Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith
Hi Isaiah
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Bruce,
Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right?
Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right?
Isaiah
Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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.
Hello and thanks again, Bruce,
I am not sure what is going wrong here. I tried what you said and I am getting this.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i <os005a1001.nii> -s <Practice> -sd </Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS00001> -all
-bash: os005a1001.nii: No such file or directory
On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
does that file exist? You don't want angle brackets <> around the name (the angle brackets typically mean "replace this with an actual name"
cheers Bruce
On Wed, 30 Jul 2014, Isaiah C. Smith wrote:
Hello and thanks again, Bruce, I am not sure what is going wrong here. I tried what you said and I am getting this.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i <os005a1001.nii> -s <Practice> -sd</Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SR S00001> -all
-bash: os005a1001.nii: No such file or directory
On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
The command is not found.
Last login: Tue Jul 29 17:42:52 on ttys001 -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i os005a1001.nii -s Practice -sd /Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS00001 -all -bash: recon-: command not found Isaiahs-MacBook-Pro:~ IsaiahSmith$ -bash: os005a1001.nii: No such file or directory On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
Hi Isaiah
remove the space. It should be:
recon-all
cheers Bruce On Wed, 30 Jul 2014, Isaiah C. Smith wrote:
The command is not found.
Last login: Tue Jul 29 17:42:52 on ttys001 -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i os005a1001.nii -s Practice -sd/Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS 00001 -all -bash: recon-: command not found Isaiahs-MacBook-Pro:~ IsaiahSmith$ -bash: os005a1001.nii: No such file or directory On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
Hello Bruce,
The I am a little confused with the results of the recon-all command? Does the recon-all -help explain the file placement?
Isaiah
On Jul 30, 2014, at 6:21 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
remove the space. It should be:
recon-all
cheers Bruce
On Wed, 30 Jul 2014, Isaiah C. Smith wrote:
The command is not found. Last login: Tue Jul 29 17:42:52 on ttys001 -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i os005a1001.nii -s Practice -sd/Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS 00001 -all -bash: recon-: command not found Isaiahs-MacBook-Pro:~ IsaiahSmith$ -bash: os005a1001.nii: No such file or directory On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
The recon-all option is no longer working and neither is the other one. I am getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Isaiahs-MacBook-Pro:~ IsaiahSmith$
On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
you need a "-" before each option, so it should be
recon-all -help
On Wed, 30 Jul 2014, Isaiah C. Smith wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Isaiahs-MacBook-Pro:~ IsaiahSmith$
On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished?
Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... ****************************************
On Jul 29, 2014, at 9:24 PM, Isaiah Smith <Isaiah.C.Smith.17@dartmouth.edumailto:Isaiah.C.Smith.17@dartmouth.edu> wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Isaiahs-MacBook-Pro:~ IsaiahSmith$
On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished?
Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error.Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Isaiahs-MacBook-Pro:~ IsaiahSmith$
On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error.Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
the format of what? On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error.Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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 files after recon-all
On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error.Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
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there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...) On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all
On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error.Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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 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.
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Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...)
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all
On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ 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.
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Hi Isaiah
you should go through the tutorials on our website - they detail all this information
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...)
