Re: [Freesurfer] trac-all -bedp error
Dear Priti
The bedpostx works fine on the data if I run it outside of tracula.
The command /home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N
bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/subjects/my_subject/dmri
gives the following error:
[: 224: NONE: unexpected operator
[: 315: NONE: unexpected operator
[: 328: xbedpostx_pre: unexpected operator
[: 487: x: unexpected operator
[: 487: -le: argument expected
But /usr/lib/fsl/4.1/fsl_sub -T 60 -m a -N bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/subjects/my_subject/dmri
works.
So I think there is a problem with fsl_sub_seychelles. Any idea how to
solve this thing?
Thanks,
Gabor
2012/5/24 Priti Srinivasan rspr...@nmr.mgh.harvard.edu
Hi Gabor,
If you run bedpostX on the data outside of tracula using the default
options, do you get the same error?
Priti
Dear all,
I've the following error right after starting trac-all -bedp -c
configuration_file:
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage
[: 223: NONE: unexpected operator
0 slices processed
[: 327: xbedpostx: unexpected operator
[: 486: x70: unexpected operator
Queuing post processing stage
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_post: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
From the created files it seems that the first error occurs at
preprocid=`${BPDIR}/fsl_sub_seychelles -T 60 -m a -N bedpostx_pre -l
${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`
Any idea how to fix this error?
Trac-all -prep finished without error.
I've Freesurfer 5.1.0, Ubuntu 11.04 and FSL 4.1.8 installed using
Neurodebian and I don't use SGE.
I'd appreciate an early answer.
Thanks,
Gabor
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Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist
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 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 ___ 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
Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist
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 gr...@nmr.mgh.harvard.edu mailto: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 ___ 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
Re: [Freesurfer] mri_surf2surf source and target annot formats
If the source is an annot, then you need to use --sval-annot Is this causing a problem? doug On 5/24/12 6:48 PM, Arno Klein wrote: hello! in mri_surf2surf, does anyone know how to specify the source and target formats if --sval is annot without using --sval-annot, as in --sfmt or --tfmt? cheers, @rno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] mri_surf2surf source and target annot formats
hi doug, we are trying to figure out if for annot we *have to* use sval-annot or if there is a way to do it with sval? cheers, satra On Fri, May 25, 2012 at 9:46 AM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: If the source is an annot, then you need to use --sval-annot Is this causing a problem? doug On 5/24/12 6:48 PM, Arno Klein wrote: hello! in mri_surf2surf, does anyone know how to specify the source and target formats if --sval is annot without using --sval-annot, as in --sfmt or --tfmt? cheers, @rno ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. ___ 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.
Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist
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.html) 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 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 ___ 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
Re: [Freesurfer] trac-all -bedp error
This is going to be updated in the next version of freesurfer. There have
been some compatibility issues with the latest version of bedpostx that
we've had to fix. For now please run bedpostx by itself. Thanks!
On Fri, 25 May 2012, Gabor Perlaki wrote:
Dear Priti
The bedpostx works fine on the data if I run it outside of tracula.
The command /home/kutato12/freesurfer/bin/fsl_sub_seychelles -T 60 -m a -N
bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/subjects/my_subject/dmri
gives the following error:
[: 224: NONE: unexpected operator
[: 315: NONE: unexpected operator
[: 328: xbedpostx_pre: unexpected operator
[: 487: x: unexpected operator
[: 487: -le: argument expected
But /usr/lib/fsl/4.1/fsl_sub -T 60 -m a -N bedpostx_pre -l
/home/kutato12/freesurfer/subjects/my_subject/dmri.bedpostX/logs
${FSLDIR}/bin/bedpostx_preproc.sh
/home/kutato12/freesurfer/subjects/my_subject/dmri
works.
So I think there is a problem with fsl_sub_seychelles. Any idea how to solve
this thing?
Thanks,
Gabor
2012/5/24 Priti Srinivasan rspr...@nmr.mgh.harvard.edu
Hi Gabor,
If you run bedpostX on the data outside of tracula using the
default
options, do you get the same error?
Priti
Dear all,
I've the following error right after starting trac-all -bedp
-c
configuration_file:
Making bedpostx directory structure
Queuing preprocessing stages
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_pre: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
Queuing parallel processing stage
[: 223: NONE: unexpected operator
0 slices processed
[: 327: xbedpostx: unexpected operator
[: 486: x70: unexpected operator
Queuing post processing stage
[: 223: NONE: unexpected operator
[: 314: NONE: unexpected operator
[: 327: xbedpostx_post: unexpected operator
[: 486: x: unexpected operator
[: 486: -le: argument expected
From the created files it seems that the first error occurs at
preprocid=`${BPDIR}/fsl_sub_seychelles -T 60 -m a -N
bedpostx_pre -l
${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh
${subjdir}`
Any idea how to fix this error?
