Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Hi, Thank you so much for assistant me in the process. I could do that. It worked. Thanks Faezeh Vedaei On Wed, Mar 2, 2016 at 6:15 PM, Faeze Vedaei wrote: > Hi > > Thank you so much for your help. I just got your meaning. I created new > LUT file by just changing randomly the RBG values for each 13 specific > regions and opened the annot file in tksurfer. And the strange issue is > that just for paracentral I used your values I had paracentral in tksurfer > GUI name, but for the rest of the regions I saw that problem I had before! > (the region's names were not the names in .ctab file). So, what do you > think about? > > Regards, > Faeze > > On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you for your response. sorry, I could not understand what you mean. >> How you found 23 230 60 values for paracentral region? I mean. Are these >> from Freesurfer LUT? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei >> wrote: >> >>> Thank you for your response. It is better to explain my question that >>> the coordinates for paracentral in .ctab file is '63 100 60', that you >>> changed these to '23 230 60' in your new version. My question is that how >>> you applied such this change on the RBG values for this region? >>> >>> Regards, >>> Faezeh >>> >>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei >>> wrote: >>> Thank you so much for you response. I should say that I know about what you are saying. My issue is that I have these 4 columns in my LUT file. Why and how can I change the numbers (RGB values) to create new LUT? Bests, Faezeh On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: > Hi, > > Thank you so much for you descriptions. I checked out the link you > just sent me. Because I do not have many experiences working with > Freesurfer, I really could not understand about how I can do such this > revising in LUT file. Can you explain more about this? I truly appreciate > your time and help. > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I really appreciate you for help me in this process. May you clarify >> me from which pattern you changed the RGB values for that region? How I >> can >> change the coordinates for the others? >> >> Regards, >> Faezeh Vedaei >> >> >> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> I should let you know that, it works! It shows paracentral name in >>> tksurfer. So, how I have to revise my .ctab file to get the right >>> result? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >>> wrote: >>> Hi, Thank you for your response. I just used the command you suggested to use by just a change in calling .ctab LUT file. I used the path: 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just calling aparc.annot.a2009s.ctab. It is strange that I created annot file for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what is your opinion? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi, > > > Here is the text format of those files. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei < > faezeved...@gmail.com> wrote: > >> Hi >> >> Thank you so much for your response. I attached here three files >> including the command lines, LUT file , and the list of names I want >> to get >> and what the result is actually. I'd appreciate if you look at them >> and let >> me know what is wrong with that. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei < >> faezeved...@gmail.com> wrote: >> >>> Hi, >>> >>> I checked again to arrange the labels in the order of LUT file, >>> but the result has not changed. Can you help me more how I can fix >>> this >>> problem? Thank you so much for your time and help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei < >>> faezeved...@gmail.com> wrote: >>> Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files >>
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Hi Thank you so much for your help. I just got your meaning. I created new LUT file by just changing randomly the RBG values for each 13 specific regions and opened the annot file in tksurfer. And the strange issue is that just for paracentral I used your values I had paracentral in tksurfer GUI name, but for the rest of the regions I saw that problem I had before! (the region's names were not the names in .ctab file). So, what do you think about? Regards, Faeze On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. sorry, I could not understand what you mean. > How you found 23 230 60 values for paracentral region? I mean. Are these > from Freesurfer LUT? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei > wrote: > >> Thank you for your response. It is better to explain my question that the >> coordinates for paracentral in .ctab file is '63 100 60', that you changed >> these to '23 230 60' in your new version. My question is that how you >> applied such this change on the RBG values for this region? >> >> Regards, >> Faezeh >> >> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei >> wrote: >> >>> Thank you so much for you response. I should say that I know about what >>> you are saying. My issue is that I have these 4 columns in my LUT file. Why >>> and how can I change the numbers (RGB values) to create new LUT? >>> >>> Bests, >>> Faezeh >>> >>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei >>> wrote: >>> Hi, Thank you so much for you descriptions. I checked out the link you just sent me. Because I do not have many experiences working with Freesurfer, I really could not understand about how I can do such this revising in LUT file. Can you explain more about this? I truly appreciate your time and help. Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > Hi, > > I really appreciate you for help me in this process. May you clarify > me from which pattern you changed the RGB values for that region? How I > can > change the coordinates for the others? > > Regards, > Faezeh Vedaei > > > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I should let you know that, it works! It shows paracentral name in >> tksurfer. So, how I have to revise my .ctab file to get the right result? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you for your response. I just used the command you suggested >>> to use by just a change in calling .ctab LUT file. I used the path: >>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >>> just >>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file >>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >>> opinion? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> > wrote: >>> Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi > > Thank you so much for your response. I attached here three files > including the command lines, LUT file , and the list of names I want > to get > and what the result is actually. I'd appreciate if you look at them > and let > me know what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei < > faezeved...@gmail.com> wrote: > >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, >> but the result has not changed. Can you help me more how I can fix >> this >> problem? Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei < >> faezeved...@gmail.com> wrote: >> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come >>> from the color LUT file. But, the issue is that I chose the label >>> files >>> from that LUT file too. It meas the source that I chose the label >>> files >>> from and the source of the region's names in tksurfer are the same. >>> The >>> problem is just I do not have the label's names I merged to create >>> annot >>> file, in the tksurfer GUI. It shows another names of that list! So,
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
