/toolbox/fast_selxavg3.m
/home/programs/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/home/programs/freesurfer/matlab/MRIread.m
outtop = /data/fMRIdata/1/users/babak/data-parent
Extension format = nii.gz
??? Error using ==> MRIread at 76
ERROR: cannot determine format of
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.haluk.lh
(MRIread)
Error in ==> flac_customize at 87
mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65
flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
[bnooryme@Vision-1 data-parent]$
---------------------------------------------------- Log File
selxavg3-sess log file
/home/programs/freesurfer/fsfast/bin/selxavg3-sess
-a rtopy.haluk.lh -sf /data/fMRIdata/1/users/babak/data-parent/haluk/subjectname -d /data/fMRIdata/1/users/babak/data-parent/
$Id: selxavg3-sess,v 1.57 2010/08/25 19:07:25 greve Exp $
uid=18368(bnooryme) gid=9999(xdem) groups=9999(xdem),13700(ogmen) context=user_u:system_r:unconfined_t
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
Linux Vision-1.EE.UH.EDU 2.6.18-238.12.1.el5 #1 SMP Sat May 7 20:18:50 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
Thu Jul 7 15:28:23 CDT 2011
preproc-sess -s haluk -d /data/fMRIdata/1/users/babak/data-parent -a rtopy.haluk.lh -nolog
preproc-sess logfile is /dev/null
$Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
bnooryme
setenv FREESURFER_HOME /home/programs/freesurfer
setenv SUBJECTS_DIR /home/programs/freesurfer/subjects
Linux Vision-1.EE.UH.EDU 2.6.18-238.12.1.el5 #1 SMP Sat May 7 20:18:50 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
/home/programs/freesurfer/fsfast/bin/preproc-sess
-s haluk -d /data/fMRIdata/1/users/babak/data-parent -a rtopy.haluk.lh -nolog
Thu Jul 7 15:28:23 CDT 2011
instem f
mc 1 f fmcpr
stc 0 fmcpr
sm 0
mask 1 brain
haluk Template -----------------------------
mktemplate-sess -s haluk -d /data/fMRIdata/1/users/babak/data-parent -fsd bold -nolog -update
Session: /data/fMRIdata/1/users/babak/data-parent/haluk ----------------
Thu Jul 7 15:28:24 CDT 2011
Detected input format at nii
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz --frame 0
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz --frame 0
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
keeping frame 0
writing to /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz...
Run: 003 ----------------
Thu Jul 7 15:28:26 CDT 2011
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz --mid-frame
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz --mid-frame
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
keeping frame 147
writing to /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz...
Thu Jul 7 15:28:28 CDT 2011
mktemplate-sess completed
haluk Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s haluk -d /data/fMRIdata/1/users/babak/data-parent -nolog -update
/data/fMRIdata/1/users/babak/data-parent/haluk
Thu Jul 7 15:28:28 CDT 2011
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_25550
/data/fMRIdata/1/users/babak/data-parent/haluk/bold
mri_convert template.nii.gz /tmp/mkbrainmask_25550/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_25550/in.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /tmp/mkbrainmask_25550/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/data/fMRIdata/1/users/babak/data-parent/haluk/bold
bet.fsl /tmp/mkbrainmask_25550/in.nii /tmp/mkbrainmask_25550/brain -m -f 0.1
/home/programs/freesurfer/bin/bet.fsl: line 150: /bin/remove_ext: No such file or directory
/home/programs/freesurfer/bin/bet.fsl: line 151: /bin/remove_ext: No such file or directory
/home/programs/freesurfer/bin/bet.fsl: line 153: /bin/imtest: No such file or directory
/home/programs/freesurfer/bin/bet.fsl: line 153: [: =: unary operator expected
/home/programs/freesurfer/bin/bet.fsl: line 231: /bin/bet2: No such file or directory
mri_binarize --i /tmp/mkbrainmask_25550/brain_mask.nii --min .01 --o /tmp/mkbrainmask_25550/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_25550/brain_mask.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/fMRIdata/1/users/babak/data-parent/haluk/bold
cmdline mri_binarize --i /tmp/mkbrainmask_25550/brain_mask.nii --min .01 --o /tmp/mkbrainmask_25550/brain_mask.nii
sysname Linux
hostname Vision-1.EE.UH.EDU
machine x86_64
user bnooryme
input /tmp/mkbrainmask_25550/brain_mask.nii
frame 0
nErode3d 0
nErode2d 0
output /tmp/mkbrainmask_25550/brain_mask.nii
Binarizing based on threshold
min 0.01
max +infinity
binval 1
binvalnot 0
I think the sliver problem means you need to update your video driver Bruce
On Jul 14, 2011, at 11:08 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
I think you can load overlays into freeview. After that it is a matter of setting the thresholds right. I think we have a fix for the "sliver" problem.
