[Freesurfer] Surface-based Interhemispheric Registration generate average surface from average subject
Hi FSexperts, I would like to compute a symmetrical template out of the anatomical images in a group of subjects. I followed the description in: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi Afterwards I recognized that no surfaces were generated. Since the computation takes quiet a while, the generation of the surfaces from the data which have already been computed would be very helpfull. Is it possible to do that? Yours pfannmoe -- Joerg Pfannmoeller ___ 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] Content of register.dof6.dat.param
Sorry, I ment the first six numbers in "register.dof6.dat.param". On Thu, 9 Apr 2015 12:33:49 +0200 pfannmo...@uni-greifswald.de wrote: > Dear Experts, > > is there a possibility to extract the "motion parameter" from a BBR > registration? Possibly the first three numbers of the > > register.dof6.dat.param > > file are the same parameter as found in column 2 - 7 in: > > fmcpr.mcdat. > > If I have a series of "register.dof6.dat.param" can I use "mcdat2mcextreg" to > calculate motion regressors from those transformations? > > Thanks pfannmoe > > > > > > -- > Joerg Pfannmoeller > ___ > 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. > -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Content of register.dof6.dat.param
Dear Experts, is there a possibility to extract the "motion parameter" from a BBR registration? Possibly the first three numbers of the register.dof6.dat.param file are the same parameter as found in column 2 - 7 in: fmcpr.mcdat. If I have a series of "register.dof6.dat.param" can I use "mcdat2mcextreg" to calculate motion regressors from those transformations? Thanks pfannmoe -- Joerg Pfannmoeller ___ 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] Content of register.dof6.dat.param
Hello Doug, can we finish the topic this week? Yours pfannmoe On Thu, 9 Apr 2015 09:41:17 -0400 (EDT) Bruce Fischl wrote: > Bruce ___ 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] Parameters for motion correction from boundary based register
Hello Doug, is there a possibility to extract the "motion parameter" from a BBR registration? Possibly, the first six numbers of the register.dof6.dat.param file are the same parameters as found in column 2 - 7 in the file: fmcpr.mcdat created by mc-afni2 during the FS-Fast preprocessing. If I have a series of "register.dof6.dat.param" files, can I use "mcdat2mcextreg" to calculate motion regressors from those transformations? Thanks 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] Content of register.dof6.dat.param
Just to make that point: Is it valid to apply "mcparams2extreg -mcfile fmc.mcdat -extreg mcextreg" after substitution of the numbers in "register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion regressors valid? On Mon, 13 Apr 2015 10:15:08 -0400 Douglas Greve wrote: > > Those numbers do not have the same interpretation as as the ones in > fmc.mcdat but they represent the same information. If you construct a > new file with the same format as fmc.mcdat but with those numbers > substituted in cols 2-7 then you should get pretty similar results. > > > On 4/9/15 7:04 AM, pfannmo...@uni-greifswald.de wrote: > > Sorry, I ment the first six numbers in "register.dof6.dat.param". > > > > > > > > On Thu, 9 Apr 2015 12:33:49 +0200 > > pfannmo...@uni-greifswald.de wrote: > > > >> Dear Experts, > >> > >> is there a possibility to extract the "motion parameter" from a BBR > >> registration? Possibly the first three numbers of the > >> > >> register.dof6.dat.param > >> > >> file are the same parameter as found in column 2 - 7 in: > >> > >> fmcpr.mcdat. > >> > >> If I have a series of "register.dof6.dat.param" can I use "mcdat2mcextreg" > >> to calculate motion regressors from those transformations? > >> > >> Thanks pfannmoe > >> > >> > >> > >> > >> > >> -- > >> Joerg Pfannmoeller > >> ___ > >> 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 -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Content of register.dof6.dat.param
Hello Doug, just a very last question. Where ist the origin of the coordinate system if the motion parameters are calculated using mc-afni2 and where is it if BBR is used? I mean the origin in the coordinate system of the input and output volume. Yours pfannmoe On Mon, 13 Apr 2015 10:36:02 -0400 Douglas Greve wrote: > yes > > On 4/13/15 10:32 AM, pfannmo...@uni-greifswald.de wrote: > > Just to make that point: Is it valid to apply "mcparams2extreg -mcfile > > fmc.mcdat -extreg mcextreg" after substitution of the numbers in > > "register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion > > regressors valid? > > > > > > > > On Mon, 13 Apr 2015 10:15:08 -0400 > > Douglas Greve wrote: > > > >> Those numbers do not have the same interpretation as as the ones in > >> fmc.mcdat but they represent the same information. If you construct a > >> new file with the same format as fmc.mcdat but with those numbers > >> substituted in cols 2-7 then you should get pretty similar results. > >> > >> > >> On 4/9/15 7:04 AM, pfannmo...@uni-greifswald.de wrote: > >>> Sorry, I ment the first six numbers in "register.dof6.dat.param". > >>> > >>> > >>> > >>> On Thu, 9 Apr 2015 12:33:49 +0200 > >>> pfannmo...@uni-greifswald.de wrote: > >>> > Dear Experts, > > is there a possibility to extract the "motion parameter" from a BBR > registration? Possibly the first three numbers of the > > register.dof6.dat.param > > file are the same parameter as found in column 2 - 7 in: > > fmcpr.mcdat. > > If I have a series of "register.dof6.dat.param" can I use > "mcdat2mcextreg" to calculate motion regressors from those > transformations? > > Thanks pfannmoe > > > > > > -- > Joerg Pfannmoeller > ___ > 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Transformation between individual subject and FsAverage
Dear Experts, if functional volume data are mapped to cortical surfaces, using mri_vol2surf and FsAverage as the target surface, a surface registration is carried out. As far as I can see the program surfreg does the surface registration. In this registration the cortical maps of the individual subject and FsAverage are aligned. Probably it is just some kind of rotation matrix. How can I output the transformation matrix? 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] Improve normalization with own average subject
Dear Experts, I am currently working with the non-linear FreeSurfer normalization. We have a small group of subjects N = 12 and in each brain we identified a single position with a fMRI localizer. The task is a group comparison of the individual results for this position. Therefore, the coordinates of each position in FSaverage was determined using mri_label2label. The radius of the region is an important quantity in my investigations. A smaller radius would help me a lot in my data processing. I tried to decrease the radius by generating a new group space template from my 12 subjects with make_average_subject. Then I used mri_label2label to determine the coordinates in the new group space template. Unfortunately, there was no difference in the radius. The intention behind this procedure was to achieve an improved normalization of the subjects. I have read much about this topic in the mailing list, but there are many details in the processing which I am not yet aware of. So, my question is if I proceeded the best possible way or if there is a better alternative to improve the normalization. Would it help to generate a new template as outlined in the second part on this web tutorial (chapter: Creating a registration template from scratch): https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates or do I need to use mris_register with my new template and my 12 subjects instead of mri_label2label in order to benfit from my new template as generated by make_average_subject (also outlined in the web tutorial in the chapter: Creating a registration template initialized with FreeSurfer template)? Even a small decrease in the radius would help to improve my results. 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.
Re: [Freesurfer] Improve normalization with own average subject
Hello, I have computed the lh.sphere.myreg3 and rh.sphere.myreg3 files for all of my subjects as outlined on the web page on this topic (chapter: Creating a registration template from scratch). Now I would like to know which points in those registered files correspond to each other. How do I have to proceed? Do I have to generate a new average subject with the command: make_average_subject --out newtemplate_from_scratch --surf-reg sphere.myreg3 --subjects subject1 ... subjectN Does this template allow me to compare the position as given by my fMRI localizer across the group with my template from scratch including the potential improvement in the correspondence of those points? Yours pfannmoe On Fri, 1 Apr 2016 08:28:18 -0400 (EDT) Bruce Fischl wrote: > Hi pfannmoe > > that page looks pretty good to me. YOu need to create a new folding atlas > which we typically store in .tif format using mris_make_template. This is > usually done by picking one subject, registering all your subjects to that > template (.tif file), recreating the template, reregistering and so on. > Usually this converges after 2-3 rounds. > > cheers > Bruce > > > On Fri, 1 Apr 2016, > pfannmo...@uni-greifswald.de wrote: > > > Dear Experts, > > > > I am currently working with the non-linear FreeSurfer normalization. > > We have a small group of subjects N = 12 and in each brain we > > identified a single position with a fMRI localizer. The task is a > > group comparison of the individual results for this position. > > Therefore, the coordinates of each position in FSaverage was > > determined using mri_label2label. The radius of the region is an > > important quantity in my investigations. A smaller radius would help > > me a lot in my data processing. I tried to decrease the radius by > > generating a new group space template from my 12 subjects with > > make_average_subject. Then I used mri_label2label to determine the > > coordinates in the new group space template. Unfortunately, there > > was no difference in the radius. The intention behind this procedure > > was to achieve an improved normalization of the subjects. I have read > > much about this topic in the mailing list, but there are many details > > in the processing which I am not yet aware of. So, my question is if > > I proceeded the best possible way or if there is a better alternative > > to improve the normalization. Would it help to generate a new template > > as outlined in the second part on this web tutorial (chapter: Creating > > a registration template from scratch): > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates > > > > or do I need to use mris_register with my new template and my 12 > > subjects instead of mri_label2label in order to benfit from my new > > template as generated by make_average_subject (also outlined in the > > web tutorial in the chapter: Creating a registration template > > initialized with FreeSurfer template)? > > > > Even a small decrease in the radius would help to improve my results. > > > > Thanks in advance > > > > pfannmoe > > > > > > > > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Time Series Revision in FS-Fast
Dear Experts, I have a question concerning the evaluation of the time series in the FS-Fast stream. There is one time series for each vertex of a brain. Can single time points or series of time points be excluded from the analysis in the following way: Remove time point 10 from the time series of vertex 220 and time point 550 from vertex 42. This means a time point exclude file can not be used in my case. Can I achieve this removal by setting the value of the time points to not-a-number or something similar? 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] selxavg3-sess error in ==> fast_selxavg3 at 434
Dear Experts, during an fsfast analysis an error occured after selxavg3-sess was executed. The corresponding commands were: mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1 selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force The output of selxavg3-sess was: >> >> >> >> >> >> >> sxa3pwd = /.../evaluation >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sessdir ### /.../evaluation/sessdir - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /.../evaluation Extension format = nii.gz 1 stim-v-base.mat Excluding 8 points nruns = 1 autostimdur = outanadir = /.../evaluation/sessdir/bold/analysis.lh Excluding 8 points Found 145573/155188 (93.8) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 1 ntptot = 108, nX = 15, DOF = 93 Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat XCond = 64.7067 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.468819(t=0.005249) 2 -0.25 -0.252194(t=0.007053) 3 0 -0.0449419(t=0.008126) 4 0.25 0.149516(t=0.00935) 5 0.5 0.319324(t=0.010795) AR1 Correction M: 0.0749452 1.26122 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean Global In-Mask Mean = (0.664951) ??? Error using ==> mrdivide Matrix dimensions must agree. Error in ==> fast_selxavg3 at 434 RescaleFactor = flac0.inorm/gmean; >> -- ERROR: fast_selxavg3() failed\n Do you have an idea what went wrong? Sincerely 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.
Re: [Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at 434
Thank you for your Help. I figured out that it was a problem with the data which caused this error. On Wed, 04 Jun 2014 12:00:08 -0400 Douglas N Greve wrote: > > This is a strange error that I cannot figure out from the terminal > output. What version of FS are you using? Here's something you can try: > > Run selxavg3-sess with --monly sxa3.m This will return right away having > created sxa3.m > > Start matlab and run sxa3. It will stop at the error below. Then type > > flac0.inorm > > gmean > > Each of these will print something out to the terminal. Send the results > to the list > > doug > > > On 06/02/2014 06:27 AM, pfannmo...@uni-greifswald.de wrote: > > Dear Experts, > > > > during an fsfast analysis an error occured after selxavg3-sess was > > executed. The corresponding commands were: > > > > mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm > > sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 > > -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg > > mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1 > > > > selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force > > > > > > > > The output of selxavg3-sess was: > > > > > > sxa3pwd = > > > > /.../evaluation > > > > sxa3cmd = > > > > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis > > analysis.lh -no-preproc -force > > > >>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > #@# sessdir ### > > /.../evaluation/sessdir > > - > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > /usr/local/freesurfer/matlab/MRIread.m > > - > > outtop = /.../evaluation > > Extension format = nii.gz > > 1 stim-v-base.mat > > Excluding 8 points > > nruns = 1 > > autostimdur = > > > > > > outanadir = /.../evaluation/sessdir/bold/analysis.lh > > Excluding 8 points > > Found 145573/155188 (93.8) voxels in mask > > Creating Design Matrix > > ... creation time = 0.008 sec > > DoMCFit = 1 > > ntptot = 108, nX = 15, DOF = 93 > > Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat > > XCond = 64.7067 (normalized) > > Computing compensation for resdual AR1 bias > > 1 -0.5 -0.468819(t=0.005249) > > 2 -0.25 -0.252194(t=0.007053) > > 3 0 -0.0449419(t=0.008126) > > 4 0.25 0.149516(t=0.00935) > > 5 0.5 0.319324(t=0.010795) > > AR1 Correction M: 0.0749452 1.26122 > > Computing contrast matrices > > OLS Beta Pass > >run 1t= 0.0 > > Global Mean > > Global In-Mask Mean = (0.664951) > > ??? Error using ==> mrdivide > > Matrix dimensions must agree. > > > > Error in ==> fast_selxavg3 at 434 > > RescaleFactor = flac0.inorm/gmean; > > > >>> -- > > ERROR: fast_selxavg3() failed\n > > > > > > Do you have an idea what went wrong? > > > > Sincerely 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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. > -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Errors in Mapping of Brodmann Areas
It would be very helpful for me. On Fri, 18 Jul 2014 09:18:15 -0400 (EDT) Bruce Fischl wrote: > Hi pfannmoe > > this is a bug in mri_label2label that we fixed a while ago. Zeke: can > post a new version and let people on the list know where it is? > > thanks > Bruce > > On Fri, 18 Jul 2014, > pfannmo...@uni-greifswald.de wrote: > > > Dear Experts, > > > > I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data > > set. This has been done with the same data on a Linux system with > > Freesurfer 5.3 without any problems. Everything works fine on the Mac > > except of the labelling of Brodmann Areas. On the Mac the regions are not > > created as a single areal with a border at the outline. Instead they > > consist of an outside border and several small regions inside the label. > > > > I already tried to create the Brodmann Areas by myself using the command: > > > > mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label > > --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid > > --regmethod surface --hemi lh > > > > > > This does not change the result. I attached a screen shot of the label in > > fsaverage and one of my subjects. Any help is highly appreciated. > > > > 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. > -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] distances on individual and mni brain
Dear Experts, I have calculated distances with mris_pmake on the individual brain of a subject. I would like to compute the distance between the corresponding points on the mni brain (fsaverage). Is there a simple way to transform the distances? Best 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] Comparison of surface and euclidean distances of fsaverage
Dear FreeSurfer experts, I computed distances on the cortex surface of fsaverage using mris_pmake. The exact syntax of the distance computation was: mris_pmake --subject fsaverage --hemi lh/rh --surface0 smoothwm --curv0 sulc --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs startVertex:X,endVertex:X . Subsequently, the euclidean distance was computed using the MNI coordinates displayed by tksurfer if the startVertex and the stopVertex are selected: distance_euc = sqrt[(startMNI_x-stopMNI_x)^2+(startMNI_y-stopMNI_y)^2+(startMNI_z-stopMNI_z)^2] . The in-surface distance must be larger or equal to the euclidean distance. However, in ~50% of the cases investigated the opposite is computed. Typical distances calculated are in the range of 7 mm. Do you have an explanation for this outcome and a possible solution? How can it be corrected? I am using FreeSurfer 5.3 and did not encounter any other problems in data evaluation. Any help us highly appreciated! Sincerely 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.
Re: [Freesurfer] Comparison of surface and euclidean distances of fsaverage
Please remove this mail. This problem was already solved. On Tue, 7 Oct 2014 16:55:16 +0200 pfannmo...@uni-greifswald.de wrote: > Dear FreeSurfer experts, > > I computed distances on the cortex surface of fsaverage using mris_pmake. The > exact syntax of the distance computation was: > > mris_pmake --subject fsaverage --hemi lh/rh --surface0 smoothwm --curv0 sulc > --curv1 sulc --mpmOverlay euclidean --mpmProg pathFind --mpmArgs > startVertex:X,endVertex:X . > > Subsequently, the euclidean distance was computed using the MNI coordinates > displayed by tksurfer if the startVertex and the stopVertex are selected: > > distance_euc = > sqrt[(startMNI_x-stopMNI_x)^2+(startMNI_y-stopMNI_y)^2+(startMNI_z-stopMNI_z)^2] > . > > The in-surface distance must be larger or equal to the euclidean distance. > However, in ~50% of the cases investigated the opposite is computed. Typical > distances calculated are in the range of 7 mm. Do you have an explanation for > this outcome and a possible solution? How can it be corrected? I am using > FreeSurfer 5.3 and did not encounter any other problems in data evaluation. > Any help us highly appreciated! > > Sincerely 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Probabilities in the Brodmann area labels
Dear FreeSurfer Experts, I am puzzeled about the probabilities in the Brodmann area labels. If I take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain vertex a probability sum < 1 should arise. This is due to the fact that 10 brains where analyzed in order to compute the probabilities and in each brain only one Brodmann area was found at each location. In my current test I recognized that values > 1 occur as often as values < 1. How is this possible? Respectfully 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] Probabilities in the Brodmann area labels
It is in fsaverage. On Tue, 9 Dec 2014 14:37:43 +0100 pfannmo...@uni-greifswald.de wrote: > Dear FreeSurfer Experts, > > I am puzzeled about the probabilities in the Brodmann area labels. If I take > the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a certain > vertex a probability sum < 1 should arise. This is due to the fact that 10 > brains where analyzed in order to compute the probabilities and in each brain > only one Brodmann area was found at each location. In my current test I > recognized that values > 1 occur as often as values < 1. How is this possible? > > Respectfully 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. > -- Joerg Pfannmoeller ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Probabilities in the Brodmann area labels
Dear Bruce, if I take BA1, BA2, BA3a and BA3b and sum the probabilities at each vertex there are 17 % of the vertices which show probabilities > 1. The largest probability is 1.7778. There is a histogramm of the values attached to this mail. Is there a possibility to correct those values? Respectfully pfannmoe On Wed, 10 Dec 2014 08:28:34 -0500 (EST) Bruce Fischl wrote: > hmmm, is it on the boundaries of the labels? And only a bit >1? That can > certainly happen due to resampling and small registration inaccuracies > > On Wed, 10 Dec 2014, > pfannmo...@uni-greifswald.de wrote: > > > It is in fsaverage. > > > > > > On Tue, 9 Dec 2014 14:37:43 +0100 > > pfannmo...@uni-greifswald.de wrote: > > > >> Dear FreeSurfer Experts, > >> > >> I am puzzeled about the probabilities in the Brodmann area labels. If I > >> take the Brodmann areas 1, 2, 3a and 3b and add their probabilities at a > >> certain vertex a probability sum < 1 should arise. This is due to the fact > >> that 10 brains where analyzed in order to compute the probabilities and in > >> each brain only one Brodmann area was found at each location. In my > >> current test I recognized that values > 1 occur as often as values < 1. > >> How is this possible? > >> > >> Respectfully 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Joerg Pfannmoeller ___ 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.