Trac-all -prep finished without error.
I've Freesurfer 5.1.0, Ubuntu 11.04 and FSL 4.1.8 installed
using
Neurodebian and I don't use SGE.
I'd appreciate an early answer.
Thanks,
Gabor
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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
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.
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Re: [Freesurfer] mri_surf2surf source and target annot formats
Currently, yes. If this is a burden for you, I could hack something. There might be other ways such as converting the annot into a segmentation (mris_annotation2label), passing that to surf2surf with --sval (and --mapmethod nnf), then converting the output back to an annotation (mris_seg2annot). This is what happens internally. doug On 05/25/2012 09:52 AM, Satrajit Ghosh wrote: hi doug, we are trying to figure out if for annot we *have to* use sval-annot or if there is a way to do it with sval? cheers, satra On Fri, May 25, 2012 at 9:46 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If the source is an annot, then you need to use --sval-annot Is this causing a problem? doug On 5/24/12 6:48 PM, Arno Klein wrote: hello! in mri_surf2surf, does anyone know how to specify the source and target formats if --sval is annot without using --sval-annot, as in --sfmt or --tfmt? cheers, @rno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. ___ 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_surf2surf source and target annot formats
hi doug, thanks. we just wanted to verify that annot's are special. no need to hack anything! cheers, satra On Fri, May 25, 2012 at 11:27 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Currently, yes. If this is a burden for you, I could hack something. There might be other ways such as converting the annot into a segmentation (mris_annotation2label), passing that to surf2surf with --sval (and --mapmethod nnf), then converting the output back to an annotation (mris_seg2annot). This is what happens internally. doug On 05/25/2012 09:52 AM, Satrajit Ghosh wrote: hi doug, we are trying to figure out if for annot we *have to* use sval-annot or if there is a way to do it with sval? cheers, satra On Fri, May 25, 2012 at 9:46 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If the source is an annot, then you need to use --sval-annot Is this causing a problem? doug On 5/24/12 6:48 PM, Arno Klein wrote: hello! in mri_surf2surf, does anyone know how to specify the source and target formats if --sval is annot without using --sval-annot, as in --sfmt or --tfmt? cheers, @rno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: 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. ___ 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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
Hi Leon, if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface… I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess) Best Sebastian On May 25, 2012, at 10:15 AM, Leon wrote: Hi, FreeSurfer experts I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue. Many thanks in advance Leon - Forwarded Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz Hi Leon can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce On Fri, 25 May 2012, Leon wrote: Hi, Bruce I checked the orig.nofix and do not see any obvious defect there (see the attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is no red label near this region. Thank you! Leon From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz That almost certainly means there is a topological defect there. Check the orig.nofix Cheers Bruce On May 23, 2012, at 2:49 PM, Leon leonad...@yahoo.com wrote: Hi, FreeSurfer experts I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue. Thanks in advance! Leon RightPreCentralGyri.jpg ___ 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. OrigNoFix_vs_WM.jpgRightPreCentralGyri.jpg___ 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. -- Sebastian Moeller telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242
Re: [Freesurfer] Longitudinal error follow up.