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all
On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
> On Thu, 31 Jul 2014, Isaiah C. Smith wrote: > > Thank you so much, Bruce. I think that I got it. Overall, I am trying to > create a source volume conduction model, calculate the lead field matrix, > and then create a source model. My instructor said that it might be possible > to do this in Freesurfer. Sorry, I am kind of new to using the terminal. > Could you tell me how to go about doing that in this program or direct me to > the part of the sit where I can start working on next steps? Or do I need to > use another program like FieldTrip for the model? Also what will the format > of the file be after the command is finished? > Nine parameter search. iteration 5 nscales = 1 ... > **************************************** > Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 > (thresh=-3.9) > 1.074 -0.133 0.048 -2.720; > 0.105 1.397 -0.148 -56.728; > -0.031 0.191 1.157 -52.936; > 0.000 0.000 0.000 1.000; > reducing scale to 0.0625 > **************************************** > Nine parameter search. iteration 6 nscales = 2 ... > **************************************** > Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 > (thresh=-3.9) > 1.076 -0.124 0.028 -1.627; > 0.096 1.401 -0.129 -58.732; > -0.015 0.165 1.156 -51.529; > 0.000 0.000 0.000 1.000; > **************************************** > Nine parameter search. iteration 7 nscales = 2 ... > **************************************** > On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu > wrote: > > The recon-all option is no longer working and neither is the > other one. I am getting an error. > Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help > ERROR: Flag help unrecognized. > help > Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: > Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 > x86_64 > recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > Isaiahs-MacBook-Pro:~ IsaiahSmith$ > On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu > wrote: > > Hi Isaiah > > recon-all -i <input file> -s <subject identifier> -sd <dir > to put subject in> -all > > should do the trick. <input file> should be a *single* > file in the right dicom series, or a .nii file. Don't use > analyze > Bruce > > On Tue, 22 Jul 2014, Isaiah C. Smith wrote: > > Hello Bruce, > Thanks for the response; I tried the inputs > from the check freesurfer page. > I just tried to do the run recon-all and got > the list of possible commands. > The input images are unix executable files > separately, but I can convert > them to .hdr/.img or .nii using mricron. They > are MRI images. How do I > direct these files to the command? And this is > the command to do the things > I previously asked, right? > Isaiah > > Hi Isaiah, > > what are the input images that you have? > What format and what > imaging > sequence? You should be able to just run > recon-all on them > (check out > recon-all -help) > > cheers > Bruce > On Tue, 22 Jul 2014, Isaiah C. Smith > wrote: > > Hello All, > > I was testing to see if the > freesurfer program works > and it does seem to work for > anything besides the > free viewer program. I do not know > what is wrong > with the others; do you have any > ideas? Also I am > trying to use the inhomogeneity > correction, convert > the images that I have to 1x1x1 > ratio, arrange the > directions of the image, and save > the program in > analyze format. If possible could > you outline that > process or give me a link that will > direct me on the > process? Thank you. Your help is > really appreciated. > > Isaiah Smith > _______________________________________________ > 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 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.
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Thanks
Sent from my iPhone
On Jul 31, 2014, at 10:47 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you should go through the tutorials on our website - they detail all this information
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...)
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all
On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
> On Jul 30, 2014, at 7:23 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: > > Hi Isaiah > > you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations) > > cheers > Bruce > >> On Thu, 31 Jul 2014, Isaiah C. Smith wrote: >> >> Thank you so much, Bruce. I think that I got it. Overall, I am trying to >> create a source volume conduction model, calculate the lead field matrix, >> and then create a source model. My instructor said that it might be possible >> to do this in Freesurfer. Sorry, I am kind of new to using the terminal. >> Could you tell me how to go about doing that in this program or direct me to >> the part of the sit where I can start working on next steps? Or do I need to >> use another program like FieldTrip for the model? Also what will the format >> of the file be after the command is finished? >> Nine parameter search. iteration 5 nscales = 1 ... >> **************************************** >> Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 >> (thresh=-3.9) >> 1.074 -0.133 0.048 -2.720; >> 0.105 1.397 -0.148 -56.728; >> -0.031 0.191 1.157 -52.936; >> 0.000 0.000 0.000 1.000; >> reducing scale to 0.0625 >> **************************************** >> Nine parameter search. iteration 6 nscales = 2 ... >> **************************************** >> Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 >> (thresh=-3.9) >> 1.076 -0.124 0.028 -1.627; >> 0.096 1.401 -0.129 -58.732; >> -0.015 0.165 1.156 -51.529; >> 0.000 0.000 0.000 1.000; >> **************************************** >> Nine parameter search. iteration 7 nscales = 2 ... >> **************************************** >> On Jul 29, 2014, at 9:24 PM, Isaiah Smith Isaiah.C.Smith.17@dartmouth.edu >> wrote: >> >> The recon-all option is no longer working and neither is the >> other one. I am getting an error. >> Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help >> ERROR: Flag help unrecognized. >> help >> Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: >> Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 >> x86_64 >> recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 >> For more details, see the log file >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> Isaiahs-MacBook-Pro:~ IsaiahSmith$ >> On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu >> wrote: >> >> Hi Isaiah >> >> recon-all -i <input file> -s <subject identifier> -sd <dir >> to put subject in> -all >> >> should do the trick. <input file> should be a *single* >> file in the right dicom series, or a .nii file. Don't use >> analyze >> Bruce >> >> On Tue, 22 Jul 2014, Isaiah C. Smith wrote: >> >> Hello Bruce, >> Thanks for the response; I tried the inputs >> from the check freesurfer page. >> I just tried to do the run recon-all and got >> the list of possible commands. >> The input images are unix executable files >> separately, but I can convert >> them to .hdr/.img or .nii using mricron. They >> are MRI images. How do I >> direct these files to the command? And this is >> the command to do the things >> I previously asked, right? >> Isaiah >> >> Hi Isaiah, >> >> what are the input images that you have? >> What format and what >> imaging >> sequence? You should be able to just run >> recon-all on them >> (check out >> recon-all -help) >> >> cheers >> Bruce >> On Tue, 22 Jul 2014, Isaiah C. Smith >> wrote: >> >> Hello All, >> >> I was testing to see if the >> freesurfer program works >> and it does seem to work for >> anything besides the >> free viewer program. I do not know >> what is wrong >> with the others; do you have any >> ideas? Also I am >> trying to use the inhomogeneity >> correction, convert >> the images that I have to 1x1x1 >> ratio, arrange the >> directions of the image, and save >> the program in >> analyze format. If possible could >> you outline that >> process or give me a link that will >> direct me on the >> process? Thank you. Your help is >> really appreciated. >> >> Isaiah Smith >> _______________________________________________ >> 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 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.
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Hello Bruce,
I am trying to check the output of the mri data that I processed I start using MNE. I placed the file in a folder called Practice in my documents, and I am using the following command:
tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
and then
freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red
e file 2014-08-01 19:53:06.207 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file e file 2014-08-01 19:53:07.387 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file
e
Do you know what is going on here?
On Jul 31, 2014, at 10:38 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
you should go through the tutorials on our website - they detail all this information
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...) On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
the format of what? On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** On Jul 29, 2014, at 9:24 PM, Isaiah Smith <Isaiah.C.Smith.17@dartmouth.edumailto:Isaiah.C.Smith.17@dartmouth.edu> wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ 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 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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
do those files exist in that path?
cheers Bruce On Sat, 2 Aug 2014, Isaiah C. Smith wrote:
Hello Bruce, I am trying to check the output of the mri data that I processed I start using MNE. I placed the file in a folder called Practice in my documents, and I am using the following command:
tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR and then
freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red e file 2014-08-01 19:53:06.207 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file e file 2014-08-01 19:53:07.387 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file
e
Do you know what is going on here?
On Jul 31, 2014, at 10:38 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah you should go through the tutorials on our website - they detail all this information cheers Bruce On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Yes, how do i view the files and where can I find where every has been placed On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...) On Thu, 31 Jul 2014, Isaiah C. Smith wrote: The files after recon-all On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: the format of what? On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd? On Jul 30, 2014, at 7:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Isaiah you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations) cheers Bruce On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** On Jul 29, 2014, at 9:24 PM, Isaiah Smith <Isaiah.C.Smith.17@dartmouth.edu> wrote: The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu rfer
_______________________________________________ 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. _______________________________________________ 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 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 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
Yes, I figured out the problem. Thanks. But for clarification, what do the $ and \ mean in the example scripts?
tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR
and then
freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red
Isaiah On Aug 2, 2014, at 7:03 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
do those files exist in that path?
cheers Bruce On Sat, 2 Aug 2014, Isaiah C. Smith wrote:
Hello Bruce, I am trying to check the output of the mri data that I processed I start using MNE. I placed the file in a folder called Practice in my documents, and I am using the following command: tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR and then freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red e file 2014-08-01 19:53:06.207 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file e file 2014-08-01 19:53:07.387 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file e Do you know what is going on here? On Jul 31, 2014, at 10:38 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
you should go through the tutorials on our website - they detail all this information
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...) On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
the format of what? On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations)
cheers Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** On Jul 29, 2014, at 9:24 PM, Isaiah Smith <Isaiah.C.Smith.17@dartmouth.edumailto:Isaiah.C.Smith.17@dartmouth.edu> wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Isaiah
recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all
should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce
On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah
Hi Isaiah,
what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help)
cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote:
Hello All,
I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated.
Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu rfer
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$ means what follows is a variable name while \ means to continue on to the next line before executing the command.
Peace,
Matt.
From: "Isaiah C. Smith" Isaiah.C.Smith.17@dartmouth.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, August 3, 2014 at 12:36 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Start Up
Yes, I figured out the problem. Thanks. But for clarification, what do the $ and \ mean in the example scripts?
tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR and then freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red Isaiah On Aug 2, 2014, at 7:03 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
do those files exist in that path?
cheers Bruce On Sat, 2 Aug 2014, Isaiah C. Smith wrote:
Hello Bruce, I am trying to check the output of the mri data that I processed I start using MNE. I placed the file in a folder called Practice in my documents, and I am using the following command: tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR and then freeview -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red e file 2014-08-01 19:53:06.207 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.white): could not open file e file 2014-08-01 19:53:07.387 Freeview[10239:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file No such file or directory MRISread failed MRISread(/Users/IsaiahSmith/Documents/LABData/Volume Conduction Models/Practice/good_output/surf/rh.pial): could not open file e Do you know what is going on here? On Jul 31, 2014, at 10:38 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah you should go through the tutorials on our website - they detail all this information cheers Bruce On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Yes, how do i view the files and where can I find where every has been placed On Jul 31, 2014, at 8:26 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: there are many, many files in many different formats (e.g. volumes in .mgz format, surfaces in our internal format, labels, parcellations, etc...) On Thu, 31 Jul 2014, Isaiah C. Smith wrote: The files after recon-all On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: the format of what? On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Thank you, I will go there now. But regarding the output of freesurfer, the format will be .ccd? On Jul 30, 2014, at 7:23 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Isaiah you might check out MNE from Matti Hamalainen (ccd). It does all this and more (using FreeSurfer surfaces and segmentations) cheers Bruce On Thu, 31 Jul 2014, Isaiah C. Smith wrote: Thank you so much, Bruce. I think that I got it. Overall, I am trying to create a source volume conduction model, calculate the lead field matrix, and then create a source model. My instructor said that it might be possible to do this in Freesurfer. Sorry, I am kind of new to using the terminal. Could you tell me how to go about doing that in this program or direct me to the part of the sit where I can start working on next steps? Or do I need to use another program like FieldTrip for the model? Also what will the format of the file be after the command is finished? Nine parameter search. iteration 5 nscales = 1 ...
Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.074 -0.133 0.048 -2.720; 0.105 1.397 -0.148 -56.728; -0.031 0.191 1.157 -52.936; 0.000 0.000 0.000 1.000; reducing scale to 0.0625
Nine parameter search. iteration 6 nscales = 2 ...
Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.076 -0.124 0.028 -1.627; 0.096 1.401 -0.129 -58.732; -0.015 0.165 1.156 -51.529; 0.000 0.000 0.000 1.000;
Nine parameter search. iteration 7 nscales = 2 ...
On Jul 29, 2014, at 9:24 PM, Isaiah SmithIsaiah.C.Smith.17@dartmouth.edu wrote:
The recon-all option is no longer working and neither is the other one. I am getting an error. Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014;root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith
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Matt Glasser