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Re: [Freesurfer] volume mapping

Failure to convert DICOM files

Kiley Seymour

23 Mar 2012 23 Mar '12

10:04 a.m.

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM).

I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below).

Any help with this would be much appreciated.

Thanks

Kiley

FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY ------------------------------------------------ /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHSfslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdlinemri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostnameFreeSurfer machine i686 user virtualuser

input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

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Kiley Seymour

25 Mar 25 Mar

7:05 a.m.

Hi again,

Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed?

Thanks

________________________________ From: Kiley Seymour kiley_seymour@yahoo.com.au To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Friday, 23 March 2012 3:04 PM Subject: mkbrainmask-sess

Dear Freesurfers,

I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below).

Any help with this would be much appreciated.

Thanks

Kiley

FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY ------------------------------------------------ /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 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_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser

input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

Douglas Greve

4:58 p.m.

It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. doug

On 3/25/12 7:05 AM, Kiley Seymour wrote:

...

Hi again,

Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed?

Thanks

K

*From:* Kiley Seymour kiley_seymour@yahoo.com.au *To:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, 23 March 2012 3:04 PM *Subject:* mkbrainmask-sess

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM).

I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below).

Any help with this would be much appreciated.

Thanks

Kiley

FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY

/media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 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_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser

input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/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

Kiley Seymour

26 Mar 26 Mar

7:31 a.m.

New subject: TR mismatch between analysis and data analysis

Dear Doug,

Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error.

ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0

I used

mri_convert f.nii f.nii -tr 2000

to try to fix the problem, but had no success (below is the output).

Your help would be very much appreciated.

Thanks in advance

Kiley

FreeSurfer:/data1/RETINOTOPY> selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc Surface data self lh -------------------------------------------------------------- selxavg3-sesslogfile is /media/sf_DATA1/RETINOTOPY/log/selxavg3-sess-bold-rtopy.self.lh-120326071335.log -------------------------------------------------------------- ------------------------------------------- /media/sf_DATA1/RETINOTOPY/IFEE2211 Mon Mar 26 07:13:35 EDT 2012 anadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output --------------------

To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.

...

...
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...
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>> >> >> >> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>

#@# IFEE2211 ############################### /media/sf_DATA1/RETINOTOPY/IFEE2211 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m ------------------------- outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz FreeSurfer Virtual Machine sudo password: freesurfer

FreeSurfer Virtual Machine sudo password: freesurfer

nruns = 4 autostimdur =

outanadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh

FreeSurfer Virtual Machine sudo password:

Found 111344/120028 (92.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 492, nX = 36, DOF = 456 Saving X matrix to /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/Xtmp.mat XCond = 1.20413 (normalized) Computing contrast matrices

FreeSurfer Virtual Machine

sudo password:

OLS Beta Pass run 1 t= 0.0 :

FreeSurfer Virtual Machine sudo password:

ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0

________________________________ From: Kiley Seymour kiley_seymour@yahoo.com.au To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Sunday, 25 March 2012 1:05 PM Subject: Re: mkbrainmask-sess

Hi again,

Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed?

Thanks

Dear Freesurfers,

I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below).

Any help with this would be much appreciated.

Thanks

Kiley

input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

Douglas N Greve

9:54 a.m.

New subject: TR mismatch between analysis and data analysis

You'll have to re-run the preprocessing (or change all the .nii files). doug

Kiley Seymour wrote:

...

Dear Doug,

Thanks for your earlier reply. I have installed fsl on my machine, and have progressed a little further through the retinotopy analysis. However, I now have the following error.

ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0

I used

mri_convert f.nii f.nii -tr 2000

to try to fix the problem, but had no success (below is the output).

Your help would be very much appreciated.

