[Freesurfer] new to Freesurfer
Hello there, I am a Graduate research assistant at a Neuroimage analysis lab.I am starting to use Freesurfer for image analysis at our labs.Could you please let me know about any prerequisites which I would need before starting to use this tool.(I presume Tcl would be gud to know).Your advice will help me a long way in my work Thanks in advance Take care Chacko Cherian. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] using Analyze
Hello all, Can freesurfer use data in Analyze format or does everything have to be converted to .mgz?? Thanks in advance. Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer installation problems
Hello all, I am having some trouble in using the freesurfer version I had downloaded.The FREESURFER_HOME file is missing and so I cannot source or setenv anytime I want to use it.Do I need to tar and unzip again or is there any other way? Thanks in advance Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] analyze format
Hello, I am having some trouble in running "Analyze" format images on freesurfer.Could someone please guide me on how to run images on this format.. THanx Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] converting .img to .mgz
Hi everybody, I ve got a small question on converting .img scans(Analyze) TO .mgz... suppose i have a raw.img(and raw.hdr) file and I want to use recon-all for converting this to .mgz do I just need to do recon-all -i raw.img -s Or is there any other way I can directly use .img files instead of converting to the native .mgz format...? Thanks a lot,in advance Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] converting .img to .mgz
That doesn't seem to work...the error it gives is > > "Unsupported datatype 132" --- Doug Greve <[EMAIL PROTECTED]> wrote: > > You can't use .img files directly in the recon. The > cmd line you have > will work, or you can > > mkdir -p subject_name/orig > mri_convert raw.img subject_name/orig/001.mgz > > Note: make sure that you look at 001.mgz in tkmedit > to make sure that it > is oriented correct, esp if the .img does not have a > .mat > > doug > > > > > Chacko Cherian wrote: > > >Hi everybody, > > > >I ve got a small question on converting .img > >scans(Analyze) TO .mgz... > > > >suppose i have a raw.img(and raw.hdr) file and I > want > >to > >use recon-all for converting this to .mgz do I just > >need to do > >recon-all -i raw.img -s > >Or is there any other way I can directly use .img > >files instead of converting to the native .mgz > >format...? > > > >Thanks a lot,in advance > > > > > >Chacko. > > > > > >__ > >Do You Yahoo!? > >Tired of spam? Yahoo! Mail has the best spam > protection around > >http://mail.yahoo.com > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the > steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tksurfer:troubleshooting surface problems
Hello everyone, I have used an Analyze format data(.img) on Freesurfer and was running the Morphometry and REconstruction tutorial on the wiki.THey were running fine till i reached the automatic topology defect correction step. I used :recon-all -fix -s and it started fxing all the defects.There were 66 defects which took me 5 hours on my machine.After this I'm not able to view the output files at ../surf/ clearly.I can only see a small piece of the surface. Could you also please tell me how to create the final surfaces because the make_final_surfaces command is also not running through. Thanks in advance, Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tesselating
Hello all, I ran an Analyze format image in Fresurfer...just the Morphometry and reconstruction tutorial..but found that it's creating a filled.mgz volume but I'm having a problem in tesselating and creating the outputs lh.orig and rh.orig for the left and right hemispheres.It displays a very tiny piece of the volume. Could you please let me know how to troubleshoot this problem.. THanks in advance. Chacko. Chacko Cherian M.S EE Graduate Assistant Department of Psychology Arizona State University. Tempe,AZ. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tesselating
yes the filled.mgz is fine...with the hemispheres distinctly labelled and no cerebellum. --- Bruce Fischl <[EMAIL PROTECTED]> wrote: > and does the filled.mgz look correct? Are the > hemisphere separately > labeled and the cerebellum gone? Also, please post > these to the list so > other people can answer! > > Bruce > > > On Thu, 22 Jun 2006, Chacko Cherian wrote: > > > Yes when I load the image in tkmedit I odnt have > any > > problems.Its perfectly clear and > coronal,horizonatal > > and sagittal are all correct. > > > > --- Bruce Fischl <[EMAIL PROTECTED]> > wrote: > > > >> when you load it in tkmedit does it display > >> properly? That is, is the > >> coronal view really coronal? > >> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> > >>> Hello all, > >>> I ran an Analyze format image in > Fresurfer...just > >> the > >>> Morphometry and reconstruction tutorial..but > found > >>> that it's creating a filled.mgz volume but I'm > >> having > >>> a problem in tesselating and creating the > outputs > >>> lh.orig and rh.orig for the left and right > >>> hemispheres.It displays a very tiny piece of the > >>> volume. > >>> Could you please let me know how to troubleshoot > >> this > >>> problem.. > >>> THanks in advance. > >>> > >>> Chacko. > >>> > >>> > >>> > >>> Chacko Cherian > >>> M.S EE > >>> Graduate Assistant > >>> Department of Psychology > >>> Arizona State University. > >>> Tempe,AZ. > >>> > >>> > >>> > __ > >>> Do You Yahoo!? > >>> Tired of spam? Yahoo! Mail has the best spam > >> protection around > >>> http://mail.yahoo.com > >>> ___ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> > >> > > > > > > __ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > > > > > > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tesselating
