Hi Claire
there is no output in the terminal window when you type the tksurfer command? Does it just return to the prompt? Bruce On Thu, 16 Oct 2014, Claire Morley wrote:
Hi Bruce, Thanks so much for your response. It`s just when I try to type the "test commands" from this link: https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. The Freeview command does work, but the commands for tkmedit, tksurfer, and qdec do not work. Therefore, my tksurfer command was simply: tksurfer bert rh pial. When I try this, the computer spits out nothing, no error, no window pops up, nada. I have made sure that the bert rh pial file does exist in the surfs and it does (I run this while in my freesurfer/subjects directory. The only thing I can think of is perhaps I installed something wrong, but I followed all of the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall. I wonder however, if in my SetUpFreeSurfer.sh file the script includes the tk tools. Since it`s a third party package, are they automatically installed? As I said before, I did this on another Mac at my other lab where Freesurfer had been previously installed and the command for tksurfer worked perfectly. So I dont think its my command but something with the configuration that`s going wrong. Could also be affecting qdec`s inability to run?
Also I see here: https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferGeneralUsag e/TkSurferQuickStart that there are two other ways to launch Tksurfer. However the one which suggests lauching it from Freesurfer with the surface button makes it sound like there is a Freesurfer GUI, however I have yet to discover one. Is there a way to launch this as well?
I really appreciate all of your help! I know this will be a lot easier once I get everything up and running.
All the best, Claire
Here is my full script from my SetUpFreeSurfer.sh file: #!/bin/bash -p
# # SetUpFreeSurfer.sh #
# This is a sample SetUpFreeSurfer.sh file. # Edit as needed for your specific setup. # The defaults should work with most installations.
# Set this to the location of the freesurfer installation. if [ -z $FREESURFER_HOME ]; then export FREESURFER_HOME=/usr/local/freesurfer/stable5-pub fi
# Set this to your subjects/ dir, usually freesurfer/subjects/ if [ -z $SUBJECTS_DIR ]; then export SUBJECTS_DIR=$FREESURFER_HOME/subjects fi
# Set this to your functional sessions dir, usually freesurfer/sessions/ if [ -z $FUNCTIONALS_DIR ]; then export FUNCTIONALS_DIR=$FREESURFER_HOME/sessions fi
# Specify the location of the MINC tools. # Necessary only if the script $FREESURFER_HOME/FreeSurferEnv.csh # does not find the tools (and issues warnings pertaining to # the following two environment variables, which have example # locations that might need user-specific modification): #export MINC_BIN_DIR=/usr/pubsw/packages/mni/current/bin #export MINC_LIB_DIR=/usr/pubsw/packages/mni/current/lib # ... or just disable the MINC toolkit (although some Freesurfer # utilities will fail!) #export NO_MINC=1
# Enable or disable fsfast (enabled by default) #export NO_FSFAST=1
# Call configuration script: source $FREESURFER_HOME/FreeSurferEnv.sh
On Wed, Oct 15, 2014 at 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Issues launching tksurfer (Bruce Fischl) 2. Re: Issues launching tksurfer (dgw) 3. Re: Transform labels in Diffusion space into MNI space (Corinna Bauer) 4. Re: mri_anatomical_stats for volume (Douglas Greve) 5. Re: problem with gyrification index extraction (Douglas Greve) 6. Re: problem with gyrification index extraction (elisa veronese) 7. Re: Transform labels in Diffusion space into MNI space (Douglas Greve) 8. Re: Transform labels in Diffusion space into MNI space (Corinna Bauer) 9. Re: Transform labels in Diffusion space into MNI space (Douglas Greve) 10. Re: Transform labels in Diffusion space into MNI space (Corinna Bauer) 11. Re: Transform labels in Diffusion space into MNI space (Corinna Bauer) 12. Re: Transform labels in Diffusion space into MNI space (Douglas N Greve) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Oct 2014 08:30:14 -0400 (EDT) From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Issues launching tksurfer To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.03.1410150829570.23626@nmr.mgh.harvard.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Claire can you send us the full output of the command from the time you type tksurfer thanks Bruce On Wed, 15 Oct 2014, Claire Morley wrote: > Good Morning, > I have a quick question regarding the launch of tksurfer. I have recently > downloaded Freesurfer onto a Mac OSX after having some experience with it on > a previous Mac. However, it had been preinstalled on that Mac, and I am > afraid that I have perhaps installed it wrong on this one as when I test the > launching of qdec and tksurfer, nothing happens. The terminal doesn`t spit > out a command error, but it never launches the program. This was also a > problem on the previous Mac for qdec but not for tksurfer. Therefore, I have > tried to install everything again from square one and am not sure why now > neither program is launching. I am simply trying to test the command > "tksurfer bert lh pial". My environment is setup with Freesurfer and I am > trying to launch from the surfs directory, as that worked on the previous > Mac, but it is still giving me nothing. Any tips you could provide me with? > > All the best, > Claire > > > -- > > We shall not cease from exploration. And the end of all our exploring will > be to arrive where we started and know the place for the first time- T.S. > Eliot > > > > ------------------------------ Message: 2 Date: Wed, 15 Oct 2014 09:00:37 -0400 From: dgw <dgwakeman@gmail.com> Subject: Re: [Freesurfer] Issues launching tksurfer To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CADM2BTh_RpZUHEOBJgWFDmQta-=qA2nmj+jkiBMrv5Zu38sFsw@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi Claire, How did you install FreeSurfer? Did you follow the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall ? HTH, D On Wed, Oct 15, 2014 at 4:02 AM, Claire Morley <clairemorley2014@u.northwestern.edu> wrote: > Good Morning, > I have a quick question regarding the launch of tksurfer. I have recently > downloaded Freesurfer onto a Mac OSX after having some experience with it on > a previous Mac. However, it had been preinstalled on that Mac, and I am > afraid that I have perhaps installed it wrong on this one as when I test the > launching of qdec and tksurfer, nothing happens. The terminal doesn`t spit > out a command error, but it never launches the program. This was also a > problem on the previous Mac for qdec but not for tksurfer. Therefore, I have > tried to install everything again from square one and am not sure why now > neither program is launching. I am simply trying to test the command > "tksurfer bert lh pial". My environment is setup with Freesurfer and I am > trying to launch from the surfs directory, as that worked on the previous > Mac, but it is still giving me nothing. Any tips you could provide me with? > > All the best, > Claire > > > -- > > We shall not cease from exploration. And the end of all our exploring will > be to arrive where we started and know the place for the first time- T.S. > Eliot > > > > _______________________________________________ > 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. > ------------------------------ Message: 3 Date: Wed, 15 Oct 2014 10:19:01 -0400 From: Corinna Bauer <corinnab83@gmail.com> Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI space To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CAJOsP4K_5Vr15qWzj6tN3AUrYVsbuO9j7bYOu4eszBjw3rtweg@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Doug, I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following: 1. mni152reg --s MAE_06072013 2. tkregister2 --mov/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152. orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152. orig.mgz.reg 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf
Up until this point, everything looks good and well registered. 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat Corinna On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote: > > Hi Corinna, once you do #1, you can concatenate the register.dat with the > mni152.2mm.reg.dat like this > > mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat > > Check > tkregister2 --mov dti.nii --targ > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat > > mri_vol2vol --mov dti.nii --targ > $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o > dti.in.mni.nii > > doug > > > > On 10/14/14 2:57 PM, Corinna Bauer wrote: > > Hello all, > I am wanting to put labels currently in diffusion space into MNI space. > Does this make sense or is there a more straight forward way? > > 1. mni152reg the subject's structural into MNI space > 2. inverse transform the MNI in the the subject's T1 space > 3. Use bbregister to align the DTI to the T1 space > 4. inverse transform the MNI into DTI space using mri_vol2vol using the > registration from step 3? > > Cheers, > > Corinna > > > _______________________________________________ > Freesurfer mailinglistFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/ listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >