[Freesurfer] Total number of vertices participating in boundary based register
Dear FreeSurfer experts, in the publication 'Accurate and robust brain image alignment using boundary-based registration', by Greve and Fischl (2009), in formula 2 a quantity termed N occurs. It is described as:'N is the total number of vertices participating'. Can I find this N in the files created by BBR? I inspected the files and found in register.dof6.dat.sum the following entries: Final costs Number of surface hits X and nhits= X. Both entries are equal and seem to be the N, which I am interested in. Can you please tell me if this is right. Sincerely yours Joerg ___ 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] tkmedit font size on scalebar
Dear FreeSurfer experts, how can I increase the font size on the tkmedit scale bar? Cheers Joerg ___ 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] beta v5.3 for fedora 18 and ubuntu 13
Just for completeness, I refer to my first contribution: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html On Mon, 13 May 2013 13:58:30 +0200 Joerg Pfannmoeller pfannmo...@uni-greifswald.de wrote: Hello Nick, just installed and tested the BETA version. Up to now no problem encountered. Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I report on the segmentation as soon as it is finished. So long Joerg On Sun, 12 May 2013 22:41:25 -0400 (EDT) Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Fedora 18, Ubuntu 13 and Gentoo 64 users, another beta of the upcoming v5.3 is available here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-BETA.tar.gz this one is just intended for the Fedora 18, Ubuntu 13, Gentoo 64 users who wished to test that the segfault problem in v5.2 and the prior beta v5.3 is fixed. Your help in testing this release is appreciated. Thanks, Nick 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. -- Joerg Pfannmoeller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Probably activation due to vessels
Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305 or -surface When you run mkanalysis-sess, specify -native instead of -mni305 or -surface, like: mkanalysis-sess -native -fwhm 5 ... doug On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.eduwrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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
Re: [Freesurfer] Probably activation due to vessels
Sorry, I have to cancel my last contribution. Another Problem crossed my way. If I have more than one run, only the first one is preprocessed if i use -per-session. What can I do about it? If I use -per-run all runs are preprocessed, but selxavg3-sess tells me that it can not determine the file format of the fmc files. Actually those files are called fmcpr, if I use -per-run. How can do I have to proceed if there is more than one run? On Mon, 6 May 2013 10:54:54 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this case, you are just specifiying -per-session and not specifying -mni305 or -surface When you run mkanalysis-sess, specify -native instead of -mni305 or -surface, like: mkanalysis-sess -native -fwhm 5 ... doug On 10/19/2012 03:59 AM, Jörg Pfannmöller wrote: Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.eduwrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like
[Freesurfer] two sample t-test of paired differences
Hello, I have two different results from a paired difference analysis lets call it A and B. How can I do a two sample t-test with those results (A-B)? Somehow I am stuck in using isxconcat-sess on the group results A and B. Help is highly appreciated. Cheers Joerg ___ 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] preproc-sess and option -mni305-1mm results in an error
A last question to this topic. Does the resolution of the MNI305 brain affected the surface based analysis or is it exclusively affecting the subcortical analysis? On Tue, 27 Nov 2012 13:30:04 -0500 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Note that each of those set commands should be a single line. The file to change is $FREESURFER_HOME/fsfast/bin/rawfunc2tal-sess doug On 11/27/2012 01:23 PM, Douglas N Greve wrote: Yep, that's a bug. I've fixed it in my version. To fix it in yours, do the following two steps: Step 1: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/subcort.mask.1mm.mgz cp subcort.mask.1mm.mgz $SUBJECTS_DIR/fsaverage/mri Step 2: In rawfunc2tal-sess, change: set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz To if($res == 2) then set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz else set subcortmask = $FREESURFER_HOME/subjects/fsaverage/mri/subcort.mask.1mm.mgz endif doug On 11/27/2012 04:48 AM, Jörg Pfannmöller wrote: Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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. -- Jörg Pfannmöller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] preproc-sess and option -mni305-1mm results in an error
Hi, if I apply the following command: preproc-sess -s sessID -fsd bold -nostc -surface fsaverage lhrh -mni305-1mm -fwhm 0 -per-run -nosmooth -force The preprocessing runs into trouble at the following point mri_vol2vol done mri_mask /...path.../bold/001/masks/brain.mni305.1mm.nii /usr/local/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz /...path.../bold/001/masks/brain.mni305.1mm.nii freadFloat: fread failed ERROR: dimension mismatch between source and mask As far as I can see freesurfer uses a 2mm mask for a 1mm brain, which results in the dimension mismatch. How can I get rid of this problem? Cheers Joerg ___ 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] Probably activation due to vessels
Hi Doug, the preprocessing is fine the quaility factor for the registration between functional and anatomical is ~0.3. Have I to use feat to do the volume analysis? Cheers pfannmoe On Thu, 18 Oct 2012 11:50:38 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is too hard to tell what is going on here from just this image. I would not immediately conclude that it is a vessel. Does the activation otherwise look ok? What about other contrasts? Is the registration accurate? When trying to debug these things, it often makes sense to analyze the data in the volume. doug On 10/17/2012 12:31 PM, Jörg Pfannmöller wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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] Probably activation due to vessels
I just noticed that the data I am currently working with are from a data set in which the freesurfer protocol for the anatomical sequence has not been used. Instead an in-house protocol is applied. On Wed, 17 Oct 2012 18:31:05 +0200 Jörg Pfannmöller pfannmo...@uni-greifswald.de wrote: It is attached to this mail. On Tue, 16 Oct 2012 16:16:54 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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. ___ 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
Re: [Freesurfer] Probably activation due to vessels
Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Probably activation due to vessels
Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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] scale bar shrink/grow problem if fsaverage is displayed
Dear freesurfers, if I display fsaverage in tksurfer (tksurfer fsaverage rh pial) and switch on the scale bar it appears to have a length of approximately 1 cm. However, If I start to zoom into the brain the color bar shrinks until a certain scale-up is reached. After it has completely vanished it starts to grow if I further scale-up the image. If I use a subject from our investigations this problem does not ocur. Can someone give my a hint about the cause of this problem? Cheers pfannmoe ___ 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] Correction of registration in preproc-sess stream
Dear Doug, I have tested the various options of register-sess. The result was a succesful registration of the functional to the anatomical image. This registration with register-sess is performed after preproc-sess failed to achieve a proper registration. The register.dof6.dat file is updated by register-sess. I would like to ask a last thing just in order to make it definite. Can I now use those data for example with selxavg3-sess in order to compute the activated areas for this subject? Greets pfannmoe On Tue, 05 Jun 2012 18:30:42 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug On 6/5/12 6:03 AM, Jörg Pfannmöller wrote: Dear Doug, I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly? Cheers pfannmoe On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5'); doug ps. Is this whole brain coverage or are you chopping off some of the brain On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote: Dear Doug, indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact? Cheers pfannmoe ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Jörg Pfannmöller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Correction of registration in preproc-sess stream
P.S.:I executed the following sequence to achieve the first level analysis with a correct registration. preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run register-sess -s session_id -fsd bold -per-run -init-header preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -noreg -regfile session_id/bold/001/register.dof6.dat -force selxavg3-sess -s session_id -analysis stim.sm0.lh -no-preproc As far as I can see this is the right procedure. Do you agree or is there another or simpler way to correct the registration and proceed with a first level analysis? ___ 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] Correction of registration in preproc-sess stream
Dear Doug, I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly? Cheers pfannmoe On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5'); doug ps. Is this whole brain coverage or are you chopping off some of the brain On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote: Dear Doug, indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact? Cheers pfannmoe ___ 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. -- Jörg Pfannmöller pfannmo...@uni-greifswald.de ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Correction of registration in preproc-sess stream
Dear Doug, indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact? Cheers pfannmoe ___ 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] Correction of registration in preproc-sess stream
Dear freesurfers, I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In the preprocessing the functional images are registered to the anatomical ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the preproc-sess registration fails it is possible to achieve a proper registration using various options of bbregister. Does it suffice to replace the register files created during the preprocessing with the ones received during the registration correction in order to attain proper preprocessed data or are there routines in steps 4 to 8 in the preprocessing which rely on the registration? Thanks in advance pfannmoe ___ 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] tfl single echo siemens verio te adjustment
Dear freesurfers, currently the freesurfer single tfl protocol for the segmentation of the cortex surface was implemented at our scanner. Siemens Verio 3T MRT NumarisVersyngo MR B17 Gradientensystem (Tim 102x8) VQ-Engine Unfortunately the echo-time (te) could not be set to the recomended value of 3.31ms. The te is defined by the system and can not be changed. Is this critical for the segmentation quality? Sincerely yours A MRT-Physician ___ 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] Grayscale Histogram Correction
Hello @all, I want to segment anatomical data recorded from an experiemental sequence. This sequence creates pictures with contrasts in a rather narrow range around two hundred if projected into an 8bit grayscale. Freesurfer fails to segment those data. However, if I rescale the brightness in tkmedit the pictures have an excellent quality. Can somebody tell me how to correct the grayscale histogram? Regards pfannmoe ___ 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.