Hi Rashimi, no idea what is causing this, as you say the scripts look OK. Have you tried re-running the longitudinal run from scratch, to make sure this is not caused by earlier data or by some I/O problem? Best, Martin On Fri, 2012-05-25 at 16:41 +, Rashmi Singh wrote: Thanks Martin, I deleted the older runs for base run and started a new run with -use– mritotal flag in the command line: Following is my script for base run for the subjects ( AA543 and AA550) that were giving me errors other than AA510.T1 #!/bin/bash SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer export SUBJECTS_DIR recon-all -base AA543.long1 -tp AA543.T0 -tp AA543.T2 -tp AA543.T3 -use-mritotal -all /dev/null FSAA543.long1 recon-all -base AA550.long1 -tp AA550.T1 -tp AA550.T2 -tp AA550.T3 -use-mritotal -all /dev/null FSAA550.long1 The base runs for AA453, AA550 and AA510 completed without error, So I ran the long run for each time point. My script for that was #!/bin/bash SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer export SUBJECTS_DIR recon-all -long AA543.T0 AA543.long1 -use-mritotal -all /dev/null FSAA543.T0long recon-all -long AA543.T2 AA543.long1 -use-mritotal -all /dev/null FSAA543.T2long recon-all -long AA543.T3 AA543.long1 -use-mritotal -all /dev/null FSAA543.T3long recon-all -long AA550.T1 AA550.long1 -use-mritotal -all /dev/null FSAA550.T1long recon-all -long AA550.T2 AA550.long1 -use-mritotal -all /dev/null FSAA550.T2long recon-all -long AA550.T3 AA550.long1 -use-mritotal -all /dev/null FSAA550.T3long recon-all -long AA510.T1 AA510.long1 -use-mritotal -all /dev/null FSAA550.T1long recon-all -long AA510.T2 AA510.long1 -use-mritotal -all /dev/null FSAA550.T2long recon-all -long AA510.T7 AA510.long1 -use-mritotal -all /dev/null FSAA550.T1long The long run for All AA510 time points and AA543.T2 and AA550.T1 and .T3 were completed without error, however surprisingly AA550.T2, AA543.T1 and AA543.T3 exited with error, the srcipt log didn't define any error other than suggesting the error to be reported. All incomplete runs exited at the same point. Attached are the script log of the runs that exited with error. I am also atatching the log file for AA543.T2 which completed the long run Message: 7 Date: Thu, 24 May 2012 18:42:17 -0400 From: Martin Reuter mreu...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error longitudinal processing To: Rashmi Singh rsi...@laureateinstitute.org Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Message-ID: 1337899337.19912.95.ca...@riemann.nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8 Hi Rashmi, the command line for running the base (subject-template) should be: recon-all -base AA510 -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all we usually don't put the '.long' after the base. I don't think this is causing your problem however. In your case for some reason the talairach transform fails. It could be that something earlier fails. You should - check the .AA510.long/mri/norm_template.mgz if it looks OK (it is the average of your time points). also the .AA510.long/mri/orig.mgz should look good. if they are OK, you need to find out why the talairach reg is failing .AA510.long/mri/transforms/talairach.xfm forgot the command for it, but it is the same as in cross sectional processing. What is weird is your log says this: INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm So probably you have an old talairach.xfm there. I think deleting the AA510.long and rerunning the base from scratch may fix everything. So maybe you want to try that first. Best, Martin On Tue, 2012-05-22 at 15:00 +, Rashmi Singh wrote: Hello, I ran longitudinal processing which exited with errors. I am attaching the output file. Please advise why this error occurred. The recon ?all run ran perfectly for all the time points for this subject. My command was as follows: recon-all -base AA510.long -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all /dev/null FSAA510.long My all other subjects longitudinal run completed without error. Thanks, Rashmi __ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this
[Freesurfer] Freesurfer and FSL
Dear experts, I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer. On Freesurfer, I've used the following commands: recon-all -i where_my_subject_is -autorecon1 -s output_name then, related to the same subject recon-all -autorecon2 -s output_name After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse. Do you know any idea what I'm doing wrong? Thank you for your attention, Ana Arruda ___ 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.
Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
Hi, Sebastian and Bruce I think I have found the reason: there are low intensity values at the precentral region (~1) that are almost invisible when viewed using the gray color scheme in FS. When I converted the wm.mgz to nifti format and viewed it in FSL using red-yellow color scheme. They are readily shown there. Is there any option in tkmedit that can show volume images with different color schemes such as red-yellow or blue, green? I found the option very helpful in detecting unwanted voxels with low intensity values when I am working on the data in FSL. Thank you for your help! Leon From: Sebastian Moeller sebastian.moell...@rwth-aachen.de To: Leon leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 1:28 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface… I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess) Best Sebastian On May 25, 2012, at 10:15 AM, Leon wrote: Hi, FreeSurfer experts I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue. Many thanks in advance Leon - Forwarded Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz Hi Leon can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce On Fri, 25 May 2012, Leon wrote: Hi, Bruce I checked the orig.nofix and do not see any obvious defect there (see the attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is no red label near this region. Thank you! Leon From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz That almost certainly means there is a topological defect there. Check the orig.nofix Cheers Bruce On May 23, 2012, at 2:49 PM, Leon leonad...@yahoo.com wrote: Hi, FreeSurfer experts I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue. Thanks in advance! Leon RightPreCentralGyri.jpg ___ 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.
Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
Hi Leon you can either change the windowing in tkmedit, or load the wm.mgz as an overlay of segmentation in either tkmedit or freeview. cheers Bruce On Fri, 25 May 2012, Leon wrote: Hi, Sebastian and Bruce I think I have found the reason: there are low intensity values at the precentral region (~1) that are almost invisible when viewed using the gray color scheme in FS. When I converted the wm.mgz to nifti format and viewed it in FSL using red-yellow color scheme. They are readily shown there. Is there any option in tkmedit that can show volume images with different color schemes such as red-yellow or blue, green? I found the option very helpful in detecting unwanted voxels with low intensity values when I am working on the data in FSL. Thank you for your help! Leon From: Sebastian Moeller sebastian.moell...@rwth-aachen.de To: Leon leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 1:28 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface? I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess) Best Sebastian On May 25, 2012, at 10:15 AM, Leon wrote: Hi, FreeSurfer experts I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue. Many thanks in advance Leon - Forwarded Message - From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz Hi Leon can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce On Fri, 25 May 2012, Leon wrote: Hi, Bruce I checked the orig.nofix and do not see any obvious defect there (see the attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is no red label near this region. Thank you! Leon ___ _ From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Leon leonad...@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz That almost certainly means there is a topological defect there. Check the orig.nofix Cheers Bruce On May 23, 2012, at 2:49 PM, Leon leonad...@yahoo.com wrote: Hi, FreeSurfer experts I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue. Thanks in advance! Leon RightPreCentralGyri.jpg ___ 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
[Freesurfer] Error during make_average_volume with --xform talairach.m3z
Hello, I am trying to run make_average_subject on my data using the --xform talairach.m3z option, but make_average_volume fails because I get an error during mri_vol2vol: ERROR: transforms/talairach.m3z does not start as 'MNI Transform File' Any suggestions? I can make an average subject perfectly fine using the talairach.xfm file. Thanks, Anne -- Anne Bailey, Ph.D. Candidate, C. Psych. Laboratory for Motor Learning and Neural Plasticity Concordia University 7141 Sherbrooke Ouest Montreal, Quebec H4R 1B6 (514) 848-2424 ext. 7567 ___ 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.
Re: [Freesurfer] fMRI time series in surface space
Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug On 05/25/2012 02:57 PM, Kushal Kapse wrote: hi, Doug as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh it shows me Done mapping volume to surface followed by Segmentation fault may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug On 05/24/2012 08:35 AM, Kushal Kapse wrote: Hi Everyone, I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, register.dof6.dat is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? Many thanks, kk ___ 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 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 ___ 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.
Re: [Freesurfer] fMRI time series in surface space
doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. please let me know thanks kk - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug On 05/25/2012 02:57 PM, Kushal Kapse wrote: hi, Doug as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh it shows me Done mapping volume to surface followed by Segmentation fault may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug On 05/24/2012 08:35 AM, Kushal Kapse wrote: Hi Everyone, I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, register.dof6.dat is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? Many thanks, kk ___ 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 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 The information in this e-mail is intended only for the person to whom it is addressed. If you
Re: [Freesurfer] fMRI time series in surface space
On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug On 05/25/2012 02:57 PM, Kushal Kapse wrote: hi, Doug as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh it shows me Done mapping volume to surface followed by Segmentation fault may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug On 05/24/2012 08:35 AM, Kushal Kapse wrote: Hi Everyone, I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, register.dof6.dat is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? Many thanks, kk ___ 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
Re: [Freesurfer] fMRI time series in surface space
@doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug On 05/25/2012 02:57 PM, Kushal Kapse wrote: hi, Doug as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh it shows me Done mapping volume to surface followed by Segmentation fault may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug On 05/24/2012 08:35 AM, Kushal Kapse wrote: Hi Everyone, I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, register.dof6.dat is produced, which includes input
Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
Hi, Sebastian Thank you very much for your information. It is very helpful. Yes, my intention is to build a surface template based on my subjects for surface-based analyses. As i am fairly new to FreeSurfer, here is my original plan and correct me if I am not heading to the correct direction: 1) Using non-linear registration approach (FNIRT in FSL) to generate a volume-based template first. 2) generate a surface based on this volume-based template 3) register all the subject's individual surface to this template for a surface-based template, based on the instructions in FreeSurfer Wiki. I checked FreeSurfer documents on how to generate a surface-based template. It seems that it starts from a random individual and do the step(3). However, the reasons for me wanting to start from a volume-based template (step1 and step2) are that having a volume-based template that corresponds to a surface-based template can be helpful if in the future I need to do both volume- and surface- based analyses and need to transfer ROIs between them. Correct me if my ideas are problematic since I am new to surface-based analyses. Many thanks Leon From: Sebastian Moeller sebastian.moell...@rwth-aachen.de To: Leon leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:01 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, On May 25, 2012, at 12:55 PM, Leon wrote: Hi, Sebastian I think you are right: the final wm surface not only considers wm.mgz and filled.mgz, but the brain.finalsurf.mgz as well. Even though I deleted these voxels with low intensity values in the wm.mgz, the lump at the precentral gyrus still show in the final wm surface. Yeaeh I struggled with this in the past, but you can always just use the orig surface. I assume this is due to the high variations of the subjects in this area, causing high intensity values in brain.finalsurf.mgz in these regions. Are you in any case building a surface for an average subject? In that case it would be better to reconstruct all input individuals and create an averaged surface from those. A lot of NHP people would be happy if a good averaged free surfer monkey would exist (that would mean that you have to build your own template out of all the individual surfaces though). Also, loading wm.mgz as a segmentation mask works for detecting the voxels with low values. Adjusting only the brightness and contrast seems not enough (see the attached file). Well in my laptops screen it works well enough. But this is really irrelevant as the orig surface does not include this bit of cortex, so the value of 1 does not hurt there… Best Sebastian Thank you! Leon From: Sebastian Moeller sebastian.moell...@rwth-aachen.de To: Leon leonad...@yahoo.com Sent: Friday, May 25, 2012 2:15 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, On May 25, 2012, at 10:51 AM, Leon wrote: Hi, Sebastian and Bruce I think I have found the reason: there are low intensity values at the precentral region (~1) that are almost invisible when viewed using the gray color scheme in FS. When I converted the wm.mgz to nifti format and viewed it in FSL using red-yellow color scheme. They are readily shown there. Now that seems weird, as far as I know the wm.mgz should only contain values around 110. But that said, the orig surface looks fine so the wm.mgz is most likely not your problem. Please have a look at brain.mgz or brain.finalsurf.mgz and look for the intensities in that area. BTW https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable gives a nice overview aout the free surfer steps and the inputs and outputs My interpretation is that the whitematter surfaces take in the intensity gradients from brain.finalsurfs.mgz and refine the orig surface. But I have last used free surfer 4.5 for surface reconstruction so things might have changed. But please humor me and show that the brain.finalsurf.mgz at corresponding slices looks fine :) Is there any option in tkmedit that can show volume images with different color schemes such as red-yellow or blue, green? I found the option very helpful in detecting unwanted voxels with low intensity values when I am working on the data in FSL. The best workaround is to use Ctrl-b to open the brightness contrast dialog and set brightness to 0 and contrast to 30 (both sliders to the right), that way even values of 1 can be seen (to some degree). Best Sebastian Thank you for your help! Leon From: Sebastian Moeller sebastian.moell...@rwth-aachen.de To: Leon leonad...@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 1:28 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz Hi Leon, if I recall correctly the wm surface is
Re: [Freesurfer] fMRI time series in surface space
i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapse kka...@mail.med.upenn.edu To: Douglas N Greve gr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug On 05/25/2012 02:57 PM, Kushal Kapse wrote: hi, Doug as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh it shows me Done mapping volume to surface followed by Segmentation fault may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? thanks kk - Original Message - From: Douglas N
Re: [Freesurfer] fMRI time series in surface space
The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug On 05/25/2012 02:57 PM, Kushal Kapse wrote: hi, Doug as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows
Re: [Freesurfer] fMRI time series in surface space
Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc:
Re: [Freesurfer] fMRI time series in surface space
well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume
Re: [Freesurfer] fMRI time series in surface space
it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with tkregister2 --mov func.nii.gz --reg register.dat --surfs doug On 05/25/2012 05:45 PM, Kushal Kapse wrote: well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug On 05/25/2012 04:03 PM, Kushal Kapse wrote: hi dough, following is the terminal output which lead to segmentation fault. i checked the data space and it is not out of size mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz
Re: [Freesurfer] fMRI time series in surface space
yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2 is their any other reason for it showing segmentation fault - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with tkregister2 --mov func.nii.gz --reg register.dat --surfs doug On 05/25/2012 05:45 PM, Kushal Kapse wrote: well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional
Re: [Freesurfer] fMRI time series in surface space
Not that I can think of. Did you try that new version? On 05/25/2012 05:58 PM, Kushal Kapse wrote: yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2 is their any other reason for it showing segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with tkregister2 --mov func.nii.gz --reg register.dat --surfs doug On 05/25/2012 05:45 PM, Kushal Kapse wrote: well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where subject comes from the register.dat file. doug please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space Hi Kushal, can you try this version of vol2surf?