Thanks in advance

Kiley

FreeSurfer:/data1/RETINOTOPY> selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc Surface data self lh

selxavg3-sess logfile is /media/sf_DATA1/RETINOTOPY/log/selxavg3-sess-bold-rtopy.self.lh-120326071335.log

/media/sf_DATA1/RETINOTOPY/IFEE2211 Mon Mar 26 07:13:35 EDT 2012 anadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1

------- matlab output --------------------
                        < M A T L A B (R) >
              Copyright 1984-2012 The MathWorks, Inc.
                R2012a (7.14.0.739) 32-bit (glnx86)
                          February 9, 2012
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.

...
...
...
...
...
> >> >> >> >>

/home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m

...
...
...
...
...
> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>

#@# IFEE2211 ############################### /media/sf_DATA1/RETINOTOPY/IFEE2211

$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m

outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz FreeSurfer Virtual Machine sudo password: freesurfer

FreeSurfer Virtual Machine sudo password: freesurfer

nruns = 4 autostimdur =

outanadir = /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh

FreeSurfer Virtual Machine sudo password:

Found 111344/120028 (92.8) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 492, nX = 36, DOF = 456 Saving X matrix to /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/Xtmp.mat XCond = 1.20413 (normalized) Computing contrast matrices

FreeSurfer Virtual Machine sudo password:

OLS Beta Pass run 1 t= 0.0 :

FreeSurfer Virtual Machine sudo password:

ERROR: TR mismatch between analysis and data analysis TR = 2, data TR = 0

*From:* Kiley Seymour kiley_seymour@yahoo.com.au *To:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Sunday, 25 March 2012 1:05 PM *Subject:* Re: mkbrainmask-sess

Hi again,

Could this error be due to the fact that I don't have a full version of fsl installed and configured on my ubuntu virtual machine? i.e. does fsfast require fsl to be installed?

Thanks

K

*From:* Kiley Seymour kiley_seymour@yahoo.com.au *To:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Friday, 23 March 2012 3:04 PM *Subject:* mkbrainmask-sess

Dear Freesurfers,

I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM).

I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat

So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below).

Any help with this would be much appreciated.

Thanks

Kiley

FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY

/media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 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_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostname FreeSurfer machine i686 user virtualuser

input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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

Kiley Seymour

27 Mar 27 Mar

6:55 a.m.

New subject: Error in fast_selxavg3 (line 254) XCond = cond(XtX);

Dear Doug,

I am aware I am becoming a regular pain. But I now encounter the following problem when running selxavg3-sess -a rtopy.self.lh -s CMRU1711. I have also attached my analysis.info and Xtmp.mat files

Thanks for all of your suggestions.

#@# CMRU1711 ############################### /media/sf_DATA1/RETINOTOPY/CMRU1711 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m ------------------------- outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz nruns = 3 autostimdur =

outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh Found 138599/149490 (92.7) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 369, nX = 33, DOF = 336 Saving X matrix to /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf.

Error in cond (line 39) s = svd(A);

Error in fast_selxavg3 (line 254) XCond = cond(XtX);

Douglas N Greve

12:17 p.m.

New subject: Error in fast_selxavg3 (line 254) XCond = cond(XtX);

Do you not have any eccen runs? doug

On 03/27/2012 06:55 AM, Kiley Seymour wrote:

...

Dear Doug,

I am aware I am becoming a regular pain. But I now encounter the following problem when running selxavg3-sess -a rtopy.self.lh -s CMRU1711. I have also attached my analysis.info and Xtmp.mat files

Thanks for all of your suggestions.

K

#@# CMRU1711 ############################### /media/sf_DATA1/RETINOTOPY/CMRU1711

$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/virtualuser/freesurfer/matlab/MRIread.m

outtop = /media/sf_DATA1/RETINOTOPY Extension format = nii.gz nruns = 3 autostimdur =

outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh Found 138599/149490 (92.7) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 369, nX = 33, DOF = 336 Saving X matrix to /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf.

Error in cond (line 39) s = svd(A);

Error in fast_selxavg3 (line 254) XCond = cond(XtX);

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Douglas Greve
Douglas N Greve
Kiley Seymour