Re: [caret-users] Create Foci
Can you upload your cdv file here (just one of them): http://pulvinar.wustl.edu/cgi-bin/upload.cgi And tell us which atlas/tutorial you were using for mapping the foci (e.g., PALS or Conte69)? On Jan 28, 2014, at 3:43 PM, Lauri wrote: > Dear caret-users, > > I am trying to create a map with a lot of different foci from many different > studies, I have tried to do it with the two different .csv files, the color > and the coordinates one with out any luck; my second option was creating one > by one all the foci, I don’t have more than 100 hundred so it won’t be a > waste of time doing it one by one, but I can’t project them with out > displaying other foci from the studies previously included. Could you provide > me with the instructions to create single foci? > > Thank you very much! > L > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Create Foci
Thank you Donna, I have uploaded the file is called CB_fMRI_foci.csv, and the atlas that I am using is the PALS, we called it PALS_B12.BOTH-HEMS.For-STEREOTAXIC-FOCI-ANALYSES. On Jan 29, 2014, at 9:51 AM, Donna Dierker wrote: > Can you upload your cdv file here (just one of them): > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > And tell us which atlas/tutorial you were using for mapping the foci (e.g., > PALS or Conte69)? > > > On Jan 28, 2014, at 3:43 PM, Lauri wrote: > >> Dear caret-users, >> >> I am trying to create a map with a lot of different foci from many different >> studies, I have tried to do it with the two different .csv files, the color >> and the coordinates one with out any luck; my second option was creating one >> by one all the foci, I don’t have more than 100 hundred so it won’t be a >> waste of time doing it one by one, but I can’t project them with out >> displaying other foci from the studies previously included. Could you >> provide me with the instructions to create single foci? >> >> Thank you very much! >> L >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Create Foci
Did you use these instructions? http://sumsdb.wustl.edu/sums/html/help/Import_Studies_Foci_INSTRUCTIONS_Mar09.pdf Erin On 1/29/14 8:51 AM, Donna Dierker wrote: Can you upload your cdv file here (just one of them): http://pulvinar.wustl.edu/cgi-bin/upload.cgi And tell us which atlas/tutorial you were using for mapping the foci (e.g., PALS or Conte69)? On Jan 28, 2014, at 3:43 PM, Lauri wrote: Dear caret-users, I am trying to create a map with a lot of different foci from many different studies, I have tried to do it with the two different .csv files, the color and the coordinates one with out any luck; my second option was creating one by one all the foci, I don’t have more than 100 hundred so it won’t be a waste of time doing it one by one, but I can’t project them with out displaying other foci from the studies previously included. Could you provide me with the instructions to create single foci? Thank you very much! L ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] display myelin mapping results
Hi Donna, I followed the procedures in Myelin_Mapping_Documentation_v2.doc and finished processing my own data. I just wonder how to display the results just as viewing conte69 results. Should I copy their spec file and replace all the files? Thank you very much! Regards, Hu -Original Message- From: caret-users-boun...@brainvis.wustl.edu [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker Sent: Monday, January 20, 2014 6:18 PM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] only got one hemisphere from surefit SureFit only segments one hemisphere at a time. You need to crop to a left or right hemisphere and run them separately. On Jan 20, 2014, at 3:36 PM, "Cheng, Hu" wrote: > Dear Caret User, > > I'm running Caret on a 64-bit Windows. I tried to segment an individual's T1w > anatomy using surefit. I set the origin at AC and select "both" in structure. > However, I only got left hemisphere segmented. The inflated surface is only > half of the brain. What did I do wrong? > Thanks for your help! > > Hu Cheng, Ph.D., DABMP > MRI Physicist, Imaging Research Facility Department of Psychological > and Brain Sciences Indiana University Bloomington, IN 47405 Tel. > 812-856-2518 Fax. 812-855-4691 > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] display myelin mapping results
You could do that, but assuming the myelin mapping results output individual myelin maps on the 164k_fs_LR standard mesh (or 32k), then you could actually look at them on the Conte69 atlas (e.g., inflated surface). You could have multiple subjects' maps loaded and toggle from one to the other. But if you want to click on the maps and "ID node" spots on the midthickness surface, for example, so you could see what the individual anatomy looks like, and how its contours overlay on the T1/T2, then you're better off using an individual spec file. To be honest, I'm not familiar with myelin mapping yet, but I am trying to learn more about it. Assuming you are on a Linux or MacOSX machine, could you do this command: find /directory/where/my/myelin/mapping/results/are/located | sort > /tmp/myelinoutputfiles.txt … then upload the resulting /tmp/myelinoutputfiles.txt here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi I'm wondering if spec or scene files already exist, and want to rule it out before you generate your own. On Jan 29, 2014, at 2:59 PM, "Cheng, Hu" wrote: > Hi Donna, > > I followed the procedures in Myelin_Mapping_Documentation_v2.doc and finished > processing my own data. I just wonder how to display the results just as > viewing conte69 results. Should I copy their spec file and replace all the > files? > Thank you very much! > > Regards, > > Hu > > > -Original Message- > From: caret-users-boun...@brainvis.wustl.edu > [mailto:caret-users-boun...@brainvis.wustl.edu] On Behalf Of Donna Dierker > Sent: Monday, January 20, 2014 6:18 PM > To: Caret, SureFit, and SuMS software users > Subject: Re: [caret-users] only got one hemisphere from surefit > > SureFit only segments one hemisphere at a time. You need to crop to a left > or right hemisphere and run them separately. > > > On Jan 20, 2014, at 3:36 PM, "Cheng, Hu" wrote: > >> Dear Caret User, >> >> I'm running Caret on a 64-bit Windows. I tried to segment an individual's >> T1w anatomy using surefit. I set the origin at AC and select "both" in >> structure. However, I only got left hemisphere segmented. The inflated >> surface is only half of the brain. What did I do wrong? >> Thanks for your help! >> >> Hu Cheng, Ph.D., DABMP >> MRI Physicist, Imaging Research Facility Department of Psychological >> and Brain Sciences Indiana University Bloomington, IN 47405 Tel. >> 812-856-2518 Fax. 812-855-4691 >> >> ___ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] not able to down Myelin_Mapping_Documentation_v2.doc
Hi Caret Users, I was not able to login to access the Myelin_Mapping_Documentation_v2.doc poseted on The http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps. I had tried my email address and my name for the usr and the assigned pwd, but none was successful. Thank you, Ping ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] not able to down Myelin_Mapping_Documentation_v2.doc
You don't use your email as the user, you use the login name from the registration email (right above the password). Tim On Wed, Jan 29, 2014 at 4:14 PM, Ping-Hong Yeh wrote: > Hi Caret Users, > > I was not able to login to access the Myelin_Mapping_Documentation_v2.doc > poseted on The http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps. > I had tried my email address and my name for the usr and the assigned pwd, > but none was successful. > > Thank you, > > Ping > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] not able to down Myelin_Mapping_Documentation_v2.doc
got it. Thanks. On Wed, Jan 29, 2014 at 6:43 PM, Yeh, Ping-Hong wrote: > Hi Tim, > > Sorry for this simple question. The problem is I don't recall I've setup > the usr name, I've only enter the email and my name. I've tried both, but > in vain. So how to retrieve the login name? > > Thanks. > ping > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
