Re: [Freesurfer] Regarding mri_convert command
Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan do you have a license? If not you need to download and install it (as noted in the error message). They are free. cheers Bruce On Wed, 12 Nov 2014, Gunjan Gautam wrote: Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at reading volume. mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz A: Volume to be resampled / resliced B: Reference Volume Error message is being shown like below: mri_convert a.nii a.resliced.nii -rl b.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from a.nii... --__--__-- ERROR: Invalid FreeSurfer license key found in license file /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.__edu http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. Actually, I have two volumes, belong to the same subject. One volume is the ground truth which will be considered as standard for the second volume which is the processed one or the extracted brain. To perform a perfect comparison between both volumes, these must generate equal number of slices in order to compare the corresponding slide. But here there is problem with my volumes, that is while performing slicing Ground Truth volume is generating 360 slice and processed volume is generating 181 slides.
Re: [Freesurfer] Missing 'recon edit' button in Freeview
Dear Freesurfer mailing list, I am having the same problem with the missing recon edit button, and I have posted two times about this- please can someone advice us if we need the recon edit, what the difference is to voxel edit and how we could get the recon edit function. Many thanks, Areti From: Zhang, Kunyu kunyu.zh...@childrens.harvard.edumailto:kunyu.zh...@childrens.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 12 November 2014 19:52 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Missing 'recon edit' button in Freeview Hi all, I seem to be missing the ‘recon edit’ button that is supposed to be next to ‘voxel edit’ in Freeview. I am using version 1.0 on Mac OS X 10.10 from the latest version (v5.3.0) of FreeSurfer. According to the FreeSurferWiki, if I check ‘recon edit’ within ‘voxel edit,’ it just locks the brush value to 255 and eraser value to 1, but for extended editing, Recon edit mode is needed. If anyone can please help me with this issue, I would greatly appreciate it! Thanks, Kunyu ___ 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] Regarding mri_convert command
Hi Gunjan FREESURFER_HOME should be an environment variable, not the name of a directory. It should point to the directory that you installed FreeSurfer in. You should run: source installation directory/SetUpFreeSurfer.csh before trying to run anything cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan do you have a license? If not you need to download and install it (as noted in the error message). They are free. cheers Bruce On Wed, 12 Nov 2014, Gunjan Gautam wrote: Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at reading volume. mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz A: Volume to be resampled / resliced B: Reference Volume Error message is being shown like below: mri_convert a.nii a.resliced.nii -rl b.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from a.nii... --__--__-- ERROR: Invalid FreeSurfer license key found in license file /home/bibl04/Data_Home/__Desktop/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.__edu http://surfer.nmr.mgh.harvard.edu to
Re: [Freesurfer] Missing 'recon edit' button in Freeview
Hi Areti Ruopeng (ccd) should be able to help you. You probably don't have the correct version cheers Bruce On Tue, 18 Nov 2014, Smaragdi A. wrote: Dear Freesurfer mailing list, I am having the same problem with the missing recon edit button, and I have posted two times about this- please can someone advice us if we need the recon edit, what the difference is to voxel edit and how we could get the recon edit function. Many thanks, Areti From: Zhang, Kunyu kunyu.zh...@childrens.harvard.edumailto:kunyu.zh...@childrens.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 12 November 2014 19:52 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Missing 'recon edit' button in Freeview Hi all, I seem to be missing the ‘recon edit’ button that is supposed to be next to ‘voxel edit’ in Freeview. I am using version 1.0 on Mac OS X 10.10 from the latest version (v5.3.0) of FreeSurfer. According to the FreeSurferWiki, if I check ‘recon edit’ within ‘voxel edit,’ it just locks the brush value to 255 and eraser value to 1, but for extended editing, Recon edit mode is needed. If anyone can please help me with this issue, I would greatly appreciate it! Thanks, Kunyu ___ 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] Regarding mri_convert command
I ran but its showing error like below: bibl04@BIBL04:~/Desktop/freesurfer$ source /Desktop/freesurfer/SetUpFreeSurfer.csh bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory May be due to the shell. What should I do now? On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan FREESURFER_HOME should be an environment variable, not the name of a directory. It should point to the directory that you installed FreeSurfer in. You should run: source installation directory/SetUpFreeSurfer.csh before trying to run anything cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan do you have a license? If not you need to download and install it (as noted in the error message). They are free. cheers Bruce On Wed, 12 Nov 2014, Gunjan Gautam wrote: Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at reading volume. mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz A: Volume to be resampled / resliced B: Reference Volume Error message is being shown like below: mri_convert a.nii a.resliced.nii -rl b.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from a.nii...