just change the values and re-run with different numbers and see what happens On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. sorry, I could not understand what you mean. > How you found 23 230 60 values for paracentral region? I mean. Are these > from Freesurfer LUT? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei wrote: >> >> Thank you for your response. It is better to explain my question that the >> coordinates for paracentral in .ctab file is '63 100 60', that you changed >> these to '23 230 60' in your new version. My question is that how you >> applied such this change on the RBG values for this region? >> >> Regards, >> Faezeh >> >> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei >> wrote: >>> >>> Thank you so much for you response. I should say that I know about what >>> you are saying. My issue is that I have these 4 columns in my LUT file. Why >>> and how can I change the numbers (RGB values) to create new LUT? >>> >>> Bests, >>> Faezeh >>> >>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei >>> wrote: Hi, Thank you so much for you descriptions. I checked out the link you just sent me. Because I do not have many experiences working with Freesurfer, I really could not understand about how I can do such this revising in LUT file. Can you explain more about this? I truly appreciate your time and help. Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > > Hi, > > I really appreciate you for help me in this process. May you clarify me > from which pattern you changed the RGB values for that region? How I can > change the coordinates for the others? > > Regards, > Faezeh Vedaei > > > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei > wrote: >> >> Hi, >> >> I should let you know that, it works! It shows paracentral name in >> tksurfer. So, how I have to revise my .ctab file to get the right result? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. I just used the command you suggested to >>> use by just a change in calling .ctab LUT file. I used the path: >>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >>> just >>> calling aparc.annot.a2009s.ctab. It is strange that I created annot >>> file for >>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >>> opinion? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >>> wrote: Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > > Hi > > Thank you so much for your response. I attached here three files > including the command lines, LUT file , and the list of names I want > to get > and what the result is actually. I'd appreciate if you look at them > and let > me know what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei > wrote: >> >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, >> but the result has not changed. Can you help me more how I can fix >> this >> problem? Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come >>> from the color LUT file. But, the issue is that I chose the label >>> files from >>> that LUT file too. It meas the source that I chose the label files >>> from and >>> the source of the region's names in tksurfer are the same. The >>> problem is >>> just I do not have the label's names I merged to create annot file, >>> in the >>> tksurfer GUI. It shows another names of that list! So, what do you >>> think >>> about? What is the problem? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >>> wrote: Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Hi, Thank you for your response. sorry, I could not understand what you mean. How you found 23 230 60 values for paracentral region? I mean. Are these from Freesurfer LUT? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei wrote: > Thank you for your response. It is better to explain my question that the > coordinates for paracentral in .ctab file is '63 100 60', that you changed > these to '23 230 60' in your new version. My question is that how you > applied such this change on the RBG values for this region? > > Regards, > Faezeh > > On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei > wrote: > >> Thank you so much for you response. I should say that I know about what >> you are saying. My issue is that I have these 4 columns in my LUT file. Why >> and how can I change the numbers (RGB values) to create new LUT? >> >> Bests, >> Faezeh >> >> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you so much for you descriptions. I checked out the link you just >>> sent me. Because I do not have many experiences working with Freesurfer, I >>> really could not understand about how I can do such this revising in LUT >>> file. Can you explain more about this? I truly appreciate your time and >>> help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei >>> wrote: >>> Hi, I really appreciate you for help me in this process. May you clarify me from which pattern you changed the RGB values for that region? How I can change the coordinates for the others? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in > tksurfer. So, how I have to revise my .ctab file to get the right result? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you for your response. I just used the command you suggested to >> use by just a change in calling .ctab LUT file. I used the path: >> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >> just >> calling aparc.annot.a2009s.ctab. It is strange that I created annot file >> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >> opinion? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> >>> Here is the text format of those files. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >> > wrote: >>> Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, > but the result has not changed. Can you help me more how I can fix > this > problem? Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei < > faezeved...@gmail.com> wrote: > >> Hi, >> >> Thank you for your response. Yes, you are right. The names come >> from the color LUT file. But, the issue is that I chose the label >> files >> from that LUT file too. It meas the source that I chose the label >> files >> from and the source of the region's names in tksurfer are the same. >> The >> problem is just I do not have the label's names I merged to create >> annot >> file, in the tksurfer GUI. It shows another names of that list! So, >> what do >> you think about? What is the problem? >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei < >> faezeved...@gmail.com> wrote: >> >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I >>> open >>> this annot file in tksurfer and click on colored regions which >>> corresponded >>> to specific labels I had chosen them, I do not have their name on >>> the >>> vertex information part at
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Those numbers only refer to the color the too will appear: hence the name color lookup table hth d Sent from my Phone > On Mar 1, 2016, at 21:33, Faeze Vedaei wrote: > > Thank you for your response. It is better to explain my question that the > coordinates for paracentral in .ctab file is '63 100 60', that you changed > these to '23 230 60' in your new version. My question is that how you applied > such this change on the RBG values for this region? > > Regards, > Faezeh > >> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei wrote: >> Thank you so much for you response. I should say that I know about what you >> are saying. My issue is that I have these 4 columns in my LUT file. Why and >> how can I change the numbers (RGB values) to create new LUT? >> >> Bests, >> Faezeh >> >>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: >>> Hi, >>> >>> Thank you so much for you descriptions. I checked out the link you just >>> sent me. Because I do not have many experiences working with Freesurfer, I >>> really could not understand about how I can do such this revising in LUT >>> file. Can you explain more about this? I truly appreciate your time and >>> help. >>> >>> Regards, >>> Faezeh Vedaei >>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: Hi, I really appreciate you for help me in this process. May you clarify me from which pattern you changed the RGB values for that region? How I can change the coordinates for the others? Regards, Faezeh Vedaei > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei > wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in > tksurfer. So, how I have to revise my .ctab file to get the right result? > > Regards, > Faezeh Vedaei > >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >> Hi, >> >> Thank you for your response. I just used the command you suggested to >> use by just a change in calling .ctab LUT file. I used the path: >> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by >> just calling aparc.annot.a2009s.ctab. It is strange that I created annot >> file for lh.G_and_S_paracentral.label, but it shows its name in >> tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what >> is your opinion? >> >> Regards, >> Faezeh Vedaei >> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >>> wrote: >>> Hi, >>> >>> >>> Here is the text format of those files. >>> >>> Regards, >>> Faezeh Vedaei >>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei > wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, but > the result has not changed. Can you help me more how I can fix this > problem? Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >> Hi, >> >> Thank you for your response. Yes, you are right. The names come from >> the color LUT file. But, the issue is that I chose the label files >> from that LUT file too. It meas the source that I chose the label >> files from and the source of the region's names in tksurfer are the >> same. The problem is just I do not have the label's names I merged >> to create annot file, in the tksurfer GUI. It shows another names of >> that list! So, what do you think about? What is the problem? >> >> Regards, >> Faezeh Vedaei >> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >>> wrote: >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I >>> open this annot file in tksurfer and click on colored regions which >>> corresponded to specific labels I had chosen them, I do not have >>> their name on the vertex information part at the bottom of tksurfer >>> GUI. It shows very different names for these regions. May you >>> explains me what is the problem I could not see the exact region's >>> name as I have them for label files? >>> >>> Thanks, >>>
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Thank you for your response. It is better to explain my question that the coordinates for paracentral in .ctab file is '63 100 60', that you changed these to '23 230 60' in your new version. My question is that how you applied such this change on the RBG values for this region? Regards, Faezeh On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei wrote: > Thank you so much for you response. I should say that I know about what > you are saying. My issue is that I have these 4 columns in my LUT file. Why > and how can I change the numbers (RGB values) to create new LUT? > > Bests, > Faezeh > > On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you so much for you descriptions. I checked out the link you just >> sent me. Because I do not have many experiences working with Freesurfer, I >> really could not understand about how I can do such this revising in LUT >> file. Can you explain more about this? I truly appreciate your time and >> help. >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> I really appreciate you for help me in this process. May you clarify me >>> from which pattern you changed the RGB values for that region? How I can >>> change the coordinates for the others? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> >>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei >>> wrote: >>> Hi, I should let you know that, it works! It shows paracentral name in tksurfer. So, how I have to revise my .ctab file to get the right result? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. I just used the command you suggested to > use by just a change in calling .ctab LUT file. I used the path: > 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just > calling aparc.annot.a2009s.ctab. It is strange that I created annot file > for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: > G_and_S_frontomarg! I excluded the part --nhits too. So, what is your > opinion? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei > wrote: > >> Hi, >> >> >> Here is the text format of those files. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >> wrote: >> >>> Hi >>> >>> Thank you so much for your response. I attached here three files >>> including the command lines, LUT file , and the list of names I want to >>> get >>> and what the result is actually. I'd appreciate if you look at them and >>> let >>> me know what is wrong with that. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >> > wrote: >>> Hi, I checked again to arrange the labels in the order of LUT file, but the result has not changed. Can you help me more how I can fix this problem? Thank you so much for your time and help. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi, > > Thank you for your response. Yes, you are right. The names come > from the color LUT file. But, the issue is that I chose the label > files > from that LUT file too. It meas the source that I chose the label > files > from and the source of the region's names in tksurfer are the same. > The > problem is just I do not have the label's names I merged to create > annot > file, in the tksurfer GUI. It shows another names of that list! So, > what do > you think about? What is the problem? > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei < > faezeved...@gmail.com> wrote: > >> Hi Freesurfer experts, >> >> I have created an annotation file by several label files using >> mris_label2annot command in Freesurfer. The problem is that when I >> open >> this annot file in tksurfer and click on colored regions which >> corresponded >> to specific labels I had chosen them, I do not have their name on the >> vertex information part at the bottom of tksurfer GUI. It shows very >> different names for these regions. May you explains me what is the >> problem >> I could not see the exact region's name as I have them for label >> files? >> >> Thanks, >> Faezeh Vedaei >> > > >>> >> > >>> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
It is just a text file (you can open it with vi or gedit whatever), just add new lines for new labels and make the colors the color you want them to be.\ hth d On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei wrote: > Thank you so much for you response. I should say that I know about what you > are saying. My issue is that I have these 4 columns in my LUT file. Why and > how can I change the numbers (RGB values) to create new LUT? > > Bests, > Faezeh > > On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: >> >> Hi, >> >> Thank you so much for you descriptions. I checked out the link you just >> sent me. Because I do not have many experiences working with Freesurfer, I >> really could not understand about how I can do such this revising in LUT >> file. Can you explain more about this? I truly appreciate your time and >> help. >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> I really appreciate you for help me in this process. May you clarify me >>> from which pattern you changed the RGB values for that region? How I can >>> change the coordinates for the others? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> >>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei >>> wrote: Hi, I should let you know that, it works! It shows paracentral name in tksurfer. So, how I have to revise my .ctab file to get the right result? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: > > Hi, > > Thank you for your response. I just used the command you suggested to > use by just a change in calling .ctab LUT file. I used the path: > 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just > calling aparc.annot.a2009s.ctab. It is strange that I created annot file > for > lh.G_and_S_paracentral.label, but it shows its name in tksurfer: > G_and_S_frontomarg! I excluded the part --nhits too. So, what is your > opinion? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei > wrote: >> >> Hi, >> >> >> Here is the text format of those files. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >> wrote: >>> >>> Hi >>> >>> Thank you so much for your response. I attached here three files >>> including the command lines, LUT file , and the list of names I want to >>> get >>> and what the result is actually. I'd appreciate if you look at them and >>> let >>> me know what is wrong with that. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >>> wrote: Hi, I checked again to arrange the labels in the order of LUT file, but the result has not changed. Can you help me more how I can fix this problem? Thank you so much for your time and help. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: > > Hi, > > Thank you for your response. Yes, you are right. The names come > from the color LUT file. But, the issue is that I chose the label > files from > that LUT file too. It meas the source that I chose the label files > from and > the source of the region's names in tksurfer are the same. The > problem is > just I do not have the label's names I merged to create annot file, > in the > tksurfer GUI. It shows another names of that list! So, what do you > think > about? What is the problem? > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > wrote: >> >> Hi Freesurfer experts, >> >> I have created an annotation file by several label files using >> mris_label2annot command in Freesurfer. The problem is that when I >> open this >> annot file in tksurfer and click on colored regions which >> corresponded to >> specific labels I had chosen them, I do not have their name on the >> vertex >> information part at the bottom of tksurfer GUI. It shows very >> different >> names for these regions. May you explains me what is the problem I >> could not >> see the exact region's name as I have them for label files? >> >> Thanks, >> Faezeh Vedaei > > >>> >> > >>> >> > > > ___ > 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 i