No, the nofix surfaces are also displaying just a small piece of the surface..similar to the ?h.orig surfaces. --- Bruce Fischl <[EMAIL PROTECTED]> wrote: > hmmm, looks okay. Can you see the ?h.orig.nofix > surfaces okay? > On Thu, 22 > Jun 2006, Chacko Cherian wrote: > > > --- Bruce Fischl <[EMAIL PROTECTED]> > wrote: > > > >> can you send us the recon-all.log file? > >> On Thu, 22 Jun 2006, Chacko Cherian > >> wrote: > >> > >>> yes the filled.mgz is fine...with the > hemispheres > >>> distinctly labelled and no cerebellum. > >>> > >>> --- Bruce Fischl <[EMAIL PROTECTED]> > >> wrote: > >>> > >>>> and does the filled.mgz look correct? Are the > >>>> hemisphere separately > >>>> labeled and the cerebellum gone? Also, please > >> post > >>>> these to the list so > >>>> other people can answer! > >>>> > >>>> Bruce > >>>> > >>>> > >>>> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >>>> > >>>>> Yes when I load the image in tkmedit I odnt > have > >>>> any > >>>>> problems.Its perfectly clear and > >>>> coronal,horizonatal > >>>>> and sagittal are all correct. > >>>>> > >>>>> --- Bruce Fischl <[EMAIL PROTECTED]> > >>>> wrote: > >>>>> > >>>>>> when you load it in tkmedit does it display > >>>>>> properly? That is, is the > >>>>>> coronal view really coronal? > >>>>>> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >>>>>> > >>>>>>> Hello all, > >>>>>>> I ran an Analyze format image in > >>>> Fresurfer...just > >>>>>> the > >>>>>>> Morphometry and reconstruction tutorial..but > >>>> found > >>>>>>> that it's creating a filled.mgz volume but > I'm > >>>>>> having > >>>>>>> a problem in tesselating and creating the > >>>> outputs > >>>>>>> lh.orig and rh.orig for the left and right > >>>>>>> hemispheres.It displays a very tiny piece of > >> the > >>>>>>> volume. > >>>>>>> Could you please let me know how to > >> troubleshoot > >>>>>> this > >>>>>>> problem.. > >>>>>>> THanks in advance. > >>>>>>> > >>>>>>> Chacko. > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> Chacko Cherian > >>>>>>> M.S EE > >>>>>>> Graduate Assistant > >>>>>>> Department of Psychology > >>>>>>> Arizona State University. > >>>>>>> Tempe,AZ. > >>>>>>> > >>>>>>> > >>>>>>> > >>>> > >> > __ > >>>>>>> Do You Yahoo!? > >>>>>>> Tired of spam? Yahoo! Mail has the best > spam > >>>>>> protection around > >>>>>>> http://mail.yahoo.com > >>>>>>> > >> ___ > >>>>>>> Freesurfer mailing list > >>>>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>>>> > >>>>>> > >>>>> > >>>> > >>> > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >> > __ > >>>>> Do You Yahoo!? > >>>>> Tired of spam? Yahoo! Mail has the best spam > >>>> protection around > >>>>> http://mail.yahoo.com > >>>>> > >>>>> > >>>>> > >>>> > >>> > >>> > >>> > __ > >>> Do You Yahoo!? > >>> Tired of spam? Yahoo! Mail has the best spam > >> protection around > >>> http://mail.yahoo.com > >>> > >>> > >>> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > __ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tesselating
Nick, Im just running one sample of an Analyze format image..freesurfer is installed on a Linux OS Centos4 platform..but its a 32-bit machine. the sample bert is displayed correctly... im using tksurfer to display lh.orig and rh.orig.. Nick,could this be the problem..im using a 32-bit machine but i ve downloaded the freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz version.. Regards Chacko. --- Nick Schmansky <[EMAIL PROTECTED]> wrote: > Chacko, > > What freesurfer distribution is being used and what > platform is it > installed upon? > > In tksurfer, does the sample subject named 'bert' > display correctly? > > I guess I don't know what you mean by not > tesselating correctly and not > displaying the volume correctly. What tool is being > used to display > lh.orig or rh.orig? tksurfer? or are you refering > to the surface > outlines as shown in tkmedit? > > Nick > > > > > No, the nofix surfaces are also displaying just a > > small piece of the surface..similar to the ?h.orig > > surfaces. > > > > --- Bruce Fischl <[EMAIL PROTECTED]> > wrote: > > > >> hmmm, looks okay. Can you see the ?h.orig.nofix > >> surfaces okay? > >> On Thu, 22 > >> Jun 2006, Chacko Cherian wrote: > >> > >> > --- Bruce Fischl <[EMAIL PROTECTED]> > >> wrote: > >> > > >> >> can you send us the recon-all.log file? > >> >> On Thu, 22 Jun 2006, Chacko Cherian > >> >> wrote: > >> >> > >> >>> yes the filled.mgz is fine...with the > >> hemispheres > >> >>> distinctly labelled and no cerebellum. > >> >>> > >> >>> --- Bruce Fischl <[EMAIL PROTECTED]> > >> >> wrote: > >> >>> > >> >>>> and does the filled.mgz look correct? Are > the > >> >>>> hemisphere separately > >> >>>> labeled and the cerebellum gone? Also, > please > >> >> post > >> >>>> these to the list so > >> >>>> other people can answer! > >> >>>> > >> >>>> Bruce > >> >>>> > >> >>>> > >> >>>> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> >>>> > >> >>>>> Yes when I load the image in tkmedit I odnt > >> have > >> >>>> any > >> >>>>> problems.Its perfectly clear and > >> >>>> coronal,horizonatal > >> >>>>> and sagittal are all correct. > >> >>>>> > >> >>>>> --- Bruce Fischl > <[EMAIL PROTECTED]> > >> >>>> wrote: > >> >>>>> > >> >>>>>> when you load it in tkmedit does it > display > >> >>>>>> properly? That is, is the > >> >>>>>> coronal view really coronal? > >> >>>>>> On Thu, 22 Jun 2006, Chacko Cherian wrote: > >> >>>>>> > >> >>>>>>> Hello all, > >> >>>>>>> I ran an Analyze format image in > >> >>>> Fresurfer...just > >> >>>>>> the > >> >>>>>>> Morphometry and reconstruction > tutorial..but > >> >>>> found > >> >>>>>>> that it's creating a filled.mgz volume > but > >> I'm > >> >>>>>> having > >> >>>>>>> a problem in tesselating and creating the > >> >>>> outputs > >> >>>>>>> lh.orig and rh.orig for the left and > right > >> >>>>>>> hemispheres.It displays a very tiny piece > of > >> >> the > >> >>>>>>> volume. > >> >>>>>>> Could you please let me know how to > >> >> troubleshoot > >> >>>>>> this > >> >>>>>>> problem.. > >> >>>>>>> THanks in advance. > >> >>>>>>> > >> >>>>>>> Chacko. > >> >>>>>>> > >> >>>>>>> > >> >>>>>>> > >> >>>>>>> Chacko Cherian > >> >>>>>>> M.S EE > >> >>>>>>> Graduate Assistant > >&
Re: [Freesurfer] tesselating
Nick, After running uname -m it says i686.Bit if it's a 64-bit build of freesurfer how come it ran all the other steps on my 32-bit machine? Chacko. --- Nick Schmansky <[EMAIL PROTECTED]> wrote: > Chacko, > > The 64bit build of freesurfer will not run on a > 32bit machine. Do you > have an older version of freesurfer that might be > running? What is the > output of: > > cat $FREESURFER_HOME/build-stamp.txt > > Are you sure your machine is really 32bits? Run > 'uname -m' and if the > machine is 64bits, it will say x86_64. > > Nick > > > Nick, > > Im just running one sample of an Analyze format > > image..freesurfer is installed on a Linux OS > Centos4 > > platform..but its a 32-bit machine. > > the sample bert is displayed correctly... > > im using tksurfer to display lh.orig and rh.orig.. > > Nick,could this be the problem..im using a 32-bit > > machine but i ve downloaded the > > > freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz > > version.. > > > > Regards > > > > Chacko. > > --- Nick Schmansky <[EMAIL PROTECTED]> > wrote: > > > >> Chacko, > >> > >> What freesurfer distribution is being used and > what > >> platform is it > >> installed upon? > >> > >> In tksurfer, does the sample subject named 'bert' > >> display correctly? > >> > >> I guess I don't know what you mean by not > >> tesselating correctly and not > >> displaying the volume correctly. What tool is > being > >> used to display > >> lh.orig or rh.orig? tksurfer? or are you > refering > >> to the surface > >> outlines as shown in tkmedit? > >> > >> Nick > >> > >> > > >> > No, the nofix surfaces are also displaying just > a > >> > small piece of the surface..similar to the > ?h.orig > >> > surfaces. > >> > > >> > --- Bruce Fischl <[EMAIL PROTECTED]> > >> wrote: > >> > > >> >> hmmm, looks okay. Can you see the > ?h.orig.nofix > >> >> surfaces okay? > >> >> On Thu, 22 > >> >> Jun 2006, Chacko Cherian wrote: > >> >> > >> >> > --- Bruce Fischl > <[EMAIL PROTECTED]> > >> >> wrote: > >> >> > > >> >> >> can you send us the recon-all.log file? > >> >> >> On Thu, 22 Jun 2006, Chacko Cherian > >> >> >> wrote: > >> >> >> > >> >> >>> yes the filled.mgz is fine...with the > >> >> hemispheres > >> >> >>> distinctly labelled and no cerebellum. > >> >> >>> > >> >> >>> --- Bruce Fischl > <[EMAIL PROTECTED]> > >> >> >> wrote: > >> >> >>> > >> >> >>>> and does the filled.mgz look correct? Are > >> the > >> >> >>>> hemisphere separately > >> >> >>>> labeled and the cerebellum gone? Also, > >> please > >> >> >> post > >> >> >>>> these to the list so > >> >> >>>> other people can answer! > >> >> >>>> > >> >> >>>> Bruce > >> >> >>>> > >> >> >>>> > >> >> >>>> On Thu, 22 Jun 2006, Chacko Cherian > wrote: > >> >> >>>> > >> >> >>>>> Yes when I load the image in tkmedit I > odnt > >> >> have > >> >> >>>> any > >> >> >>>>> problems.Its perfectly clear and > >> >> >>>> coronal,horizonatal > >> >> >>>>> and sagittal are all correct. > >> >> >>>>> > >> >> >>>>> --- Bruce Fischl > >> <[EMAIL PROTECTED]> > >> >> >>>> wrote: > >> >> >>>>> > >> >> >>>>>> when you load it in tkmedit does it > >> display > >> >> >>>>>> properly? That is, is the > >> >> >>>>>> coronal view really coronal? > >> >> >>>>>> On Thu, 22 Jun 2006, Chacko Cherian > wrote: > >> >> >>
[Freesurfer] Spherical morphometry
Hello everyone, In spherical morphometry,to create the spherical surfaces,Im using the step 8.1 in the Wiki tutorial. Could someone please explain what the colors stand for? DOING "tksurfer subj001 rh sphere" gives me a sphere on the display.But I'm not able to map it and provide the overlay info rh.curv. the command "tksurfer -subjid subj001 -morph" gives me the error "Flag unrecognized".. THanks in advance. Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Spherical morphometry
THanks Bruce. I ve been having some problems with display..in the sense that when I minimize the diplay window and open it back there's nothing in it.Just wnated to confirm whether this is any sort of graphics driver problem. THanx Chacko. --- Bruce Fischl <[EMAIL PROTECTED]> wrote: > Hi Chacko, > > after tksurfer is loaded, from the gui do > file->curvature->load > curvature->rh.curv (or rh.sulc) > > cheers, > Bruce > On Thu, 29 Jun 2006, Chacko Cherian wrote: > > > Hello everyone, > > > > In spherical morphometry,to create the spherical > > surfaces,Im using the step 8.1 in the Wiki > tutorial. > > Could someone please explain what the colors stand > > for? > > DOING "tksurfer subj001 rh sphere" gives me a > sphere > > on the display.But I'm not able to map it and > provide > > the overlay info rh.curv. > > the command "tksurfer -subjid subj001 -morph" > gives me > > the error "Flag unrecognized".. > > > > THanks in advance. > > > > Chacko. > > > > __ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Spherical morphometry
The other question that I have is about templates.I suppose Freesurfer uses MNI templates.How do I add my templates on to Freesurfer if I want to use say monkey or mice data? THAnks Chacko. --- Bruce Fischl <[EMAIL PROTECTED]> wrote: > Hi Chacko, > > after tksurfer is loaded, from the gui do > file->curvature->load > curvature->rh.curv (or rh.sulc) > > cheers, > Bruce > On Thu, 29 Jun 2006, Chacko Cherian wrote: > > > Hello everyone, > > > > In spherical morphometry,to create the spherical > > surfaces,Im using the step 8.1 in the Wiki > tutorial. > > Could someone please explain what the colors stand > > for? > > DOING "tksurfer subj001 rh sphere" gives me a > sphere > > on the display.But I'm not able to map it and > provide > > the overlay info rh.curv. > > the command "tksurfer -subjid subj001 -morph" > gives me > > the error "Flag unrecognized".. > > > > THanks in advance. > > > > Chacko. > > > > __ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection around > > http://mail.yahoo.com > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] printing out from tksurfer and tkmedit
Hello everyone, How can I can I print out the display images from tksurfer and tkmedit other than manually saving them into tiff and then printing them.IS there any way to print them directly? THAnx Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] printing out from tksurfer and tkmedit
Thanks Don.That would be really useful. Chacko. --- Don Hagler <[EMAIL PROTECTED]> wrote: > If there is interest, I could post my shell script > for generating a tcl > script and running tksurfer (with an option to write > to rgb). I have > another one that will render all w files in a > particular directory (as > rgb's) and another that will render all frames from > an mgh (painted surface) > file (as tif's). > > With the older version of tksurfer, you can render > offscreen, which is > convenient for batches of files (because otherwise > your monitor is unusable > for a long time). > > > >From: Bruce Fischl <[EMAIL PROTECTED]> > >To: Kevin Teich <[EMAIL PROTECTED]> > >CC: Chacko Cherian <[EMAIL PROTECTED]>, > >freesurfer@nmr.mgh.harvard.edu > >Subject: Re: [Freesurfer] printing out from > tksurfer and tkmedit > >Date: Fri, 30 Jun 2006 11:39:03 -0400 (EDT) > > > >but you could write a tcl script to do it > automatically > >On Fri, 30 Jun 2006, Kevin Teich wrote: > > > >>>How can I can I print out the display images from > tksurfer and > >>>tkmedit other than manually saving them into tiff > and then printing > >>>them.IS there any way to print them directly? > >> > >>No, sorry, saving TIFFs is the only output that > tkmedit and tksurfer > >>do of that kind. > >> > >> > >___ > >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 > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] printing out from tksurfer and tkmedit
when i want to print-out the outputs using "Save TIFF as" it isn't giving me any results.Is there something else that I need to do to save the outputs as TIFF files?? --- Bruce Fischl <[EMAIL PROTECTED]> wrote: > but you could write a tcl script to do it > automatically > On Fri, 30 Jun 2006, > Kevin Teich wrote: > > >> How can I can I print out the display images from > tksurfer and > >> tkmedit other than manually saving them into tiff > and then printing > >> them.IS there any way to print them directly? > > > > No, sorry, saving TIFFs is the only output that > tkmedit and tksurfer > > do of that kind. > > > > > __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness table.
Hello all, The cortical thickness table which is located in the stats folder..i am currently opening it with my vi editor.Is there any way to open it directly as a spreadsheet to print it out?? THanks Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] autorecon1
Hello everyone, I was running recon-all -autorecon1 -s bert and it exited with errors.. Processing... Not implemented yet in cache _volume _range _has _ changed()... IS there anything wrong in the way i've run the command?? THanks in advance for your help. Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] autorecon1
Hello everyone, looks like the error is at the skull stripping step...here's how it exited... [EMAIL PROTECTED] Skull Stripping Fri Jul 14 16:40:38 MST 2006 /ud/chacko/freesurfer/subjects/bert/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Fri Jul 14 16:40:38 MST 2006 --- Chacko Cherian <[EMAIL PROTECTED]> wrote: > here's the recon-all.log file... > > --- Nick Schmansky <[EMAIL PROTECTED]> > wrote: > > > Can you send the recon-all.log file? The 'Not > > implemented...' message is > > a normal warning message (part of the MNI tools) > and > > is generally not the > > source of an exit error. > > > > > > > Hello everyone, > > > I was running recon-all -autorecon1 -s bert and > it > > > exited with errors.. > > > Processing... > > > Not implemented yet in cache _volume _range _has > _ > > > changed()... > > > IS there anything wrong in the way i've run the > > > command?? > > > > > > THanks in advance for your help. > > > > > > Chacko. > > > > > > > __ > > > Do You Yahoo!? > > > Tired of spam? Yahoo! Mail has the best spam > > protection around > > > http://mail.yahoo.com > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > __ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam > protection around > http://mail.yahoo.com > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] general question concerning orientation
Hello everyone, orientation i guess is quite an issue. Well how does,Freesurfer determine orientation of the image.Do I have to know how the image has been processed before it reaches me or is there any other way to find out?Does it have to do with the 'flip'? I checked the orientation of an image on SPM and on Freesurfer. Left on SPM is Right on Freesurfer and vice versa is what I got. Essentially how do I determine L-R orientation? Thanks in advance, Chacko Cherian. Arizona State University. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error message
Hello everyone, I got this message while running bert on my Linux machine.Is it because the NVIDIA graphics driver is not updated?? GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by display: :0.0 Thanks in advance Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Group-Specific template
Hello everyone, I would like to run a group-specific template on Freesurfer and compare my results with the default template(which is MNI,I assume)? Is this possible?Can I do cortical thickness measurement also in the same way? Thanks in advance, Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error running tkmedit
Hello everyone, I am using a Red Hat Enterprise Linux AS release 3(Taroon update 6) version.While running tkmedit for the bert data..this is what i get.. tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory. I tried the CentOS(without x86_64) version and the rh9 versions of freesurfer but both gave me the same error message. Could someone pls clarify. Thanks in advance Chacko. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all exited with ERRORS
Hello all, I was running recon-all for one of my images and this happened to be the error that i got.what is libstdc++?? Could someone please clarify, Thanks in advance Chacko. "mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006" __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all exited with errors
Hello all, I was running recon-all for one of my images and this happened to be the error that i got.Could someone please clarify, Thanks in advance Chacko. "mri_watershed: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Linux elmo 2.6.12.1 #2 Thu Jul 14 11:14:31 MST 2005 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Wed Jul 26 13:09:41 MST 2006" __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] GLIBCXX
Hello all, Could someone please clarify why this library cannot provide the correct 'GLIBCXX_3.4'. Thanks in advance. Chacko. mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz mri_watershed: /usr/lib/libstdc++.so.6: version `GLIBCXX_3.4' not found (required by mri_watershed) Linux ibmlnx4 2.4.21-32.0.1.ELsmp #1 SMP Tue May 17 17:52:23 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Jul 28 09:35:51 MST 2006 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dicom files
Hello all, I have 180 slices of a subject in DICOM format.I am trying to run the 'recon-all' procedure for this subject. Are these slices seen by Freesurfer as individual acquisitions or as a single dicom file? In case they are percieved as individual acquisitions,do I need to manually type all the file names(for each slice) for the recon-all procedure or is there a simpler way. THanks in advance Chacko Cherian. Arizona State University Graduate Research Assistant __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dicom format
I got this error while running a single subject in DICOM format.the 'recon-all -autorecon1 -subjid ' stopped at this stage. INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux ibmlnx2.samaritan.edu 2.4.20-24.9 #1 Mon Dec 1 11:35:51 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 2 14:16:22 MST 2006 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error at autorecon2
Hello all, Here's an error I got while doing 'recon-all -autorecon2 -s . Could someone please clarify. Thank you. Chacko Cherian. [EMAIL PROTECTED] EM Registration Wed Aug 2 16:35:22 MST 2006 /home/ttest/freesurfer/subjects/case1/case1/case1/mri mri_em_register -mask brainmask.mgz nu.mgz /home/ttest/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/home/ttest/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault (core dumped) Linux ibmlnx2.samaritan.edu 2.4.20-24.9 #1 Mon Dec 1 11:35:51 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 2 16:35:41 MST 2006 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] query regarding T2/T1
Hello all, Can we use tkmedit for T2-weighted images or is it restricted to T1 -weighted? Thanks Chacko. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Slackware 10.0.0
Hello all, I have a small query.Just wanted to know which stable Freesurfer version I should install for Linux Slackware 10.0.0 version. Has anybody experienced any issues usig this platform. Thanks in advance. Chacko Cherian. Arizona State University. __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error message at SkullLTA
Hello all, I got this error message while running one of my subjects. i checked the /mri directory but nu_noneck.mgz was not created instead nu.mgz was there. THanks in advance. Chacko Cherian. Arizona State University. reading labels out of gcam file... removing structures at least 25 mm from brain... 12620067 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 18 minutes and 46 seconds. #-- [EMAIL PROTECTED] SkullLTA Wed Aug 9 08:35:57 MST 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck. mgz /ud/chacko/freesurfer/average/RB_all_withskull_2006-02-15. gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacin g = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/ud/chacko/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization= 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 9 08:36:35 MST 2006 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] subject failed autorecon1
Hi all, One of my subjects failed autorecon1 giving me this error: mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.646 0.464 -0.179 -16.319; -0.497 0.598 -0.245 -56.371; -0.008 0.303 0.757 179.232; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux zoe 2.6.15-25-386 #1 PREEMPT Wed Jun 14 11:25:49 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Tue Aug 15 16:21:26 MST 2006 Thanks in advance Chacko Cherian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error message regarding mri_ca_register_
Hello all, I got this error message while running one of my subjects: ERROR: mri_ca_register with non-zero status Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 14 09:35:29 MST 2006 Does anyone knw wat this could possibly mean? THanks in advance. Chacko Cherian. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Ubuntu linx
Hello all, I am using an Ubuntu linux machine to run a few subjects.I ve been having trouble using tksurfer on it but tkmedit seems to be working pretty fine.Could someone please let me know why this problem has occured?Is it something to do with the souce code and the graphics libraries? Thanks in advance Chacko Cherian. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mritotal.log
Hello all, I wanted to know where the mritotal.log file is created.I checked the /scripts directory but couldnt find it there. I'd like to have a look at the Final objective function value for the subjects I'm running. Thanks in advance Chacko Cherian. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] parameters for N3 correction
Hello users, Is there any information available regarding the parameters used for N3 correction in the autorecon process? Thanks, Chacko. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] is this ok?
Thanks Bruce. I Am using version 3.0.3,..wat can i do to to get better pial surface images? IS it something to do with the skull stripping stage or is it the motion artifacts which cause a reduction in the overall resoution of the image? Chacko. - Original Message From: Bruce Fischl <[EMAIL PROTECTED]> To: Chacko Cherian <[EMAIL PROTECTED]> Cc: Freesurfer Sent: Monday, November 6, 2006 4:25:05 PM Subject: Re: [Freesurfer] is this ok? Hi Chako, I wouldn't worry too much about the inflated - it looks okay. Probably a result of the large motion artifact in your data. The pial surface is more worrisome - what version are you running? They are usually *much* better than this. Bruce On Mon, 6 Nov 2006, Chacko Cherian wrote: > Hello freesurer users, > > Is it ok to have such edges on the inflated surface?Is there something I can > do to rectify this? > THe second image is the brainmask and wm volume as seen using tkmedit. > > (tkmedit subj1 brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white) > > THanks in advance > > Best, > > Chacko Cherian > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] command for aseg stats to export to spreadsheet(excel)
Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko. Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] command for aseg stats to export to spreadsheet(excel)
Thank you Jenni. How do i use asegstats2table?What is the command?Is it a tcl script file?If so,could you also mention where it is located. Regards Chacko. - Original Message From: Jenni Pacheco <[EMAIL PROTECTED]> To: Chacko Cherian <[EMAIL PROTECTED]>; Freesurfer Sent: Wednesday, November 22, 2006 3:04:28 PM Subject: RE: [Freesurfer] command for aseg stats to export to spreadsheet(excel) You can use asegstats2table. Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chacko Cherian Sent: Wednesday, November 22, 2006 5:02 PM To: Freesurfer Subject: [Freesurfer] command for aseg stats to export to spreadsheet(excel) Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko. Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] regarding .plt files
Hello users, I am using the latest stable version of FreeSurfer and there are two files wm.plt and gm.plt which are created after the recon-all process.What do these signify and how do I open them? Thanks in advance Chacko. Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] version 3.0.2
Hello all, I'd like to know whether the good_output and bert, analysis were done on version 3.0.2? If so could anyone please pass me a link to that version? Thanks Chacko. Have a burning question? Go to www.Answers.yahoo.com and get answers from real people who know. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Longitudinal analysis
Hello users, Is there a typo on the longitudinal analysis page on the wiki.. does the command go like this?? recon-all-long -long -subjid tp1 -subjid tp2 Thanks Chacko. Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Longitudinal analysis
Sorry Nick,I dont seem to get it..it says recon-all-long:Command not found --- Nick Schmansky <[EMAIL PROTECTED]> wrote: > Chacko, > > Which wiki page are you referring to? > > Recon-all-long is used like this: > > recon-all-long -long -tp1 tp1 -subjid tp2 ... > > where ... refers to what flags you want to use (like > -all). > > Nick > > > On Mon, 2007-01-22 at 10:35 -0800, Chacko Cherian > wrote: > > Hello users, > > > > Is there a typo on the longitudinal analysis page > on > > the wiki.. > > > > does the command go like this?? > > recon-all-long -long -subjid tp1 -subjid tp2 > > > > > > Thanks > > > > Chacko. > > > > > > > > > > > > > > > > > > > > > > > Expecting? Get great news right away with email > Auto-Check. > > Try the Yahoo! Mail Beta. > > > http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] thickness reproducibility-longitudinal?
Hello all, http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility Is this page on thickness reproducibility intended for longitudinal analysis or is it just a general group analysis procedure? THanks in advance, Chacko. Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] group-analysis error
Hello all, Here's an error that i got while running group analysis on a couple of subjects...i checked the rh.orig file and the rh.sphere.reg and i could open both using tksurfer. Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig): surface doesn't match /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file orig No such file or directory mris_make_average_surface: could not read orig file for rh. No such file or directory Thanks in advance Chacko. Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] group-analysis error
Hello all, I also noticed that the program searches for the talairach transform in the wrong directory??could someone tell me why.. THanks Chacko. [EMAIL PROTECTED] processing subject 8/25 subj13... Reading /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/surf/rh.sphere.reg Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm Read /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/T1.mgz Surface area: 802.9 cm^2 Applying linear transform Talairach transform /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/AD/subj13/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj13/mri/transforms/talairach.xfm --- Chacko Cherian <[EMAIL PROTECTED]> wrote: > Hello all, > > Here's an error that i got while running group > analysis on a couple of subjects...i checked the > rh.orig file and the rh.sphere.reg and i could open > both using tksurfer. > > > > Reading > /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg > mrisReadTriangleFile(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.orig): > surface doesn't match > /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/AD_norm_group_analysis/subj1/surf/rh.sphere.reg > > No such file or directory > mrisReadTriangleFile failed. > > No such file or directory > MRISreadOriginalProperties: could not read surface > file orig > No such file or directory > mris_make_average_surface: could not read orig file > for rh. > > No such file or directory > > > > > > Thanks in advance > > > Chacko. > > > > > Finding fabulous fares is fun. > Let Yahoo! FareChase search your favorite travel > sites to find flight and hotel bargains. > http://farechase.yahoo.com/promo-generic-14795097 > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all -long errors
Hello users, I was running longitudinal analysis for a couple of scans and recon-all exited with this error. CTABread(/usr/local/freesurfer/ASegStatsLUT.txt): could not open file No such file or directory atlas_icv = 1.74537e+06 Loading mri/aseg.mgz Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1836053 # brainmaskvolume 1836053.0 # nbrainsegvoxels 1347237 # brainsegvolume 1347237.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids ERROR: reading /usr/local/freesurfer/ASegStatsLUT.txt Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Thu Jan 25 11:38:22 MST 2007 there were also a couple of lines like these where it couldn't find gc for labels. GCAmaxLikelihoodBorderLabel(138, 152, 124): couldn't find gc for label 28 GCAmaxLikelihoodBorderLabel(203, 103, 130): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(154, 177, 130): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(154, 178, 130): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(203, 103, 131): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(207, 126, 136): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(207, 126, 137): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(207, 127, 137): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(150, 145, 150): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(150, 146, 150): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(150, 146, 151): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(159, 157, 163): couldn't find gc for label 3 GCAmaxLikelihoodBorderLabel(135, 159, 163): couldn't find gc for label 42 GCAmaxLikelihoodBorderLabel(136, 159, 163): couldn't find gc for label 42 Thsnks in advance Chacko. Expecting? Get great news right away with email Auto-Check. Try the Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/newmail_tools.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] surf2surf
Hello users, I wanted to use mri_surf2surf for surface smoothing but it gives me an error saying --s is not an option. mri_surf2surf --hemi lh \ --s average \ --sval lh.gender_age.thickness.mgh \ --fwhm 10 \ --tval lh.gender_age.thickness.10.mgh it didnt work with srcsubject either.The average subject is in the $SUBJECTS_DIR. THAnks in advance Chacko. Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] surf2surf
Doug, mri_surf2surf --hemi lh \ --srcsubject fsaverage \ --srcsurfval lh.ADnorm.thickness.mgh \ --fwhm 10 \ --trgsurfval lh.ADnorm.thickness.10.mgh ERROR: Option --srcsubject unknown this is the error that i'm getting. --- Doug Greve <[EMAIL PROTECTED]> wrote: > You might be using a slightly order version that > does not support the > --s option. If so, then you'll need to spec the src > and trg subjects > explicitly. > > Chacko Cherian wrote: > > >Hello users, > > > >I wanted to use mri_surf2surf for surface smoothing > >but it gives me an error saying --s is not an > option. > > > >mri_surf2surf --hemi lh \ > > > >--s average \ > > --sval lh.gender_age.thickness.mgh \ > > --fwhm 10 \ > > --tval lh.gender_age.thickness.10.mgh > > > >it didnt work with srcsubject either.The average > >subject is in the $SUBJECTS_DIR. > > > >THAnks in advance > > > >Chacko. > > > > > > > > > > > > > > > > > >Don't get soaked. Take a quick peak at the > forecast > >with the Yahoo! Search weather shortcut. > >http://tools.search.yahoo.com/shortcuts/#loc_weather > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the > steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TIV in group analysis
Hello all, Is calculation of TIV taken into consideration while performing the group analysis? Thanks Chacko Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. http://games.yahoo.com/games/front ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] my_average and fsaverage
Hello users, I created an average subject(my_average) with 25 subjects.Now when I compare the fsaverage and my_average inflated views,the display shows fsaverage as way bigger than my_average.Is this normal?Is it something to do with how fsaverage is scaled and displayed? Area-wise my_average is greater than fsaverage. Thanks in advance, Chacko. Don't get soaked. Take a quick peak at the forecast with the Yahoo! Search weather shortcut. http://tools.search.yahoo.com/shortcuts/#loc_weather ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] transforms
Hello all, Is there some information on the wiki about the srctoDst voxel-to-voxel transform and the rastoRAas transform? THAnks Chacko. Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] input registration matrix
Hello All, After making changes using tkregister2 the input registration matrix changes.IS there an 'optimum' input registration matrix that i should try to get.I notice that the closer the values(last column of the input reg matrix) are to zero the better the outcome. Thanks in advance. Chacko. Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] input registration matrix
Hello all, To rectify the talairach transform, I am editing brainmask.mgz using tkregister2 and aligning the subject and talairach volume. THank you. Chacko. What are you trying to register? > > > > Chacko Cherian wrote: > > >Hello All, > > > >After making changes using tkregister2 the input > >registration matrix changes.IS there an 'optimum' > >input registration matrix that i should try to > get.I > >notice that the closer the values(last column of > the > >input reg matrix) are to zero the better the > outcome. > > > >Thanks in advance. > > > >Chacko. > > > > > > > > > > > >Now that's room service! Choose from over 150,000 > hotels > >in 45,000 destinations on Yahoo! Travel to find > your fit. > >http://farechase.yahoo.com/promo-generic-14795097 > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the > steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. http://autos.yahoo.com/new_cars.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkregister2:views mixed up.
Hello ALL, Has anybody had trouble with tkregister2..I loaded the transform and the coronal and horizontal views are mixed up.Coronal view of the subject is coupled with the horizontal view of the talairach volume. Thanks in advance Regards, Chacko. TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2:views mixed up.
No, It has the same problem in tkmedit too. --- Doug Greve <[EMAIL PROTECTED]> wrote: > Does it view correctly in tkmedit? > > Chacko Cherian wrote: > > >Hello ALL, > > > >Has anybody had trouble with tkregister2..I loaded > the > >transform and the coronal and horizontal views are > >mixed up.Coronal view of the subject is coupled > with > >the horizontal view of the talairach volume. > > > >Thanks in advance > >Regards, > > > >Chacko. > > > > > > > > > >TV dinner still cooling? > >Check out "Tonight's Picks" on Yahoo! TV. > >http://tv.yahoo.com/ > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the > steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. http://tools.search.yahoo.com/toolbar/features/mail/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2:views mixed up.
It has the problem in tkmedit,after I load the transform..i checked brainmask.img and T1.img after loading the transform and they had this problem..The header and geometry info look fine.. --- Doug Greve <[EMAIL PROTECTED]> wrote: > That means that the geometry info in the file is > messed up. Where did > the data come from? Are the dicoms messed up too? > > Chacko Cherian wrote: > > >No, It has the same problem in tkmedit too. > > > > > >--- Doug Greve <[EMAIL PROTECTED]> wrote: > > > > > > > >>Does it view correctly in tkmedit? > >> > >>Chacko Cherian wrote: > >> > >> > >> > >>>Hello ALL, > >>> > >>>Has anybody had trouble with tkregister2..I > loaded > >>> > >>> > >>the > >> > >> > >>>transform and the coronal and horizontal views > are > >>>mixed up.Coronal view of the subject is coupled > >>> > >>> > >>with > >> > >> > >>>the horizontal view of the talairach volume. > >>> > >>>Thanks in advance > >>>Regards, > >>> > >>>Chacko. > >>> > >>> > >>> > >>> > >>> > >> > >> > >> > >>>TV dinner still cooling? > >>>Check out "Tonight's Picks" on Yahoo! TV. > >>>http://tv.yahoo.com/ > >>>___ > >>>Freesurfer mailing list > >>>Freesurfer@nmr.mgh.harvard.edu > >>> > >>> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >>> > >>> > >>> > >>> > >>-- > >>Douglas N. Greve, Ph.D. > >>MGH-NMR Center > >>[EMAIL PROTECTED] > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>In order to help us help you, please follow the > >>steps in: > >>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >>___ > >>Freesurfer mailing list > >>Freesurfer@nmr.mgh.harvard.edu > >> > >> > >> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > >Never miss an email again! > >Yahoo! Toolbar alerts you the instant new Mail > arrives. > >http://tools.search.yahoo.com/toolbar/features/mail/ > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the > steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Never miss an email again! Yahoo! Toolbar alerts you the instant new Mail arrives. http://tools.search.yahoo.com/toolbar/features/mail/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2:views mixed up.
Yes,It is perfectly fine with the --regheader optionmwhich means no problem with geometry info. But how do I fix the talairach.xfm? Thanks a lot! Chacko. --- Doug Greve <[EMAIL PROTECTED]> wrote: > I mean to just load the orig.mgz into tkmedit and > see if it is oriented > correctly. Assuming that it is oriented correctly, > then it sounds like > the talairach transform is messed up pretty badly. > When you run > tkregister2, try adding --regheader. This will > ignore the info in the > talairaach.xfm file and force it to use the geometry > info. it will > likely be very far off, but the basic orientation > should be ok. > > Chacko Cherian wrote: > > >It has the problem in tkmedit,after I load the > >transform..i checked brainmask.img and T1.img after > >loading the transform and they had this > problem..The > >header and geometry info look fine.. > > > > > >--- Doug Greve <[EMAIL PROTECTED]> wrote: > > > > > > > >>That means that the geometry info in the file is > >>messed up. Where did > >>the data come from? Are the dicoms messed up too? > >> > >>Chacko Cherian wrote: > >> > >> > >> > >>>No, It has the same problem in tkmedit too. > >>> > >>> > >>>--- Doug Greve <[EMAIL PROTECTED]> wrote: > >>> > >>> > >>> > >>> > >>> > >>>>Does it view correctly in tkmedit? > >>>> > >>>>Chacko Cherian wrote: > >>>> > >>>> > >>>> > >>>> > >>>> > >>>>>Hello ALL, > >>>>> > >>>>>Has anybody had trouble with tkregister2..I > >>>>> > >>>>> > >>loaded > >> > >> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>the > >>>> > >>>> > >>>> > >>>> > >>>>>transform and the coronal and horizontal views > >>>>> > >>>>> > >>are > >> > >> > >>>>>mixed up.Coronal view of the subject is coupled > >>>>> > >>>>> > >>>>> > >>>>> > >>>>with > >>>> > >>>> > >>>> > >>>> > >>>>>the horizontal view of the talairach volume. > >>>>> > >>>>>Thanks in advance > >>>>>Regards, > >>>>> > >>>>>Chacko. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>> > >>> > >>> > >>>> > >>>> > >>>> > >>>> > >>>>>TV dinner still cooling? > >>>>>Check out "Tonight's Picks" on Yahoo! TV. > >>>>>http://tv.yahoo.com/ > >>>>>___ > >>>>>Freesurfer mailing list > >>>>>Freesurfer@nmr.mgh.harvard.edu > >>>>> > >>>>> > >>>>> > >>>>> > >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>>> > >>>> > >>>> > >>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>-- > >>>>Douglas N. Greve, Ph.D. > >>>>MGH-NMR Center > >>>>[EMAIL PROTECTED] > >>>>Phone Number: 617-724-2358 > >>>>Fax: 617-726-7422 > >>>> > >>>>In order to help us help you, please follow the > >>>>steps in: > >>>>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >>>> > >>>> > >>>>___ > >>>>Freesurfer mailing list > >>>>Freesurfer@nmr.mgh.harvard.edu > >>>> > >>>> > >>>> > >>>> > >>>> > >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >> > >> > >> > >>>Never miss an email again! > >>>Yahoo! Toolbar alerts you the instant new Mail > >>> > >>> > >>arrives. > >> > >>http://tools.search.yahoo.com/toolbar/features/mail/ > >> > >> > >>> > >>> > >>> > >>> > >>-- > >>Douglas N. Greve, Ph.D. > >>MGH-NMR Center > >>[EMAIL PROTECTED] > >>Phone Number: 617-724-2358 > >>Fax: 617-726-7422 > >> > >>In order to help us help you, please follow the > >>steps in: > >>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > >> > >> > >> > >>>___ > >>> > >>> > >>Freesurfer mailing list > >>Freesurfer@nmr.mgh.harvard.edu > >> > >> > >> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > >Never miss an email again! > === message truncated === Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] longitudinal analysis - error
Hello all, This is an error I got while running the longitudinal analysis on one of our subjects.It didnt create the filled.mgz volume and so the surfaces weren't created. [EMAIL PROTECTED] Fill Tue Feb 13 20:59:04 MST 2007 /ud/chacko/freesurfer/subjects/apoe/1279MRI4/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... fill: could not scan threshold from 'norm.mgz'Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Tue Feb 13 20:59:04 MST 2007 THanks in advance Chacko. It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] longitudinal analysis error
Hello all, I got an error while running longitudinal analysis using recon-all -long and the process exited with errors. THis is the error message: mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz -topofix norm.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... fill: could not scan threshold from 'norm.mgz'Linux snuffy 2.6.17-10-generic #2 SMP Tue Dec 5 22:28:26 UTC 2006 i686 GNU/Linux recon-all-long exited with ERRORS at Tue Feb 13 20:59:04 MST 2007 Could someone give me suggestions on what could have gone wrong..thanks in advance. Regards Chacko. We won't tell. Get more on shows you hate to love (and love to hate): Yahoo! TV's Guilty Pleasures list. http://tv.yahoo.com/collections/265 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QDEC
Hello developers, How can I get access to QDEC? Regards Chacko. Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] viewing group analysis results
Hello users, I am doing the group analysis stats results...using FDR correction 0.01 and checking the pial surface with curvature and overlay. I see this line come up whenever i change the FDR..is this some kind of error which I need to be concerned about? surfer: Error sending tcl command OverlayLayerChanged: bad window path name ".fsgdf-0" Thanks in advance. Regards Chacko. Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