Re: [Freesurfer] Regarding mri_convert command
I think if the file existed you would have gotten a syntax error. Does it exist? If not, then either you didn't install FreeSurfer there or something went wrong with your installation cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: I ran but its showing error like below: bibl04@BIBL04:~/Desktop/freesurfer$ source /Desktop/freesurfer/SetUpFreeSurfer.csh bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory May be due to the shell. What should I do now? On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan FREESURFER_HOME should be an environment variable, not the name of a directory. It should point to the directory that you installed FreeSurfer in. You should run: source installation directory/SetUpFreeSurfer.csh before trying to run anything cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014
Re: [Freesurfer] Regarding mri_convert command
I followed the installation process from http://freesurfer.net/fswiki/LinuxInstall. while running setenv FREESURFER_HOME /usr/local/freesurfer it shows that setenv command not found. Is it necessary to place FreeSurfer directory in to /usr/local ? I have it on my desktop. On Tue, Nov 18, 2014 at 6:47 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think if the file existed you would have gotten a syntax error. Does it exist? If not, then either you didn't install FreeSurfer there or something went wrong with your installation cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: I ran but its showing error like below: bibl04@BIBL04:~/Desktop/freesurfer$ source /Desktop/freesurfer/SetUpFreeSurfer.csh bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory May be due to the shell. What should I do now? On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan FREESURFER_HOME should be an environment variable, not the name of a directory. It should point to the directory that you installed FreeSurfer in. You should run: source installation directory/SetUpFreeSurfer.csh before trying to run anything cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54
Re: [Freesurfer] Regarding mri_convert command
Hi Gunjan if you are using bash, you need to run the instructions for bash at: http://freesurfer.net/fswiki/SetupConfiguration for example, it says: If using bash or sh, type: export FREESURFER_HOME=freesurfer_installation_directory/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: I followed the installation process from http://freesurfer.net/fswiki/LinuxInstall. while running setenv FREESURFER_HOME /usr/local/freesurfer it shows that setenv command not found. Is it necessary to place FreeSurfer directory in to /usr/local ? I have it on my desktop. On Tue, Nov 18, 2014 at 6:47 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think if the file existed you would have gotten a syntax error. Does it exist? If not, then either you didn't install FreeSurfer there or something went wrong with your installation cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: I ran but its showing error like below: bibl04@BIBL04:~/Desktop/freesurfer$ source /Desktop/freesurfer/SetUpFreeSurfer.csh bash: /Desktop/freesurfer/SetUpFreeSurfer.csh: No such file or directory May be due to the shell. What should I do now? On Tue, Nov 18, 2014 at 6:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan FREESURFER_HOME should be an environment variable, not the name of a directory. It should point to the directory that you installed FreeSurfer in. You should run: source installation directory/SetUpFreeSurfer.csh before trying to run anything cheers Bruce On Tue, 18 Nov 2014, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want
Re: [Freesurfer] Regarding mri_convert command
Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan do you have a license? If not you need to download and install it (as noted in the error message). They are free. cheers Bruce On Wed, 12 Nov 2014, Gunjan Gautam wrote: Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at reading volume. mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz A: Volume to be resampled / resliced B: Reference Volume Error message is being shown like below: mri_convert a.nii a.resliced.nii -rl b.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from a.nii... --__--__-- ERROR: Invalid FreeSurfer license key found in license file
[Freesurfer] Issue with smoothing in local gyrification process
Hello Freesurfer Gurus, I am trying to compute LGI analysis using Qdec and have successfully loaded my qdec.table.dat file as well as created .Qrecrc to include the new pial_lgi measure. However, when I try to analyze using this measure (or with any measure for that matter), an error pops up saying that it was not able to locate the fwhm10.fsaverage.mgh file. I am guessing that this is the smoothed file and therefore that I need to run recon-all -qcache -measure pial_lgi -average -s, but when I run this while in my subjects directory, it tells me the -average flag is unrecognized. (I also tried this with -fsaverage and got the same error). Can you please help troubleshoot what might be going on? The lh pial files have already been created. When those are created I am guessing the smoothed files aren't created automatically as well? I was getting these instructions from the Schaer article here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/#!po=31.2500 Thank you so much for your help! 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.
[Freesurfer] Fwd: outer pial error
Solved it, thank you
-- Forwarded message --
From: Octavian Lie octavian@gmail.com
Date: Mon, Nov 17, 2014 at 8:11 AM
Subject: outer pial error
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Dear All,
I tried to get an outer pial surface on a previously processed pt subjid,
and I got the following error.
(recon-all was running another subject in a separate window, for what's
worth)
Please advise,
Octavian
recon-all -localGI -s subjid
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217
INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer
-rw-rw-r-- 1 ovl ovl 3224039 Nov 17 07:58
/usr/local/fs5.3/freesurfer/subjects/subjid/scripts/recon-all.log
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/fs5.3/freesurfer/subjects/subjid/surf
#
#@# Local Gyrification Index lh Mon Nov 17 08:03:50 CST 2014
mris_compute_lgi --i lh.pial
=
rm -Rf
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/fs5.3/freesurfer/subjects/subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
*make_outer_surface('/usr/local/fs5.3/freesurfer/subjects/*
*subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/fs5.3/freesurfer/subjects/**subjid/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit*
=
ERROR:: Too many arguments.
Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23
09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subjid exited with ERRORS at Mon Nov 17 08:03:54 CST 2014
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[Freesurfer] Longitudinal analysis and hippocampal subfields
Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-logob489c8] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.iemailto:erikohan...@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ 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] Longitudinal analysis and hippocampal subfields
Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik *Erik O'Hanlon* Postdoctoral researcher *RCSI* Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland *T: *8093740 *E: *erikohan...@rcsi.ie mailto:erikohan...@rcsi.ie *W: *www.rcsi.ie http://www.rcsi.ie *RCSI* DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Longitudinal analysis and hippocampal subfields
Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:part1.06080901.05020203@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.iemailto:erikohan...@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Longitudinal analysis and hippocampal subfields
Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik *From:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] *Sent:* 18 November 2014 17:04 *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik *Erik O'Hanlon* Postdoctoral researcher *RCSI* Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland *T: *8093740 *E: *erikohan...@rcsi.ie mailto:erikohan...@rcsi.ie *W: *www.rcsi.ie http://www.rcsi.ie *RCSI* DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Regarding mri_convert command
Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto: zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto: fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan do you have a license? If not you need to download and install it (as noted in the error message). They are free. cheers Bruce On Wed, 12 Nov 2014, Gunjan Gautam wrote: Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at reading volume. mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz A: Volume to be resampled / resliced B: Reference Volume Error message is being shown
Re: [Freesurfer] Regarding mri_convert command
Hi Gunjan just run recon-all and it will do everything that we know how to do (including those steps) cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan do you have a license? If not you need to download and install it
Re: [Freesurfer] Regarding mri_convert command
Thank you I will be thankful if you could let me know about the link related to recon-all, in order to know about the parameters(input volume info etc) associated to it and other usage. On Nov 19, 2014 12:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan just run recon-all and it will do everything that we know how to do (including those steps) cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system. Best regards, Gunjan On Nov 12, 2014 9:15 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, Are you using your own version of VirtualBox, with freesurfer installed on it by you? Or the VirtualBox version of freesurfer made by us and downloaded from our website? I am confused because in your email below, freesurfer appears to be installed on the Desktop whereas the prepackaged version made by us is installed in /usr/local -Zeke On 11/12/2014 08:54 AM, Gunjan Gautam wrote: Hello Sir, License file is present in the folder but with the name LICENSE. Should I download it again ? Best Regards, Gunjan On Nov 12, 2014 7:01 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
Re: [Freesurfer] Regarding mri_convert command
Hi Gunjan, it's all on the wiki. You should go through our tutorials cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: Thank you I will be thankful if you could let me know about the link related to recon-all, in order to know about the parameters(input volume info etc) associated to it and other usage. On Nov 19, 2014 12:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan just run recon-all and it will do everything that we know how to do (including those steps) cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had to ask someone to get it downloaded and send me through Google drive. This was how I installed it in my system.
Re: [Freesurfer] Regarding mri_convert command
Ok, I go through that. Thanks, Gunjan On Nov 19, 2014 12:37 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan, it's all on the wiki. You should go through our tutorials cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: Thank you I will be thankful if you could let me know about the link related to recon-all, in order to know about the parameters(input volume info etc) associated to it and other usage. On Nov 19, 2014 12:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gunjan just run recon-all and it will do everything that we know how to do (including those steps) cheers Bruce On Wed, 19 Nov 2014, Gunjan Gautam wrote: Ok, I try this tomorrow morning. I will be thankful if you could tell me about getting brain mask and performing skull stripping otherwise I'll have to wait for 12 hours to get your replies as our working hours doesn't match. On Nov 18, 2014 8:45 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Gunjan, this may be related to an Ubuntu specific issue we address on the Freesurfer download page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download Specifically the part thats states the following: *** On Ubuntu, you might have to do this if qdec or freeview complain about libjpeg or libtiff: cd /usr/lib (/usr/lib/i386 or /usr/lib/x86_64 on some Ubuntu distros) sudo ln -s libjpeg.so.8 libjpeg.so.62 sudo ln -s libtiff.so.4 libtiff.so.3 *** -Zeke On 11/18/2014 03:55 AM, Gunjan Gautam wrote: Hello Sir, I have place the license.txt in the same directory that contains build-stamp.txt as there were no directory with name FREESURFER_HOME. freeview command is not working and showing below message freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory. What next I need to do in order to generate a output brain mask. Best Regards, Gunjan On Thu, Nov 13, 2014 at 12:24 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Im having a little difficulty following all the avenues of your attempts to get this working, but the bottom line is that the error message below is complaining that you do not have a valid license file. You need to go to this page and register and get the valid license file: https://surfer.nmr.mgh.harvard.edu/registration.html Once you get a valid license file you will need to place it in your $FREESURFER_HOME directory (the same directory that contains build-stamp.txt) and give it the name .license or license.txt. Try both. -Zeke On 11/12/2014 01:29 PM, Gunjan Gautam wrote: Sir earlier I was trying to use FreeSurfer using Virtual Box in my Windows machine. There the mri_convert command did not work so I switched to a Linux machine. Now, I'm using centos6_x86_64 version as my machine has the Ubuntu 12.04 platform and here also facing the same problem. I want to share one thing that in my institute I tried hard to download FreeSurfer but every time it resulted into a time-out situation so I had
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
That's super! Thanks again Martin Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:part1.06060905.0900@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.iemailto:erikohan...@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Frontal WM ROI
Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ 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] QAtools errors with aseg QA
Hi there, Just trying out the QAtools and I notice that there are a number of (standard_in) 1: syntax error reports for each subcortical label: checking subcortical label: Endosteum, . +/- . (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error As best as I can tell its in some bc calculations that are being done and I assume these errors are why there are no aseg reports made. All the other calculations and snapshots seem to work just fine. I am running FreeSurfer 5.3 and QAtools 1.1 on Ubuntu 12.04. Thanks in advance. Cheers, -Morgan ___ 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] How does freesurfer smoothes the data?
I'm not sure what you mean by that, but I'm pretty sure the answer is no :-) doug On 11/17/14 3:01 PM, ye tian wrote: Hello Doug and Bruce, Thank you! Another quick question, is there an option to select bandwidth using cross-validation? Sincerely, Ye On Mon, Nov 17, 2014 at 9:40 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: The way it is implemented is as a nearest neighbor smoothing which is an approximation to convolving with a Gaussian. doug On 11/17/14 8:02 AM, Bruce Fischl wrote: Hi Ye, yes, it is a Gaussian kernel along the surface cheers Bruce On Mon, 17 Nov 2014, ye tian wrote: Hello freesurfers, I would like to understand intuitively how data is smoothed by Freesurfer. Is it an analogue to kernel smoothing, with the different FWHM equivalent to different bandwidths? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 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] Frontal WM ROI
The unsegmented is all the WM that is further than 5mm from cortex. You can change the threshold so that it labels all of WM regardless of the distance. Other than that, I don't have much to suggest. doug On 11/18/14 6:13 PM, Michele Cavallari wrote: Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks ___ 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.