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Thank you so much for you response. I should say that I know about what you are saying. My issue is that I have these 4 columns in my LUT file. Why and how can I change the numbers (RGB values) to create new LUT? Bests, Faezeh On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: > Hi, > > Thank you so much for you descriptions. I checked out the link you just > sent me. Because I do not have many experiences working with Freesurfer, I > really could not understand about how I can do such this revising in LUT > file. Can you explain more about this? I truly appreciate your time and > help. > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I really appreciate you for help me in this process. May you clarify me >> from which pattern you changed the RGB values for that region? How I can >> change the coordinates for the others? >> >> Regards, >> Faezeh Vedaei >> >> >> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> I should let you know that, it works! It shows paracentral name in >>> tksurfer. So, how I have to revise my .ctab file to get the right result? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >>> wrote: >>> Hi, Thank you for your response. I just used the command you suggested to use by just a change in calling .ctab LUT file. I used the path: 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just calling aparc.annot.a2009s.ctab. It is strange that I created annot file for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what is your opinion? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei wrote: > Hi, > > > Here is the text format of those files. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei > wrote: > >> Hi >> >> Thank you so much for your response. I attached here three files >> including the command lines, LUT file , and the list of names I want to >> get >> and what the result is actually. I'd appreciate if you look at them and >> let >> me know what is wrong with that. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> I checked again to arrange the labels in the order of LUT file, but >>> the result has not changed. Can you help me more how I can fix this >>> problem? Thank you so much for your time and help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> > wrote: >>> Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files from that LUT file too. It meas the source that I chose the label files from and the source of the region's names in tksurfer are the same. The problem is just I do not have the label's names I merged to create annot file, in the tksurfer GUI. It shows another names of that list! So, what do you think about? What is the problem? Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei < faezeved...@gmail.com> wrote: > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command in Freesurfer. The problem is that when I > open > this annot file in tksurfer and click on colored regions which > corresponded > to specific labels I had chosen them, I do not have their name on the > vertex information part at the bottom of tksurfer GUI. It shows very > different names for these regions. May you explains me what is the > problem > I could not see the exact region's name as I have them for label > files? > > Thanks, > Faezeh Vedaei > >>> >> > >>> >> > ___ 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] The name of regions of annotation file issue viewing by tksurfer
The 4 number columns represent: Red Green Blue and Alpha The numbers range from 0-255. They can be combined to create any color. Play around, and you will see what it does. hth, d On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei wrote: > Hi, > > Thank you so much for you descriptions. I checked out the link you just sent > me. Because I do not have many experiences working with Freesurfer, I really > could not understand about how I can do such this revising in LUT file. Can > you explain more about this? I truly appreciate your time and help. > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: >> >> Hi, >> >> I really appreciate you for help me in this process. May you clarify me >> from which pattern you changed the RGB values for that region? How I can >> change the coordinates for the others? >> >> Regards, >> Faezeh Vedaei >> >> >> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> I should let you know that, it works! It shows paracentral name in >>> tksurfer. So, how I have to revise my .ctab file to get the right result? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >>> wrote: Hi, Thank you for your response. I just used the command you suggested to use by just a change in calling .ctab LUT file. I used the path: 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just calling aparc.annot.a2009s.ctab. It is strange that I created annot file for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what is your opinion? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei wrote: > > Hi, > > > Here is the text format of those files. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei > wrote: >> >> Hi >> >> Thank you so much for your response. I attached here three files >> including the command lines, LUT file , and the list of names I want to >> get >> and what the result is actually. I'd appreciate if you look at them and >> let >> me know what is wrong with that. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> I checked again to arrange the labels in the order of LUT file, but >>> the result has not changed. Can you help me more how I can fix this >>> problem? >>> Thank you so much for your time and help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >>> wrote: Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files from that LUT file too. It meas the source that I chose the label files from and the source of the region's names in tksurfer are the same. The problem is just I do not have the label's names I merged to create annot file, in the tksurfer GUI. It shows another names of that list! So, what do you think about? What is the problem? Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command in Freesurfer. The problem is that when I > open this > annot file in tksurfer and click on colored regions which > corresponded to > specific labels I had chosen them, I do not have their name on the > vertex > information part at the bottom of tksurfer GUI. It shows very > different > names for these regions. May you explains me what is the problem I > could not > see the exact region's name as I have them for label files? > > Thanks, > Faezeh Vedaei >>> >> > >>> >> > > > ___ > 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. > ___ Freesurfe
