[Freesurfer] question about longitudinal data processing
Dear FreeSurfers, I have one question, related to longitudinal data processing. According to the wiki page about Longitudinal Processing, as the first step, all time points should be processed with the default workflow. All of my data, including all time points, were already processed using FreeSurfer v. 4.0.2 and I would like to process the longitudinal data using v.5.0 or later. In this case, can I use the FS results from v. 4.0.2 as the input to the second step of longitudinal processing? OR, should I re-process my data with a new version from the first step? Thank you very much for your help and answers in advance. -- Sungeun Kim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error with libtix8.1.8.4.so
Hello, Thank you for all help in advance. Recently, I installed the FreeSurfer ver.4.5.0 (centos4_x86_64-stable-pub-v4.5.0) on my mint 8 linux (x86_64). When I tried to run a command (recon-all) on my terminal, I didn't see any problem and all help messages were returned. But I tried to run tkmedit and tksurfer, I got an error message: "tkmedit.bin: error while loading shared libraries: libtix8.1.8.4.so: cannot open shared object file: No such file or directory" To check the dependency of tkmedit, I ran "which tkmedit' and "ldd `which tkmedit`" on a terminal. Two commands returned ..>which tkmedit /usr/local/freesurfer/bin/tkmedit ..> ldd `which tkmedit` not a dynamic executable Here is my LD_LIBRARY_PATH: ..>echo $LD_LIBRARY_PATH /lib:/usr/lib:/lib32:/usr/lib32:/usr/local/lib64:/usr/local/lib I am using freesurfer often for my research. So, any help or suggestion to resolve this issue would be really helpful to me. -- Sungeun Kim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] automatic subdivision of segmented subcortical structures
Thank you Bruce. I haven't thought about it specifically. But, if I can uniformly subdivide them, it would be very helpful to me. Best wishes, Sungeun On Fri, Mar 27, 2009 at 4:55 PM, Bruce Fischl wrote: > Hi Sungeun, > > Koen Van Leemput (ccd) have some prototypes for doing this in hippocampus, > but we haven't written anything for elsewhere. What specifically were you > thinking about? Just a uniform subdivision? Along the major eigendirection > for example? > > cheers, > Bruce > > > > On Fri, 27 Mar 2009, Sungeun Kim wrote: > > Hello, >> >> I am looking for any automated method to sub-divide segmented subcortical >> structures by FreeSurfer. Is there anyone who knows how to do this? >> >> Thanks in advance. >> >> >> -- Sungeun Kim, Ph.D. Postdoctoral Fellow Indiana University Center for NeuroImaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] automatic subdivision of segmented subcortical structures
Hello, I am looking for any automated method to sub-divide segmented subcortical structures by FreeSurfer. Is there anyone who knows how to do this? Thanks in advance. -- Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister segmentation fault
Yes, I have been using tkregister and I am not familiar with tkregister2. Doug Greve wrote: tkregister2 is the latest. Have you been using tkregister? Sungeun Kim wrote: Thank you for the quick answer. I am trying to know how to use tkregister2, but I would like to know why the latest tkregister suddenly doesn't work. Sungeun. Doug Greve wrote: Did you mean to use tkregister2? tkregister has not been used in years (we should actually remove it from the dist). doug Sungeun Kim wrote: Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan => subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: .bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister segmentation fault
Thank you for the quick answer. I am trying to know how to use tkregister2, but I would like to know why the latest tkregister suddenly doesn't work. Sungeun. Doug Greve wrote: Did you mean to use tkregister2? tkregister has not been used in years (we should actually remove it from the dist). doug Sungeun Kim wrote: Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan => subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: .bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister segmentation fault
Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan => subject's T1/COR's register: reg image transform matrix: -0.45 0.00 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.00 0.00 0.00 1.00 register: done reading target COR images register: input file type: bshort (x,y,t: .bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
