Hi all,
I'm trying to analyze a retinotopic mapping dataset using FsFast but some things don't seem to work the way they should.
When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following error:
"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
However, I checked that rtopy.self.lh does in fact exist. I also made sure that the folder contains the file analysis.info. Why do I still get this error message?
Here is the contents of analysis.info:
# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $ # MKACMD /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force # DATE Thu May 24 11:50:39 CEST 2012
analysis rtopy.self.lh mcstem fmcpr funcstem fmcsurfsm5 fsd bold TR 3.12 RegDOF 6 RawSpace surface self lh mask brain RawFWHM 0 RawSTC none UseB0DC 0 inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype retinotopy nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 parname rtopy.par period 49.92
Any ideas? Thanks for your help! Michael
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
Hi Michael, is rtopy.self.lh in the current directory (the one that you are running selxavg from)? doug
On 05/24/2012 07:57 AM, Michael Bannert wrote:
Hi all,
I'm trying to analyze a retinotopic mapping dataset using FsFast but some things don't seem to work the way they should.
When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following error:
"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
However, I checked that rtopy.self.lh does in fact exist. I also made sure that the folder contains the file analysis.info http://analysis.info. Why do I still get this error message?
Here is the contents of analysis.info http://analysis.info:
# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $ # MKACMD /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force # DATE Thu May 24 11:50:39 CEST 2012
analysis rtopy.self.lh mcstem fmcpr funcstem fmcsurfsm5 fsd bold TR 3.12 RegDOF 6 RawSpace surface self lh mask brain RawFWHM 0 RawSTC none UseB0DC 0 inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype retinotopy nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 parname rtopy.par period 49.92
Any ideas? Thanks for your help! Michael
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for your help! No, the current directory is the "Project" directory (refering to naming conventions in http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is identical to $FUNCTIONALS_DIR.
The rtopy.self.lh folder is in the "Sess0x" directory and contains only the file called "analysis.info".
I actually tried two different commands:
A: selxavg-sess -s ex01s05 -a rtopy.self.lh B: selxavg3-sess -s ex01s05 -a rtopy.self.lh
I suspect that version B is the correct one. I accidentally posted the wrong code in the previous email. Sorry! I tried both with the same negative outcome.
I now moved the rtopy.self.lh folder into the "Project" folder and tried running the command again. (I think I have to run this command from "Project" because otherwise Freesurfer tells me that it can't find the session.) That gave me the following output:
!selxavg3-sess -s ex01s05 -a rtopy.self.lh
Surface data self lh -------------------------------------------------------------- selxavg3-sess logfile is /Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log -------------------------------------------------------------- ------------------------------------------- /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05 Thu May 24 18:23:04 CEST 2012 anadir = /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- matlab: Command not found. cat: stdout: Broken pipe ------------------------------------------ ERROR: fast_selxavg3() failed\n
Btw: I'm running all these commands from inside a Matlab shell. I hope this isn't a problem.
Thanks for your support!
Best regards, Michael
On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:
Hi Michael, is rtopy.self.lh in the current directory (the one that you are running selxavg from)? doug
On 05/24/2012 07:57 AM, Michael Bannert wrote:
Hi all,
I'm trying to analyze a retinotopic mapping dataset using FsFast but some things don't seem to work the way they should.
When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following error:
"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
However, I checked that rtopy.self.lh does in fact exist. I also made sure that the folder contains the file analysis.info http://analysis.info. Why do I still get this error message?
Here is the contents of analysis.info http://analysis.info:
# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $ # MKACMD /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force # DATE Thu May 24 11:50:39 CEST 2012
analysis rtopy.self.lh mcstem fmcpr funcstem fmcsurfsm5 fsd bold TR 3.12 RegDOF 6 RawSpace surface self lh mask brain RawFWHM 0 RawSTC none UseB0DC 0 inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype retinotopy nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 parname rtopy.par period 49.92
Any ideas? Thanks for your help! Michael
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
yes, B is correct. The error says that it cannot find matlab. Is it in your path? doug
On 5/25/12 9:16 AM, Michael Bannert wrote:
Hi Doug,
Thanks for your help! No, the current directory is the "Project" directory (refering to naming conventions in http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is identical to $FUNCTIONALS_DIR.
The rtopy.self.lh folder is in the "Sess0x" directory and contains only the file called "analysis.info http://analysis.info/".
I actually tried two different commands:
A: selxavg-sess -s ex01s05 -a rtopy.self.lh B: selxavg3-sess -s ex01s05 -a rtopy.self.lh
I suspect that version B is the correct one. I accidentally posted the wrong code in the previous email. Sorry! I tried both with the same negative outcome.
I now moved the rtopy.self.lh folder into the "Project" folder and tried running the command again. (I think I have to run this command from "Project" because otherwise Freesurfer tells me that it can't find the session.) That gave me the following output:
!selxavg3-sess -s ex01s05 -a rtopy.self.lh
Surface data self lh
selxavg3-sess logfile is /Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log
/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05 Thu May 24 18:23:04 CEST 2012 anadir = /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1
------- matlab output -------------------- matlab: Command not found. cat: stdout: Broken pipe
ERROR: fast_selxavg3() failed\n
Btw: I'm running all these commands from inside a Matlab shell. I hope this isn't a problem.
Thanks for your support!
Best regards, Michael
On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:
Hi Michael, is rtopy.self.lh in the current directory (the one that you are running selxavg from)? doug
On 05/24/2012 07:57 AM, Michael Bannert wrote:
Hi all,
I'm trying to analyze a retinotopic mapping dataset using FsFast but some things don't seem to work the way they should.
When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following error:
"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
However, I checked that rtopy.self.lh does in fact exist. I also made sure that the folder contains the file analysis.info http://analysis.info http://analysis.info. Why do I still get this error message?
Here is the contents of analysis.info http://analysis.info http://analysis.info:
# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $ # MKACMD /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess
-a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force # DATE Thu May 24 11:50:39 CEST 2012
analysis rtopy.self.lh mcstem fmcpr funcstem fmcsurfsm5 fsd bold TR 3.12 RegDOF 6 RawSpace surface self lh mask brain RawFWHM 0 RawSTC none UseB0DC 0 inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype retinotopy nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 parname rtopy.par period 49.92
Any ideas? Thanks for your help! Michael
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
Hi Doug,
Yes, that was the problem. I think Freesurfer expects that you start Matlab by typing "matlab" in the terminal (as opposed to "matlab2010a" which is what I usually do). So I created a new symbolic that takes care of that.
Now I got the error message "ERROR: TR mismatch between analysis and data" I'm now re-running the preprocessing as suggested here (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-March/023012.htm...)
Fingers crossed! :)
Thanks for your help! Michael
On May 25, 2012, at 3:44 PM, Douglas Greve wrote:
yes, B is correct. The error says that it cannot find matlab. Is it in your path? doug
On 5/25/12 9:16 AM, Michael Bannert wrote:
Hi Doug,
Thanks for your help! No, the current directory is the "Project" directory (refering to naming conventions in http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is identical to $FUNCTIONALS_DIR.
The rtopy.self.lh folder is in the "Sess0x" directory and contains only the file called "analysis.info".
I actually tried two different commands:
A: selxavg-sess -s ex01s05 -a rtopy.self.lh B: selxavg3-sess -s ex01s05 -a rtopy.self.lh
I suspect that version B is the correct one. I accidentally posted the wrong code in the previous email. Sorry! I tried both with the same negative outcome.
I now moved the rtopy.self.lh folder into the "Project" folder and tried running the command again. (I think I have to run this command from "Project" because otherwise Freesurfer tells me that it can't find the session.) That gave me the following output:
!selxavg3-sess -s ex01s05 -a rtopy.self.lh
Surface data self lh
selxavg3-sess logfile is /Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log
/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05 Thu May 24 18:23:04 CEST 2012 anadir = /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1
------- matlab output -------------------- matlab: Command not found. cat: stdout: Broken pipe
ERROR: fast_selxavg3() failed\n
Btw: I'm running all these commands from inside a Matlab shell. I hope this isn't a problem.
Thanks for your support!
Best regards, Michael
On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:
Hi Michael, is rtopy.self.lh in the current directory (the one that you are running selxavg from)? doug
On 05/24/2012 07:57 AM, Michael Bannert wrote:
Hi all,
I'm trying to analyze a retinotopic mapping dataset using FsFast but some things don't seem to work the way they should.
When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the following error:
"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"
However, I checked that rtopy.self.lh does in fact exist. I also made sure that the folder contains the file analysis.info http://analysis.info. Why do I still get this error message?
Here is the contents of analysis.info http://analysis.info:
# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve Exp $ # MKACMD /Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force # DATE Thu May 24 11:50:39 CEST 2012
analysis rtopy.self.lh mcstem fmcpr funcstem fmcsurfsm5 fsd bold TR 3.12 RegDOF 6 RawSpace surface self lh mask brain RawFWHM 0 RawSTC none UseB0DC 0 inorm 100 acfbins 0 fixacf 1 acffwhm 20 acfsvd 0 designtype retinotopy nskip 0 polyfit 2 HPFCutoffHz 0 HeteroGCor 0 parname rtopy.par period 49.92
Any ideas? Thanks for your help! Michael
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Michael Bannert, Dipl.-Psych. Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen Otfried-Müller-Str. 25, 72076 Tübingen, Germany Phone: +49 - (0)7071 / 29 - 89031
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Michael Bannert