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Hi, Thank you so much for you descriptions. I checked out the link you just sent me. Because I do not have many experiences working with Freesurfer, I really could not understand about how I can do such this revising in LUT file. Can you explain more about this? I truly appreciate your time and help. Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > Hi, > > I really appreciate you for help me in this process. May you clarify me > from which pattern you changed the RGB values for that region? How I can > change the coordinates for the others? > > Regards, > Faezeh Vedaei > > > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I should let you know that, it works! It shows paracentral name in >> tksurfer. So, how I have to revise my .ctab file to get the right result? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you for your response. I just used the command you suggested to >>> use by just a change in calling .ctab LUT file. I used the path: >>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just >>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file >>> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >>> opinion? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >>> wrote: >>> Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > Hi > > Thank you so much for your response. I attached here three files > including the command lines, LUT file , and the list of names I want to > get > and what the result is actually. I'd appreciate if you look at them and > let > me know what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, but >> the result has not changed. Can you help me more how I can fix this >> problem? Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come from >>> the color LUT file. But, the issue is that I chose the label files from >>> that LUT file too. It meas the source that I chose the label files from >>> and >>> the source of the region's names in tksurfer are the same. The problem >>> is >>> just I do not have the label's names I merged to create annot file, in >>> the >>> tksurfer GUI. It shows another names of that list! So, what do you think >>> about? What is the problem? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei < >>> faezeved...@gmail.com> wrote: >>> Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name on the vertex information part at the bottom of tksurfer GUI. It shows very different names for these regions. May you explains me what is the problem I could not see the exact region's name as I have them for label files? Thanks, Faezeh Vedaei >>> >>> >> > >>> >> > ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Faezeh, Check this page out for details. The values are just numbers in the columns of the file: https://en.wikipedia.org/wiki/RGB_color_model hth d On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei wrote: > Hi, > > I really appreciate you for help me in this process. May you clarify me from > which pattern you changed the RGB values for that region? How I can change > the coordinates for the others? > > Regards, > Faezeh Vedaei > > > On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: >> >> Hi, >> >> I should let you know that, it works! It shows paracentral name in >> tksurfer. So, how I have to revise my .ctab file to get the right result? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. I just used the command you suggested to use >>> by just a change in calling .ctab LUT file. I used the path: >>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just >>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for >>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >>> opinion? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >>> wrote: Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > > Hi > > Thank you so much for your response. I attached here three files > including the command lines, LUT file , and the list of names I want to > get > and what the result is actually. I'd appreciate if you look at them and > let > me know what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei > wrote: >> >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, but >> the result has not changed. Can you help me more how I can fix this >> problem? >> Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come from >>> the color LUT file. But, the issue is that I chose the label files from >>> that >>> LUT file too. It meas the source that I chose the label files from and >>> the >>> source of the region's names in tksurfer are the same. The problem is >>> just I >>> do not have the label's names I merged to create annot file, in the >>> tksurfer >>> GUI. It shows another names of that list! So, what do you think about? >>> What >>> is the problem? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >>> wrote: Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name on the vertex information part at the bottom of tksurfer GUI. It shows very different names for these regions. May you explains me what is the problem I could not see the exact region's name as I have them for label files? Thanks, Faezeh Vedaei >>> >>> >> > >>> >> > > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
Hi, I really appreciate you for help me in this process. May you clarify me from which pattern you changed the RGB values for that region? How I can change the coordinates for the others? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in > tksurfer. So, how I have to revise my .ctab file to get the right result? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you for your response. I just used the command you suggested to use >> by just a change in calling .ctab LUT file. I used the path: >> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just >> calling aparc.annot.a2009s.ctab. It is strange that I created annot file >> for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >> opinion? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> >>> Here is the text format of those files. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >>> wrote: >>> Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, but > the result has not changed. Can you help me more how I can fix this > problem? Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you for your response. Yes, you are right. The names come from >> the color LUT file. But, the issue is that I chose the label files from >> that LUT file too. It meas the source that I chose the label files from >> and >> the source of the region's names in tksurfer are the same. The problem is >> just I do not have the label's names I merged to create annot file, in >> the >> tksurfer GUI. It shows another names of that list! So, what do you think >> about? What is the problem? >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > > wrote: >> >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I open >>> this annot file in tksurfer and click on colored regions which >>> corresponded >>> to specific labels I had chosen them, I do not have their name on the >>> vertex information part at the bottom of tksurfer GUI. It shows very >>> different names for these regions. May you explains me what is the >>> problem >>> I could not see the exact region's name as I have them for label files? >>> >>> Thanks, >>> Faezeh Vedaei >>> >> >> > >>> >> > ___ 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] The name of regions of annotation file issue viewing by tksurfer
yes, just follow the pattern of the file. You will probably want to use different RGB values to get different colored labels. hth d On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei wrote: > Hi, > > I should let you know that, it works! It shows paracentral name in tksurfer. > So, how I have to revise my .ctab file to get the right result? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: >> >> Hi, >> >> Thank you for your response. I just used the command you suggested to use >> by just a change in calling .ctab LUT file. I used the path: >> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just >> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for >> lh.G_and_S_paracentral.label, but it shows its name in tksurfer: >> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your >> opinion? >> >> Regards, >> Faezeh Vedaei >> >> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> >>> Here is the text format of those files. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >>> wrote: Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: > > Hi, > > I checked again to arrange the labels in the order of LUT file, but the > result has not changed. Can you help me more how I can fix this problem? > Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei > wrote: >> >> Hi, >> >> Thank you for your response. Yes, you are right. The names come from >> the color LUT file. But, the issue is that I chose the label files from >> that >> LUT file too. It meas the source that I chose the label files from and >> the >> source of the region's names in tksurfer are the same. The problem is >> just I >> do not have the label's names I merged to create annot file, in the >> tksurfer >> GUI. It shows another names of that list! So, what do you think about? >> What >> is the problem? >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >> wrote: >>> >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I open >>> this >>> annot file in tksurfer and click on colored regions which corresponded >>> to >>> specific labels I had chosen them, I do not have their name on the >>> vertex >>> information part at the bottom of tksurfer GUI. It shows very different >>> names for these regions. May you explains me what is the problem I >>> could not >>> see the exact region's name as I have them for label files? >>> >>> Thanks, >>> Faezeh Vedaei >> >> > >>> >> > > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
Hi, I should let you know that, it works! It shows paracentral name in tksurfer. So, how I have to revise my .ctab file to get the right result? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. I just used the command you suggested to use > by just a change in calling .ctab LUT file. I used the path: > 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just > calling aparc.annot.a2009s.ctab. It is strange that I created annot file > for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: > G_and_S_frontomarg! I excluded the part --nhits too. So, what is your > opinion? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei > wrote: > >> Hi, >> >> >> Here is the text format of those files. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >> wrote: >> >>> Hi >>> >>> Thank you so much for your response. I attached here three files >>> including the command lines, LUT file , and the list of names I want to get >>> and what the result is actually. I'd appreciate if you look at them and let >>> me know what is wrong with that. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >>> wrote: >>> Hi, I checked again to arrange the labels in the order of LUT file, but the result has not changed. Can you help me more how I can fix this problem? Thank you so much for your time and help. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. Yes, you are right. The names come from > the color LUT file. But, the issue is that I chose the label files from > that LUT file too. It meas the source that I chose the label files from > and > the source of the region's names in tksurfer are the same. The problem is > just I do not have the label's names I merged to create annot file, in the > tksurfer GUI. It shows another names of that list! So, what do you think > about? What is the problem? > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > wrote: > >> Hi Freesurfer experts, >> >> I have created an annotation file by several label files using >> mris_label2annot command in Freesurfer. The problem is that when I open >> this annot file in tksurfer and click on colored regions which >> corresponded >> to specific labels I had chosen them, I do not have their name on the >> vertex information part at the bottom of tksurfer GUI. It shows very >> different names for these regions. May you explains me what is the >> problem >> I could not see the exact region's name as I have them for label files? >> >> Thanks, >> Faezeh Vedaei >> > > >>> >> > ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Faezeh, Please run the exact commands including the file I attached, not the aparc.annot.a2009s.ctab, and check the result using the freeview command I provided. Then let me know what label freeview shows. hth d On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. I just used the command you suggested to use by > just a change in calling .ctab LUT file. I used the path: > 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just > calling aparc.annot.a2009s.ctab. It is strange that I created annot file for > lh.G_and_S_paracentral.label, but it shows its name in tksurfer: > G_and_S_frontomarg! I excluded the part --nhits too. So, what is your > opinion? > > Regards, > Faezeh Vedaei > > On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei wrote: >> >> Hi, >> >> >> Here is the text format of those files. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei >> wrote: >>> >>> Hi >>> >>> Thank you so much for your response. I attached here three files >>> including the command lines, LUT file , and the list of names I want to get >>> and what the result is actually. I'd appreciate if you look at them and let >>> me know what is wrong with that. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >>> wrote: Hi, I checked again to arrange the labels in the order of LUT file, but the result has not changed. Can you help me more how I can fix this problem? Thank you so much for your time and help. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: > > Hi, > > Thank you for your response. Yes, you are right. The names come from > the color LUT file. But, the issue is that I chose the label files from > that > LUT file too. It meas the source that I chose the label files from and the > source of the region's names in tksurfer are the same. The problem is > just I > do not have the label's names I merged to create annot file, in the > tksurfer > GUI. It shows another names of that list! So, what do you think about? > What > is the problem? > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > wrote: >> >> Hi Freesurfer experts, >> >> I have created an annotation file by several label files using >> mris_label2annot command in Freesurfer. The problem is that when I open >> this >> annot file in tksurfer and click on colored regions which corresponded to >> specific labels I had chosen them, I do not have their name on the vertex >> information part at the bottom of tksurfer GUI. It shows very different >> names for these regions. May you explains me what is the problem I could >> not >> see the exact region's name as I have them for label files? >> >> Thanks, >> Faezeh Vedaei > > >>> >> > > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
Hi, Thank you for your response. I just used the command you suggested to use by just a change in calling .ctab LUT file. I used the path: 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just calling aparc.annot.a2009s.ctab. It is strange that I created annot file for lh.G_and_S_paracentral.label, but it shows its name in tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what is your opinion? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei wrote: > Hi, > > > Here is the text format of those files. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei > wrote: > >> Hi >> >> Thank you so much for your response. I attached here three files >> including the command lines, LUT file , and the list of names I want to get >> and what the result is actually. I'd appreciate if you look at them and let >> me know what is wrong with that. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> I checked again to arrange the labels in the order of LUT file, but the >>> result has not changed. Can you help me more how I can fix this problem? >>> Thank you so much for your time and help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >>> wrote: >>> Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files from that LUT file too. It meas the source that I chose the label files from and the source of the region's names in tksurfer are the same. The problem is just I do not have the label's names I merged to create annot file, in the tksurfer GUI. It shows another names of that list! So, what do you think about? What is the problem? Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command in Freesurfer. The problem is that when I open > this annot file in tksurfer and click on colored regions which > corresponded > to specific labels I had chosen them, I do not have their name on the > vertex information part at the bottom of tksurfer GUI. It shows very > different names for these regions. May you explains me what is the problem > I could not see the exact region's name as I have them for label files? > > Thanks, > Faezeh Vedaei > >>> >> > ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Faezeh, It is strange that the LUT file you sent doesn't seem to be named anything similar to the file you called. You are calling new/002_S_0413/labels/aparc.annot.a2009s.ctab There also seem to be some basic issues with the command --s should just have the name of the subject not a separate directory as well. Why are you using the --nhits option? Here is an example, of what I think is closer to what you want: mris_label2annot --s 002_S_0413 --h lh --ctab faezeh_lut.ctab --a myaparc_test --l 002_S_0413/labels/lh.G_and_S_paracentral.label Work from there and see if that gets you the first one, then just add as you go. Also check that you are properly loading the data in freeview: freeview -f 002_S_0413/surf/lh.inflated:annot=lh.myaparc_test.annot hth d On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei wrote: > Hi, > > > Here is the text format of those files. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: >> >> Hi >> >> Thank you so much for your response. I attached here three files including >> the command lines, LUT file , and the list of names I want to get and what >> the result is actually. I'd appreciate if you look at them and let me know >> what is wrong with that. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> I checked again to arrange the labels in the order of LUT file, but the >>> result has not changed. Can you help me more how I can fix this problem? >>> Thank you so much for your time and help. >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >>> wrote: Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files from that LUT file too. It meas the source that I chose the label files from and the source of the region's names in tksurfer are the same. The problem is just I do not have the label's names I merged to create annot file, in the tksurfer GUI. It shows another names of that list! So, what do you think about? What is the problem? Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command in Freesurfer. The problem is that when I open > this > annot file in tksurfer and click on colored regions which corresponded to > specific labels I had chosen them, I do not have their name on the vertex > information part at the bottom of tksurfer GUI. It shows very different > names for these regions. May you explains me what is the problem I could > not > see the exact region's name as I have them for label files? > > Thanks, > Faezeh Vedaei >>> >> > > > ___ > 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. > faezeh_lut.ctab Description: Binary data ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi, Here is the text format of those files. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > Hi > > Thank you so much for your response. I attached here three files including > the command lines, LUT file , and the list of names I want to get and what > the result is actually. I'd appreciate if you look at them and let me know > what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei > wrote: > >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, but the >> result has not changed. Can you help me more how I can fix this problem? >> Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come from the >>> color LUT file. But, the issue is that I chose the label files from that >>> LUT file too. It meas the source that I chose the label files from and the >>> source of the region's names in tksurfer are the same. The problem is just >>> I do not have the label's names I merged to create annot file, in the >>> tksurfer GUI. It shows another names of that list! So, what do you think >>> about? What is the problem? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >>> wrote: >>> Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name on the vertex information part at the bottom of tksurfer GUI. It shows very different names for these regions. May you explains me what is the problem I could not see the exact region's name as I have them for label files? Thanks, Faezeh Vedaei >>> >>> >> > mris_label2annot --s new/002_S_0413/ --h lh --ctab new/002_S_0413/labels/aparc.annot.a2009s.ctab --a MYAPARC2 --l new/002_S_0413/labels/lh.G_and_S_paracentral.label --l new/002_S_0413/labels/lh.G_and_S_subcentral.label --l new/002_S_0413/labels/lh.G_cingul-Post-ventral.label --l new/002_S_0413/labels/lh.G_Ins_lg_and_S_cent_ins.label --l new/002_S_0413/labels/lh.G_oc-temp_med-Parahip.label --l new/002_S_0413/labels/lh.S_calcarine.label --l new/002_S_0413/labels/lh.S_central.label --l new/002_S_0413/labels/lh.S_circular_insula_ant.label --l new/002_S_0413/labels/lh.S_circular_insula_inf.label --l new/002_S_0413/labels/lh.S_circular_insula_sup.label --l new/002_S_0413/labels/lh.S_interm_prim-Jensen.label --l new/002_S_0413/labels/lh.S_oc_sup_and_transversal.label --l new/002_S_0413/labels/lh.S_oc-temp_lat.label --nhits nhits.mgh The regions I am looking for: * lh.S_oc-temp_lat.label * lh.S_oc_sup_and_transversal.label * lh.S_central.label * lh.S_circular_insula_inf.label * lh.G_oc-temp_med-Parahip.label * lh.S_circular_insula_ant.label * lh.S_interm_prim-Jensen.label * lh.G_Ins_lg_and_S_cent_ins.label * lh.G_and_S_subcentral.label * lh.G_cingul-Post-ventral.label * lh.S_calcarine.label * lh.G_and_S_paracentral.label * lh.S_circular_insula_sup.label And the regions I got in tksurfer: * Cingual_post_dorsal * G_and_transv_frontc * Front_inf_opecular * Cuneus * G_and_S_occipital_inf * G_and_S_cingul_Ant * G_front_inf_orbital * G_and_S_paracentral 0 Unknown 0 0 00 1 G_and_S_frontomargin 23 220 600 2 G_and_S_occipital_inf23 60 1800 3 G_and_S_paracentral 63 100 600 4 G_and_S_subcentral 63 20 2200 5 G_and_S_transv_frontopol 13 0 2500 6 G_and_S_cingul-Ant 26 60 00 7 G_and_S_cingul-Mid-Ant 26 60 750 8 G_and_S_cingul-Mid-Post 26 60 1500 9 G_cingul-Post-dorsal 25 60 2500 10 G_cingul-Post-ventral60 25 250 11 G_cuneus180 20 200 12 G_front_inf-Opercular 220 20 1000 13 G_front_inf-Orbital 140 60 600 14 G_front_inf-Triangul180 220 1400 15 G_front_middle 140 100 1800 16 G_front_sup 180 20 1400 17 G_Ins_lg_and_S_cent_ins 23 10 100 18 G_insular_short 225 140 1400 19 G_occipital_middle 180 60 1800 20 G_occipital_sup 20 220 600 21 G_oc-temp_lat-fusifor60 20 1400 22 G_oc-temp_med-Lingual 220 180 1400 23 G_oc-temp_med-Parahip65 100 200 24 G_orbital 220 60 200 25 G_pariet_inf-Angular 20 60 2200 26 G_pariet_inf-Supramar 100 100 600 27 G_parietal_sup 220
Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer
Hi Faezeh, Can you send these in the text of the email. It is very hard to deal with these files? The LUT file shouldn't be an excel file it should be a plain text document (please attach). Thanks, D On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei wrote: > Hi > > Thank you so much for your response. I attached here three files including > the command lines, LUT file , and the list of names I want to get and what > the result is actually. I'd appreciate if you look at them and let me know > what is wrong with that. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: >> >> Hi, >> >> I checked again to arrange the labels in the order of LUT file, but the >> result has not changed. Can you help me more how I can fix this problem? >> Thank you so much for your time and help. >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei >> wrote: >>> >>> Hi, >>> >>> Thank you for your response. Yes, you are right. The names come from the >>> color LUT file. But, the issue is that I chose the label files from that LUT >>> file too. It meas the source that I chose the label files from and the >>> source of the region's names in tksurfer are the same. The problem is just I >>> do not have the label's names I merged to create annot file, in the tksurfer >>> GUI. It shows another names of that list! So, what do you think about? What >>> is the problem? >>> >>> Regards, >>> Faezeh Vedaei >>> >>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >>> wrote: Hi Freesurfer experts, I have created an annotation file by several label files using mris_label2annot command in Freesurfer. The problem is that when I open this annot file in tksurfer and click on colored regions which corresponded to specific labels I had chosen them, I do not have their name on the vertex information part at the bottom of tksurfer GUI. It shows very different names for these regions. May you explains me what is the problem I could not see the exact region's name as I have them for label files? Thanks, Faezeh Vedaei >>> >>> >> > > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
Hi Thank you so much for your response. I attached here three files including the command lines, LUT file , and the list of names I want to get and what the result is actually. I'd appreciate if you look at them and let me know what is wrong with that. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, but the > result has not changed. Can you help me more how I can fix this problem? > Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei > wrote: > >> Hi, >> >> Thank you for your response. Yes, you are right. The names come from the >> color LUT file. But, the issue is that I chose the label files from that >> LUT file too. It meas the source that I chose the label files from and the >> source of the region's names in tksurfer are the same. The problem is just >> I do not have the label's names I merged to create annot file, in the >> tksurfer GUI. It shows another names of that list! So, what do you think >> about? What is the problem? >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >> wrote: >> >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I open >>> this annot file in tksurfer and click on colored regions which corresponded >>> to specific labels I had chosen them, I do not have their name on the >>> vertex information part at the bottom of tksurfer GUI. It shows very >>> different names for these regions. May you explains me what is the problem >>> I could not see the exact region's name as I have them for label files? >>> >>> Thanks, >>> Faezeh Vedaei >>> >> >> > mris_label2annot.docx Description: MS-Word 2007 document LUT file (ctab).xlsx Description: MS-Excel 2007 spreadsheet label's name.docx Description: MS-Word 2007 document ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Faezeh, Please provide more details (those i described in the earlier email). Thanks d On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei wrote: > Hi, > > I checked again to arrange the labels in the order of LUT file, but the > result has not changed. Can you help me more how I can fix this problem? > Thank you so much for your time and help. > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: >> >> Hi, >> >> Thank you for your response. Yes, you are right. The names come from the >> color LUT file. But, the issue is that I chose the label files from that LUT >> file too. It meas the source that I chose the label files from and the >> source of the region's names in tksurfer are the same. The problem is just I >> do not have the label's names I merged to create annot file, in the tksurfer >> GUI. It shows another names of that list! So, what do you think about? What >> is the problem? >> >> Regards, >> Faezeh Vedaei >> >> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei >> wrote: >>> >>> Hi Freesurfer experts, >>> >>> I have created an annotation file by several label files using >>> mris_label2annot command in Freesurfer. The problem is that when I open this >>> annot file in tksurfer and click on colored regions which corresponded to >>> specific labels I had chosen them, I do not have their name on the vertex >>> information part at the bottom of tksurfer GUI. It shows very different >>> names for these regions. May you explains me what is the problem I could not >>> see the exact region's name as I have them for label files? >>> >>> Thanks, >>> Faezeh Vedaei >> >> > > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
Hi, I checked again to arrange the labels in the order of LUT file, but the result has not changed. Can you help me more how I can fix this problem? Thank you so much for your time and help. Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. Yes, you are right. The names come from the > color LUT file. But, the issue is that I chose the label files from that > LUT file too. It meas the source that I chose the label files from and the > source of the region's names in tksurfer are the same. The problem is just > I do not have the label's names I merged to create annot file, in the > tksurfer GUI. It shows another names of that list! So, what do you think > about? What is the problem? > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > wrote: > >> Hi Freesurfer experts, >> >> I have created an annotation file by several label files using >> mris_label2annot command in Freesurfer. The problem is that when I open >> this annot file in tksurfer and click on colored regions which corresponded >> to specific labels I had chosen them, I do not have their name on the >> vertex information part at the bottom of tksurfer GUI. It shows very >> different names for these regions. May you explains me what is the problem >> I could not see the exact region's name as I have them for label files? >> >> Thanks, >> Faezeh Vedaei >> > > ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Faeze, It is difficult to help without more details, but in my experience, (exact command, the color lut file in text in the email and what the error in the naming was, which label went to which entry in the color lut.) You need to put the labels in the order of your custom color lut file. hth d On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. Yes, you are right. The names come from the > color LUT file. But, the issue is that I chose the label files from that LUT > file too. It meas the source that I chose the label files from and the > source of the region's names in tksurfer are the same. The problem is just I > do not have the label's names I merged to create annot file, in the tksurfer > GUI. It shows another names of that list! So, what do you think about? What > is the problem? > > Regards, > Faezeh Vedaei > > On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei > wrote: >> >> Hi Freesurfer experts, >> >> I have created an annotation file by several label files using >> mris_label2annot command in Freesurfer. The problem is that when I open this >> annot file in tksurfer and click on colored regions which corresponded to >> specific labels I had chosen them, I do not have their name on the vertex >> information part at the bottom of tksurfer GUI. It shows very different >> names for these regions. May you explains me what is the problem I could not >> see the exact region's name as I have them for label files? >> >> Thanks, >> Faezeh Vedaei > > > > ___ > 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] The name of regions of annotation file issue viewing by tksurfer
Hi, Thank you for your response. Yes, you are right. The names come from the color LUT file. But, the issue is that I chose the label files from that LUT file too. It meas the source that I chose the label files from and the source of the region's names in tksurfer are the same. The problem is just I do not have the label's names I merged to create annot file, in the tksurfer GUI. It shows another names of that list! So, what do you think about? What is the problem? Regards, Faezeh Vedaei On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command in Freesurfer. The problem is that when I open > this annot file in tksurfer and click on colored regions which corresponded > to specific labels I had chosen them, I do not have their name on the > vertex information part at the bottom of tksurfer GUI. It shows very > different names for these regions. May you explains me what is the problem > I could not see the exact region's name as I have them for label files? > > Thanks, > Faezeh Vedaei > ___ 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] The name of regions of annotation file issue viewing by tksurfer
Hi Faeze, I believe the name comes from the Color LUT file. Try changing the name in there. hth d On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei wrote: > Hi Freesurfer experts, > > I have created an annotation file by several label files using > mris_label2annot command in Freesurfer. The problem is that when I open this > annot file in tksurfer and click on colored regions which corresponded to > specific labels I had chosen them, I do not have their name on the vertex > information part at the bottom of tksurfer GUI. It shows very different > names for these regions. May you explains me what is the problem I could not > see the exact region's name as I have them for label files? > > Thanks, > Faezeh Vedaei > > ___ > 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