doug
On 7/14/11 10:26 PM, Babak wrote:
Thanks Doug, I fixed that problem and completed the analysis process, but tksurfer doesn't work on my system. It seems to be the Sliver problem, and I used the freeview to look at my surfaces and volumes. I'm not sure however if I can use freeview for retinotopic mapping. Could you kindly give me some insight on that?
Thanks Again, Babak
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, July 08, 2011 3:57 PM To: Babak Subject: Re: [Freesurfer] retinotopy manual?
does /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.haluk.lh.n ii.gz exist? If not, then you need to run the preprocessing (or exclude -no-preproc)
Babak wrote:
Hi Doug,
Another freeSurfer newbie question . I followed your steps for retinotopic mapping in freesurfer
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16562.html),
and got as far as selxavg3. I have attached the error and log file that I got, if you could kindly have a look.
Thanks a lot,
Babak
---------------------------------------------------- Log File
[bnooryme@Vision-1 data-parent]$ selxavg3-sess -a rtopy.haluk.lh -sf /data/fMRIdata/1/users/babak/data-parent/haluk/subjectname -d /data/fMRIdata/1/users/babak/data-parent -no-preproc
Surface data haluk lh
selxavg3-sess logfile is
/data/fMRIdata/1/users/babak/data-parent/log/selxavg3-sess-bold-rtopy.haluk. lh-110708131238.log
/data/fMRIdata/1/users/babak/data-parent/haluk
Fri Jul 8 13:12:38 CDT 2011
anadir = /data/fMRIdata/1/users/babak/data-parent/haluk/bold/rtopy.haluk.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------- matlab output --------------------
Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen.
< M A T L A B (R)>
Copyright 1984-2009 The MathWorks, Inc.
Version 7.9.0.529 (R2009b) 64-bit (glnxa64)
August 12, 2009
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
/home/programs/freesurfer/fsfast/toolbox/fast_selxavg3.m
#@# haluk ###############################
/data/fMRIdata/1/users/babak/data-parent/haluk
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
/home/programs/freesurfer/fsfast/toolbox/fast_selxavg3.m
/home/programs/freesurfer/fsfast/toolbox/fast_ldanaflac.m
/home/programs/freesurfer/matlab/MRIread.m
outtop = /data/fMRIdata/1/users/babak/data-parent
Extension format = nii.gz
??? Error using ==> MRIread at 76
ERROR: cannot determine format of
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/fmcpr.sm5.haluk.lh
(MRIread)
Error in ==> flac_customize at 87
mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65
flac0 = flac_customize(flac0);
ERROR: fast_selxavg3() failed\n
[bnooryme@Vision-1 data-parent]$
---------------------------------------------------- Log File
selxavg3-sess log file
/home/programs/freesurfer/fsfast/bin/selxavg3-sess
-a rtopy.haluk.lh -sf /data/fMRIdata/1/users/babak/data-parent/haluk/subjectname -d /data/fMRIdata/1/users/babak/data-parent/
$Id: selxavg3-sess,v 1.57 2010/08/25 19:07:25 greve Exp $
uid=18368(bnooryme) gid=9999(xdem) groups=9999(xdem),13700(ogmen) context=user_u:system_r:unconfined_t
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
Linux Vision-1.EE.UH.EDU 2.6.18-238.12.1.el5 #1 SMP Sat May 7 20:18:50 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
Thu Jul 7 15:28:23 CDT 2011
preproc-sess -s haluk -d /data/fMRIdata/1/users/babak/data-parent -a rtopy.haluk.lh -nolog
preproc-sess logfile is /dev/null
$Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $
bnooryme
setenv FREESURFER_HOME /home/programs/freesurfer
setenv SUBJECTS_DIR /home/programs/freesurfer/subjects
Linux Vision-1.EE.UH.EDU 2.6.18-238.12.1.el5 #1 SMP Sat May 7 20:18:50 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
/home/programs/freesurfer/fsfast/bin/preproc-sess
-s haluk -d /data/fMRIdata/1/users/babak/data-parent -a rtopy.haluk.lh -nolog
Thu Jul 7 15:28:23 CDT 2011
instem f
mc 1 f fmcpr
stc 0 fmcpr
sm 0
mask 1 brain
haluk Template -----------------------------
mktemplate-sess -s haluk -d /data/fMRIdata/1/users/babak/data-parent -fsd bold -nolog -update
Session: /data/fMRIdata/1/users/babak/data-parent/haluk ----------------
Thu Jul 7 15:28:24 CDT 2011
Detected input format at nii
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz --frame 0
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz --frame 0
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
keeping frame 0
writing to /data/fMRIdata/1/users/babak/data-parent/haluk/bold/template.nii.gz...
Run: 003 ----------------
Thu Jul 7 15:28:26 CDT 2011
/data/fMRIdata/1/users/babak/data-parent/haluk/bold/003
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz --mid-frame
mri_convert /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz --mid-frame
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/f.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
keeping frame 147
writing to /data/fMRIdata/1/users/babak/data-parent/haluk/bold/003/template.nii.gz...
Thu Jul 7 15:28:28 CDT 2011
mktemplate-sess completed
haluk Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s haluk -d /data/fMRIdata/1/users/babak/data-parent -nolog -update
/data/fMRIdata/1/users/babak/data-parent/haluk
Thu Jul 7 15:28:28 CDT 2011
mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
FSLMATHS fslmaths.fsl
Scratch Dir is /tmp/mkbrainmask_25550
/data/fMRIdata/1/users/babak/data-parent/haluk/bold
mri_convert template.nii.gz /tmp/mkbrainmask_25550/in.nii
mri_convert template.nii.gz /tmp/mkbrainmask_25550/in.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /tmp/mkbrainmask_25550/in.nii...
# ---------- Using FSL's BET to Extract Brain------------------ #
/data/fMRIdata/1/users/babak/data-parent/haluk/bold
bet.fsl /tmp/mkbrainmask_25550/in.nii /tmp/mkbrainmask_25550/brain -m -f 0.1
/home/programs/freesurfer/bin/bet.fsl: line 150: /bin/remove_ext: No such file or directory
/home/programs/freesurfer/bin/bet.fsl: line 151: /bin/remove_ext: No such file or directory
/home/programs/freesurfer/bin/bet.fsl: line 153: /bin/imtest: No such file or directory
/home/programs/freesurfer/bin/bet.fsl: line 153: [: =: unary operator expected
/home/programs/freesurfer/bin/bet.fsl: line 231: /bin/bet2: No such file or directory
mri_binarize --i /tmp/mkbrainmask_25550/brain_mask.nii --min .01 --o /tmp/mkbrainmask_25550/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_25550/brain_mask.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/fMRIdata/1/users/babak/data-parent/haluk/bold
cmdline mri_binarize --i /tmp/mkbrainmask_25550/brain_mask.nii --min .01 --o /tmp/mkbrainmask_25550/brain_mask.nii
sysname Linux
hostname Vision-1.EE.UH.EDU
machine x86_64
user bnooryme
input /tmp/mkbrainmask_25550/brain_mask.nii
frame 0
nErode3d 0
nErode2d 0
output /tmp/mkbrainmask_25550/brain_mask.nii
Binarizing based on threshold
min 0.01
max +infinity
binval 1
binvalnot 0
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve