Re: [Freesurfer] [FSFAST]
Thank you, i will! Walid > On Apr 10, 2018, at 8:03 AM, Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > > You can do it with the tpexclude file. Do a search through the archives > for docs on how to use it > > > On 04/09/2018 06:56 PM, Walid Yassin wrote: >> Hello Doug, >> >> Thank you for your previous answer. >> I have another question in the mkanalysis. When I run mkanalysis is it >> possible to analyse only a part of my run? >> I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore >> the first 20s and the last 30s and analyse the 50 in the middle? >> >> Walid >> >> On Mar 21, 2018, at 0:10, Douglas Greve <dgr...@mgh.harvard.edu >> <mailto:dgr...@mgh.harvard.edu>> wrote: >> >>> Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess >>> -help to get more info >>> >>> >>> On 3/20/18 4:28 AM, Walid Yassin wrote: >>>> Hello all, >>>> >>>> I would like to pose my question again in case it got missed. >>>> >>>> Thank you. >>>> >>>> WY >>>> >>>> On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin >>>> <walidyassi...@gmail.com <mailto:walidyassi...@gmail.com>> wrote: >>>> >>>>Hi Doug, >>>> >>>>Is it possible to run retinotopy-like analysis to reveal areas >>>>in the brain responsible for a certain phase of a presented stimuli? >>>>Say, instead of presenting 0 - 360 degrees of rotating wedge per >>>>cycle, we would like to present arbitrary scale of 0 - 100 of a >>>>particular stimulus feature, that does not necessarily differ in >>>>their retinotopic locations. >>>> >>>>We thought, if we pretend that scale-0 is equivalent to a wedge >>>>of 0 degree, and scale-50 is equivalent to a wedge of 180 >>>>degrees, and so on, we would be able to map the cortical area >>>>corresponding to each value of the scale. >>>>However, the retinotopy protocol of freesurfer requires the >>>>input of a stimulus type “e.g. polar or eccen” and direction >>>>“e.g. pos or neg”, so our analysis won’t work as we intend. >>>> >>>>Running Freesurfer v5.3.0 >>>> >>>>Thank you >>>> >>>>Walid >>>> >>>> >>>> >>>> >>>> ___ >>>> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > 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
Re: [Freesurfer] [FSFAST]
Hello Doug, Thank you for your previous answer. I have another question in the mkanalysis. When I run mkanalysis is it possible to analyse only a part of my run? I mean if my stimuli was 100s per run, can i tell mkanalysis to ignore the first 20s and the last 30s and analyse the 50 in the middle? Walid > On Mar 21, 2018, at 0:10, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > > Sorry, yes you can use an A-B blocked paradigm. Run mkanalysis-sess -help to > get more info > >> On 3/20/18 4:28 AM, Walid Yassin wrote: >> Hello all, >> >> I would like to pose my question again in case it got missed. >> >> Thank you. >> >> WY >> >>> On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin <walidyassi...@gmail.com> >>> wrote: >>> Hi Doug, >>> >>> Is it possible to run retinotopy-like analysis to reveal areas in the brain >>> responsible for a certain phase of a presented stimuli? >>> Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we >>> would like to present arbitrary scale of 0 - 100 of a particular stimulus >>> feature, that does not necessarily differ in their retinotopic locations. >>> >>> We thought, if we pretend that scale-0 is equivalent to a wedge of 0 >>> degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we >>> would be able to map the cortical area corresponding to each value of the >>> scale. >>> However, the retinotopy protocol of freesurfer requires the input of a >>> stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our >>> analysis won’t work as we intend. >>> >>> Running Freesurfer v5.3.0 >>> >>> Thank you >>> >>> Walid >> >> >> >> ___ >> 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. ___ 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] [FSFAST]
Hello all, I would like to pose my question again in case it got missed. Thank you. WY On Mon, Mar 19, 2018 at 3:47 PM, Walid Yassin <walidyassi...@gmail.com> wrote: > Hi Doug, > > Is it possible to run retinotopy-like analysis to reveal areas in the > brain responsible for a certain phase of a presented stimuli? > Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we > would like to present arbitrary scale of 0 - 100 of a particular stimulus > feature, that does not necessarily differ in their retinotopic locations. > > We thought, if we pretend that scale-0 is equivalent to a wedge of 0 > degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we > would be able to map the cortical area corresponding to each value of the > scale. > However, the retinotopy protocol of freesurfer requires the input of a > stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our > analysis won’t work as we intend. > > Running Freesurfer v5.3.0 > > Thank you > > Walid ___ 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] [FSFAST]
Hi Doug, Is it possible to run retinotopy-like analysis to reveal areas in the brain responsible for a certain phase of a presented stimuli? Say, instead of presenting 0 - 360 degrees of rotating wedge per cycle, we would like to present arbitrary scale of 0 - 100 of a particular stimulus feature, that does not necessarily differ in their retinotopic locations. We thought, if we pretend that scale-0 is equivalent to a wedge of 0 degree, and scale-50 is equivalent to a wedge of 180 degrees, and so on, we would be able to map the cortical area corresponding to each value of the scale. However, the retinotopy protocol of freesurfer requires the input of a stimulus type “e.g. polar or eccen” and direction “e.g. pos or neg”, so our analysis won’t work as we intend. Running Freesurfer v5.3.0 Thank you Walid ___ 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] LGI
Hello, Sorry for raising this questions again. I posted this questions a while ago (Twice), but i haven't gotten an answer yet. Can i at least know if i can tweak something for this to work? or just give up? I tried downgrading Xquatrz, to 2.7.8, but it still doesn't work! My matlab is 2016a, could this be the problem? Thank you for letting me know WY On Sat, Jun 25, 2016 at 10:39 AM, Walid Yassin <walidyassi...@gmail.com> wrote: > Hello again, > > Sorry for posting twice, but does someone know what might be the problem? > > Thank you in advance. > > I’m trying to run recon-all -lgi - s Subjectname on my data but i am > getting this error! > > *** > > Error in dsearchn (line 79) > [d(i),t(i)] = min(sum((x-yi).^2,2)); > > Error in mesh_vertex_nearest (line 29) > nearestIndex = dsearchn(vertices,points); > > > Error in reorganize_verticeslist (line 28) > > [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); > > > Error in make_roi_paths (line 93) > reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, > verticeslist, step); > > > >> > ERROR: make_roi_paths did not complete successfully! > > > *** > > > *I checked the archives and saw a reply by Marie to someone who had the > same problem.* > *She recommended changing the info inside “SearchProjectionByPial.m" in the > ~/Application/freesurfer/matlab directory to:* > > > > *** > > function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, > step) > > % step is typically set between 5 and 10. Default is 7, increasing it will > % limit redundancies in the resulting path file. > > verticeslist=[]; > si=max(size(perim)); > for t=1:step:si > > [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); > verticeslist= [verticeslist nearestIndexMT]; > end > verticeslist=unique(vertices list); > > *** > > > Which i did, but i am still getting this error!* > Any recommendations on what to do next? I am running MATLAB_R2016. > > Thank you in advance, > > WY > > ___ 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] Freeview recon button
Thanks a lot Bruce! I will wait for v6 and check freeview then. for the gyrification question i added a link. Here it is: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html Thank you again! Best, Walid On Fri, Jul 1, 2016 at 12:08 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Walid > Recon editing mode is in the upcoming v6. Our recent hardware woes slowed > things down a bit, but we are still hoping to get It out soon > What was the gyrification question? > Cheers > Bruce > > On Jun 30, 2016, at 10:39 PM, Walid Yassin <walidyassi...@gmail.com> > wrote: > > Hello freesurfers, > > I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have > the Recon edit button. > I saw that someone asked about this questions twice in the archive but was > never answered. > > There was a note in the wiki page that reads "*Note*: Recon edit mode is > only available in the most recent release of freeview". I thought that the > most recent release of freeview comes with the most recent release of > freesurfer. > Can someone please let me know if there is a separate download link to the > recent release of freeview? > > Thank you in advance, > > Also If someone can answer my previous question regarding the Gyrification > i would really really appreciate it. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html > > Thank you again, > > > Best regards, > > Walid > > ___ > 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. > > ___ 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] Freeview recon button
Hello freesurfers, I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have the Recon edit button. I saw that someone asked about this questions twice in the archive but was never answered. There was a note in the wiki page that reads "*Note*: Recon edit mode is only available in the most recent release of freeview". I thought that the most recent release of freeview comes with the most recent release of freesurfer. Can someone please let me know if there is a separate download link to the recent release of freeview? Thank you in advance, Also If someone can answer my previous question regarding the Gyrification i would really really appreciate it. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html Thank you again, Best regards, Walid ___ 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] LGI
Hello again, Sorry for posting twice, but does someone know what might be the problem? Thank you in advance. I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error! *** Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! *** *I checked the archives and saw a reply by Marie to someone who had the same problem.* *She recommended changing the info inside “SearchProjectionByPial.m" in the ~/Application/freesurfer/matlab directory to:* *** function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(vertices list); *** Which i did, but i am still getting this error!* Any recommendations on what to do next? I am running MATLAB_R2016. Thank you in advance, WY ___ 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] LGI
*Hello,* *I’m trying to run recon-all -lgi - s Subjectname on my data but i am getting this error!* *** Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! *** *I checked the archives and saw a reply by Marie to someone who had the same problem.* *She recommended changing the info inside “SearchProjectionByPial.m" in the ~/Application/freesurfer/matlab directory to:* *** function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(vertices list); *** *Which i did, but i am still getting this error!* *Any recommendations on what to do next? I am running MATLAB_R2016.* *Thank you in advance,* *WY* ___ 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] [FreeSurfer/TRACULA]
Hello, Where can we find the link to tract the inferior fronto-occipital fascicles? Just want to know the reference name to add it to my path list. Best, Walid ___ 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] Referencing
Hello, We would like to cite Freesurfer for using its subcortical segmentation, but we are limited in the number of references for a case study.we can assign 1 reference to that, can you please let us know which of these 2 should we use. Fischl et al., 2002; Fischl et al., 2004a?Thanks W. Please consider your environmental responsibility. Before printing this e-mail message, ask yourself whether you really need a hard copy. ___ 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.
