Re: [Freesurfer] volume of CSF for hemispheres
Hello Bruce, Could you please give me a link to this coordinate tutorial. I don't think I can find it. Thank you, Tanja. On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think Doug just put up a coordinate tutorial. For each voxel in the aseg label you are interested, compute it's tal coords and if the x is negative assign it to one pool and if it is positive assign it to the other cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Thank you, Bruce. Could you recommend me any tutorial on this? Or probably can you just mention some steps or commands, where I should insert coordinates? Tanja. On Wed, Feb 16, 2011 at 3:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja we don't do this by default, but I guess you could use the Talairach x coordinate to try to differentiate. cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fixing hippocampus segmentation
Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] installation problem in ubuntu
Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] installation problem in ubuntu
Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.cowrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] installation problem in ubuntu
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co wrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] fixing hippocampus segmentation
Hi Tanja, Can you send us an image? Is parahippocampal white matter significantly darker than 110? Bruce On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova tetian...@gmail.com wrote: Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank you, Tanja. ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] volume of CSF for hemispheres
Hi Tanja, type 'coordinates' into the wiki search on our page. doug On 2/21/11 4:11 AM, Tetiana Dadakova wrote: Hello Bruce, Could you please give me a link to this coordinate tutorial. I don't think I can find it. Thank you, Tanja. On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja, I think Doug just put up a coordinate tutorial. For each voxel in the aseg label you are interested, compute it's tal coords and if the x is negative assign it to one pool and if it is positive assign it to the other cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Thank you, Bruce. Could you recommend me any tutorial on this? Or probably can you just mention some steps or commands, where I should insert coordinates? Tanja. On Wed, Feb 16, 2011 at 3:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tanja we don't do this by default, but I guess you could use the Talairach x coordinate to try to differentiate. cheers Bruce On Wed, 16 Feb 2011, Tetiana Dadakova wrote: Dear list, I would like to calculate CSF volume separately for left and right hemispheres. In aseg.stats file I have volumes for 3rd, 4th and 5th ventricles as a whole. Is there any possibility to get volume values for right/left parts of 3rd, 4th and 5th ventricles? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_mask
Hello Freesurfers, I'm trying to mask the rawavg.mgz from some subjects with the brain.mgz after doing some manual segmentation corrections by using mri_mask command, I have donne it before and it always works but with this subject, the command line is excacly the same so I have no idea what could be wrong: mri_mask rawavg.mgz brain.mgz outbrain.mgz ERROR: dimension mismatch between source and mask. Can any one help me with this? Bests, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_mask
The rawavg.mgz and brain.mgz are of different sizes. You'll need to transfer one to the other. You can do this with mri_vol2vol using brain as the mov and rawavg as the target and --regheader. doug On 2/21/11 11:49 AM, Gabriel Go.Es. wrote: Hello Freesurfers, I'm trying to mask the rawavg.mgz from some subjects with the brain.mgz after doing some manual segmentation corrections by using mri_mask command, I have donne it before and it always works but with this subject, the command line is excacly the same so I have no idea what could be wrong: mri_mask rawavg.mgz brain.mgz outbrain.mgz ERROR: dimension mismatch between source and mask. Can any one help me with this? Bests, Gabriel ___ 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 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] overlay sig.mgh onto T1 vol
Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I have only one point of the sig.mgh (in the slice 128) which is outside the volume. There's another way to do this? Thanks for the help! Fernanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] overlay sig.mgh onto T1 vol
Hi Fernanda if that's a surface overlay you'll need to sample it into the volume with mri_surf2vol cheers Bruce On Mon, 21 Feb 2011, Fernanda Palhano wrote: Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I have only one point of the sig.mgh (in the slice 128) which is outside the volume. There's another way to do this? Thanks for the help! Fernanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] installation problem in ubuntu
run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can unistall it, if i'm the admin user? Thanks in advance, Carolina 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co wrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! Jie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] overlay sig.mgh onto T1 vol
use tkmedit fsaverage orig.mgz -overlay teste_sig.mgz doug On 2/21/11 3:46 PM, Fernanda Palhano wrote: Hi Bruce, Thank you for the prompt reply. I tried using mri_surf2vol : mri_surf2vol --surfval qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh --identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o teste_sig.mgz gdiagno = -1 Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: -- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; -- subjects dir /Applications/freesurfer/subjects/dados_Riba/ surface value path qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh hemi lh mksurfmask 0 projfrac 0 outvol path teste_sig.mgz template path fsaverage/mri/T1.mgz --- Anat2Vol Registration (TkReg) 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; - height = 256 width = 256 depth = 256 xsize = 1.00 ysize = 1.00 zsize = 1.00 cdc = -1.00 0.00 0.00 rdc = 0.00 0.00 -1.00 sdc = 0.00 1.00 0.00 xyz0 = 0.00 0.00 0.00 Gdiag_no -1 Reading surface /Applications/freesurfer/subjects/dados_Riba//fsaverage/surf/lh.white Done reading source surface INFO: reading qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh as MGH Done loading source values (nvtxs = 163842) INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 73965 voxels in the volume INFO: writing output volume to teste_sig.mgz done And then, use tkmedit to view it: [Fernanda-Palhanos-Mac-Pro:freesurfer/subjects/dados_Riba] fernandapalhano% tkmedit fsaverage teste_sig.mgz mghRead(/Applications/freesurfer/subjects/dados_Riba//fsaverage/mri/teste_sig.mgz, -1): could not open file Error: Loading volume teste_sig.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. Am I using wrong parameters in mri_surf2vol? Thanks again, Fernanda On Mon, Feb 21, 2011 at 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Fernanda if that's a surface overlay you'll need to sample it into the volume with mri_surf2vol cheers Bruce On Mon, 21 Feb 2011, Fernanda Palhano wrote: Hello, Does anyone knows if is it possible to overlay the surface file sig.mgh onto a T1 vol? I tried the command: tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were the thresholds I used in qdec), but it seems like I have only one point of the sig.mgh (in the slice 128) which is outside the volume. There's another way to do this? Thanks for the help! Fernanda The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] question about weighted regression analysis
So I created a weighted regression analysis to look at the effect of memory load in a particular brain region. Basically, I weighted the paradigms by a behavioral measure that reflected the number of items actually remembered (as set size was increased). As far as Doug told me there are basically 2 ways to weight your paradigm files. Version 1: Have 2 conditions, baseline (condition 0) and all the set sizes (condition 1). Condition 1 would then be weighted by the behavioral measure. Version 2: Have 3 conditions, baseline (condition 0), and then I represented each presentation as two different conditions, one with a weight that is always 1 (condition 1), the other weighted according to the behavioral measure (condition 2). The difference, as far as I understand it, in version 1, it is assumed that the response amplitude is ) when the weight is 0 (ie. that when you are attending to 0 items, brain activity = 0). Whereas, version 2, tests the slope of the HRF amplitude vs weight without the assumption above. However, I'm a bit confused as to the results I got. When I looked at the data from both versions, version 1 provided a much higher amount of activation and more areas activated than version 2. However, I believe version 2 better fits with the multiple regression analysis that is done in Brain Voyager. Can anyone give me a better explanation of what the difference between these analysis models is? Katie ___ 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] Gammafit parameters
Hi all, We are trying to use -gammafit when running the mkanalysis-sess command. In the FsFast Tutorial, the flag -gammafit 2.25 1.25 is used. Are those numbers the default? If not, what is the default? Thanks in advance. Best, Mandy Nagy ___ 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.