Re: [Freesurfer] Freesurfer and FSL
Hi Ana, if this is on a single subject, anything can happen. Also you can run that in a single step: recon-all -i ... -autorecon1 -autorecon2 -s output_name Best, Martin On Fri, 2012-05-25 at 18:48 +0100, Ana Arruda wrote: Dear experts, I'm an MSc student and part of my final project is related to the measurement of the volume of the hippocampus. The last thing I have to do is to compare two softwares, FSL and Freesurfer. On Freesurfer, I've used the following commands: recon-all -i where_my_subject_is -autorecon1 -s output_name then, related to the same subject recon-all -autorecon2 -s output_name After approximately 12 hours, and after comparing the results of Freesurfer and FSL, I found that those obtained with Freesurfer are bigger than those obtained with FSL. According to the literature the results are the reverse. Do you know any idea what I'm doing wrong? Thank you for your attention, Ana Arruda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
Re: [Freesurfer] fMRI time series in surface space
doug, did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.what output format does the new version vol2surf likes? thanks kk - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space Not that I can think of. Did you try that new version? On 05/25/2012 05:58 PM, Kushal Kapse wrote: yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2 is their any other reason for it showing segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with tkregister2 --mov func.nii.gz --reg register.dat --surfs doug On 05/25/2012 05:45 PM, Kushal Kapse wrote: well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are correct 2- vol2surf needs functional file as src and register.dat fileare these both supposed to be in same directorybecause during processing it says cannot find target reference for orig.mgz.. They do not have to be. I did not see that error below. Is that something new? It's looking for
Re: [Freesurfer] fMRI time series in surface space
I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug On 5/25/12 8:19 PM, Kushal Kapse wrote: doug, did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.what output format does the new version vol2surf likes? thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space Not that I can think of. Did you try that new version? On 05/25/2012 05:58 PM, Kushal Kapse wrote: yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2 is their any other reason for it showing segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with tkregister2 --mov func.nii.gz --reg register.dat --surfs doug On 05/25/2012 05:45 PM, Kushal Kapse wrote: well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of mri_vol2surf issues 1- mri_vol2surf command needs to specify register.dat file i have been using register.dat file for vol2surf from reg-feat2anat output.is that the register.dat file i am supposed to used?.or if i am wrong, which register.dat file am i suppose to usebasically, where does tht file come from No, you are
Re: [Freesurfer] fMRI time series in surface space
i tried .nii.gz and they didnt work.i will try .mgz file and keep u updated,... thanks kk - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: Kushal Kapse kka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 8:23:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug On 5/25/12 8:19 PM, Kushal Kapse wrote: doug, did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.what output format does the new version vol2surf likes? thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space Not that I can think of. Did you try that new version? On 05/25/2012 05:58 PM, Kushal Kapse wrote: yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2 is their any other reason for it showing segmentation fault - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with tkregister2 --mov func.nii.gz --reg register.dat --surfs doug On 05/25/2012 05:45 PM, Kushal Kapse wrote: well... it seems the seg fault occured due to i was using a 4D func file and not 3ddoes the vol2surf does only on 3d func data ?how would i do that for 4D time series? please let me know thanks kk - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug On 05/25/2012 04:56 PM, Kushal Kapse wrote: orig.mgz file is on 15446_03908/mri/orig.mgz yes the subject name and the directory path is correct - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls If either of those are not correct, then it will not determine the path correctly. Does that orig.mgz file exist? On 05/25/2012 04:50 PM, Kushal Kapse wrote: i was talking about this issue mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file i didnt understand when u said in last email where subject comes from the register.dat file.would you please explain me this thanks kk - Original Message - From: Kushal Kapsekka...@mail.med.upenn.edu To: Douglas N Grevegr...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space @doug no doug...this orig.mgzerror was before segmentation fault error started showing up.hence i wanna see if why it gave that lemme take a look and will keep u updated - Original Message - From: Douglas N Grevegr...@nmr.mgh.harvard.edu To: Kushal Kapsekka...@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space On 05/25/2012 04:30 PM, Kushal Kapse wrote: doug, thanks dougbefore i do thati have two questions which may take care of
