Re: [Freesurfer] local GI calculation Error
Thanks Marie,Yes at the end I found a threat with the same problem and saw the solution, so I did the recon and re-run the GLI and worked fine, but i didn't re-run the -autorecon3, I would run this separately, I guess it will cause no problems. Regards,GabrielEl 19/10/12, Marie Schaer escribió:Hi Gabriel,It may be the case that because of the surface topology, the lGI fails on one vertex. Most of the time, just recomputing the surface creation solves the problem. Can you try to run recon-all -autorecon2-wm -autorecon3 -randomness -hemi lh -s c_36 and then rerun the lgi computation on this hemisphere?It should solve the problem. Let me know,Marie On Oct 19, 2012, at 3:43 PM, Gabriel Gonzalez Escamilla wrote:Dear FS expertsI'm trying to calculate the local GI of my subjects but I'm having trouble with one of them, When I run recon-all -s MySubject -localGI it always give me the same message:... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012When I checked the mris_euler_number on the pial surface I get no topological defect:[root@localhost surf]$ mris_euler_number lh.pialeuler # = v-e+f = 2g-2: 134601 - 403797 + 269198 = 2 --> 0 holes F =2V-4: 269198 = 269202-4 (0) 2E=3F: 807594 = 807594 (0)total defect index = 0Also try as: mris_compute_lgi --i lh.pial --echoAnd get the following message: ... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.endifendifecho ""echorm -f ${MLF}rm -f /tmp/clgi_15928_.mif ( $RunIt && ! -e ${tmpdir}/${input}_lgi.asc ) thenif ( 1 && ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) thenecho "ERROR: compute_lgi did not create output file '${tmpdir}/${input}_lgi.asc'!"echo ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!exit 1exit 1The right hemisphere works perfectly...with this last command, but left just does not work.Any ideas about this? any way to fix it??? Can anyone help me?Best Regards,Gabriel
___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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Re: [Freesurfer] error finding data on bourget
You can't use dcmdir-info-mgh as of data collected in August because the file naming has changed. Instead, use dcmunpack (you cannot use the -mgh or -martinos flags anymore either). doug On 10/19/2012 03:09 PM, qtngu...@nmr.mgh.harvard.edu wrote: > Dear Freesurfer experts, > > I'm trying to run structural reconstruction for two subjects DODASD016 and > DODASD017. > > DODASD016 was scanned last Wed Oct 10 and last week I was able to > findsession DODASD016, run dcmdir-info-mgh, and run recon-all using > pbsubmit. However, after this was done I was unable to unpack the Bold& > DTI Data from Bourget. We believe that the recon-all didn't work and when > we tried to re-run: > > (for DODASD016) dcmdir-info-mgh > /cluster/archive/301/siemens/TrioTim-35006-20121010-153034-596000 > (and for DODASD017) dcmdir-info-mgh > /cluster/archive/301/siemens/TrioTim-35006-20121017-153207-445000 > > ...I got the error message "ERROR: finding data" > > Can you help me resolve this issue? Or can you direct me to someone who > can help? > > Thank you! > > Trang > ___ > 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] error finding data on bourget
Dear Freesurfer experts, I'm trying to run structural reconstruction for two subjects DODASD016 and DODASD017. DODASD016 was scanned last Wed Oct 10 and last week I was able to findsession DODASD016, run dcmdir-info-mgh, and run recon-all using pbsubmit. However, after this was done I was unable to unpack the Bold & DTI Data from Bourget. We believe that the recon-all didn't work and when we tried to re-run: (for DODASD016) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121010-153034-596000 (and for DODASD017) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121017-153207-445000 ...I got the error message "ERROR: finding data" Can you help me resolve this issue? Or can you direct me to someone who can help? Thank you! Trang ___ 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
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] local GI calculation Error
Hi Gabriel,
It may be the case that because of the surface topology, the lGI fails on one
vertex. Most of the time, just recomputing the surface creation solves the
problem. Can you try to run recon-all -autorecon2-wm -autorecon3 -randomness
-hemi lh -s c_36 and then rerun the lgi computation on this hemisphere?
It should solve the problem. Let me know,
Marie
On Oct 19, 2012, at 3:43 PM, Gabriel Gonzalez Escamilla wrote:
> Dear FS experts
>
> I'm trying to calculate the local GI of my subjects but I'm having trouble
> with one of them, When I run recon-all -s MySubject -localGI it always give
> me the same message:
>
>
> ... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.
> WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high
> (lGI=47.3485)...
> ...lGI computation will be stopped. This may be caused by topological
> defects, check mris_euler_number on the pial surface.
>
> ERROR: compute_lgi did not create output file
> '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
> Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012
>
>
>
> When I checked the mris_euler_number on the pial surface I get no topological
> defect:
>
> [root@localhost surf]$ mris_euler_number lh.pial
> euler # = v-e+f = 2g-2: 134601 - 403797 + 269198 = 2 --> 0 holes
> F =2V-4: 269198 = 269202-4 (0)
> 2E=3F:807594 = 807594 (0)
> total defect index = 0
>
>
> Also try as: mris_compute_lgi --i lh.pial --echo
> And get the following message:
>
> ... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.
> WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high
> (lGI=47.3485)...
> ...lGI computation will be stopped. This may be caused by topological
> defects, check mris_euler_number on the pial surface.
> endif
> endif
> echo ""
> echo
> rm -f ${MLF}
> rm -f /tmp/clgi_15928_.m
> if ( $RunIt && ! -e ${tmpdir}/${input}_lgi.asc ) then
> if ( 1 && ! -e
> /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc
> ) then
> echo "ERROR: compute_lgi did not create output file
> '${tmpdir}/${input}_lgi.asc'!"
> echo ERROR: compute_lgi did not create output file
> '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
> ERROR: compute_lgi did not create output file
> '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!
> exit 1
> exit 1
>
>
> The right hemisphere works perfectly...with this last command, but left just
> does not work.
> Any ideas about this? any way to fix it??? Can anyone help me?
>
>
> Best Regards,
> Gabriel
>
> ___
> Freesurfer mailing list
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>
>
> 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.
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[Freesurfer] local GI calculation Error
Dear FS expertsI'm trying to calculate the local GI of my subjects but I'm having trouble with one of them, When I run recon-all -s MySubject -localGI it always give me the same message:... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s c_36 exited with ERRORS at Fri Oct 19 09:22:54 CEST 2012When I checked the mris_euler_number on the pial surface I get no topological defect:[root@localhost surf]$ mris_euler_number lh.pialeuler # = v-e+f = 2g-2: 134601 - 403797 + 269198 = 2 --> 0 holes F =2V-4: 269198 = 269202-4 (0) 2E=3F: 807594 = 807594 (0)total defect index = 0Also try as: mris_compute_lgi --i lh.pial --echoAnd get the following message: ... remeasuring lGI value for vertex iV = 57301. It may take a few minutes.WARNING -- Problem for vertex iV = 57301, lGI value is aberrantly high (lGI=47.3485)..lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.endifendifecho ""echorm -f ${MLF}rm -f /tmp/clgi_15928_.mif ( $RunIt && ! -e ${tmpdir}/${input}_lgi.asc ) thenif ( 1 && ! -e /root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc ) thenecho "ERROR: compute_lgi did not create output file '${tmpdir}/${input}_lgi.asc'!"echo ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!ERROR: compute_lgi did not create output file '/root/trabajo/freesurfer/subjects/c_36/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'!exit 1exit 1The right hemisphere works perfectly...with this last command, but left just does not work.Any ideas about this? any way to fix it??? Can anyone help me?Best Regards,Gabriel
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Re: [Freesurfer] withe matter of cortical Lables
Thanks Doug,I did create my own ctab and works perfectly!Regards,GabrielEl 18/10/12, Douglas N Greve escribió:Hi Gabriel, don't use the ASegStatsLUT.txt ctab file. It will only report the volumes of structure in the ctab, and that ctab does not have the WM parcellations. You can use FreeSurferColotLUT.txt instead. When you use --empty, this will report on *everything* in the ctab, which will probably be overwhelming. If you run it without --empty, then some subjects may have a different number of structures. The only alternative is to create your own ctab with only the structures you are interested in.dougOn 10/17/2012 02:36 PM, Gabriel Gonzalez Escamilla wrote:> Dear Freesurfer Experts>> Sorry for many mail, but I'm working on may things at the time.>> Apart from my corticalGM problems I'm trying to obtain the WM volumes > from some regions in the apparc.annot such as precuneus, for this I'm > using>> mri_aparc2aseg --s MySubj --labelwm --annot aparc --o > /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz>> to convert the apparc into a volume file, and then obtaining such > voxels correponding to the asigned WM using:>> mri_segstats --seg > /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz --sum > /root/trabajo/freesurfer/subjects/MySUbj/stats/Newaparc+aseg.stats > --pv /root/trabajo/freesurfer/subjects/MySubj/mri/norm.mgz --empty > --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in > /root/trabajo/freesurfer/subjectsMySubj/mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol > --surf-ctx-vol --totalgray --ctab > /root/trabajo/freesurfer/ASegStatsLUT.txt --subject MySubj>>> the problem is that even when it seems to work, some of the structures > have no WM volume in the stat table, but they do have assigned voxels > on the Newaparc+aseg (see attached image),> Is there something I've been doing wrong? the command gives me the > same results when I use the aparc+aseg.mgz created during recon-all > process.>> Can anyone guide me?>> Best Regards,> Gabriel ___> Freesurfer mailing list> Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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] error while compiling utils
Hi Kim You are missing some packages. https://help.ubuntu.com/community/CompilingEasyHowTo You should install teh essential package for compiling in ubuntu by sudo apt-get install build-essential and sudo apt-get install linux-libc-dev to get Linux headers in /usr/include/linux. When building you should ensure that you meet the dependency before compiling. Cheers Knut J On 10/18/2012 11:10 PM, Kim, Daniel wrote: Hi Freesurfer users, I'm trying to compile utils on my Ubuntu 10.04 64 bit machine and I am getting a considerable amount of error while compiling afni.c - I am using gcc-4.4.3, g++-4.4.3 for compilers - I have successfully installed VXL and MNI as per the developer's guide (I am not building any GUI apps) - Had to add "-I/usr/src/linux-headers-2.6.32-43/include" under CFLAGS in utils/Makefile since without it, it would spit out error message saying it cannot find - under the utils folder, "make" gives an error along the lines of "expected specifier-qualifier-list before 'size_t'" (attaching error log file) - tried using older compiler gcc-3.3, g++3.3 but problems seems worse I'm a bit stuck here and hoping that someone has had experience similar to this who can lend me some help? Thanks very much! cheers Danny Kim Children's Brain Mapping Centre BC Children's Hospital ___ 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] 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
