Re: [Freesurfer] Probably activation due to vessels
When you use -per-session, it uses the first image of the first run as the template. All runs are motion-corrected to this template, and the template is registered to the anatomical. In this way, all images get aligned to the anatomical. The -per-session command means that there is only one template and so only one register.dof6.dat. If you want one for each run you would use -per-run. doug On 05/07/2013 10:51 AM, Jörg Pfannmöller wrote: > Hi, the problem is that there is only one register.dof6.dat in the bold > folder. I expected a register.dof6.dat in each run folder. I did not see an > error message, but have attached a log file to this mail. A solution of this > problem would help me to simplify my workflow and improve the analysis. > Thanks in advance. Joerg > > > On Mon, 06 May 2013 10:48:14 -0400 > Douglas N Greve wrote: > >> If you use -per-session, all of them should be processed. Why do you >> think they are not? Also, just saying something is not working is not >> very informative. Send command lines and terminal output of the error. >> thanks! >> doug >> >> On 05/06/2013 05:46 AM, Jörg Pfannmöller wrote: >>> 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 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 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 Greve 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 Greve 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
Re: [Freesurfer] Probably activation due to vessels
If you use -per-session, all of them should be processed. Why do you think they are not? Also, just saying something is not working is not very informative. Send command lines and terminal output of the error. thanks! doug On 05/06/2013 05:46 AM, Jörg Pfannmöller wrote: > 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 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 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 Greve 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 Greve 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 Grevewrote: > Hi Jorg, can you tell us a l
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 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 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 Greve 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 Greve 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 Grevewrote: > > > > > >> 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). > > >>
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 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 Greve 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 Greve 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 Grevewrote: > > > >> 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 > >>> > >>>
Re: [Freesurfer] Probably activation due to vessels
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 Greve 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 Greve 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 Grevewrote: > >> 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: s
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 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 Greve 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 Greve 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
Re: [Freesurfer] Probably activation due to vessels
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 Greve 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 Greve 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
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 wrote: > It is attached to this mail. > > > > On Tue, 16 Oct 2012 16:16:54 -0400 > Douglas N Greve 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 Greve 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
Re: [Freesurfer] Probably activation due to vessels
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 Greve 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 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] 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 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
Re: [Freesurfer] Probably activation due to vessels
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, Jörg Pfannmöller 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.
