[Freesurfer] Freesurfer Start Up
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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Start Up
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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Start Up
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 -s -sd -all -bash: os005a1001.nii: No such file or directory On Jul 22, 2014, at 4:44 PM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Start Up
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/SRS1 -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 mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Start Up
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 mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Start Up
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 mailto:isaiah.c.smith...@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 mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. 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<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to y
Re: [Freesurfer] Freesurfer Start Up
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 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 >> 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 >> wrote: >> >> Hi Isaiah >> >> recon-all -i -s -sd > to put subject in> -all >> >> should do the trick. 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 >>
Re: [Freesurfer] Freesurfer Start Up
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" > 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 >> 1 -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 >> wrote: >> >> Hi Isaiah >> >> recon-all -i -s -sd > put subject in> -all >> >> should do the trick. 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 >> C
Re: [Freesurfer] Freesurfer Start Up
The files after recon-all > On Jul 31, 2014, at 7:10 AM, "Bruce Fischl" > 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 >>> 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 >>>> 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 >>>> wrote: >>>> >>>> Hi Isaiah >>>> >>>> recon-all -i -s -sd >>> to put subject in> -all >>>> >>>> should do the trick. 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
Re: [Freesurfer] Freesurfer Start Up
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" > 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" >>> 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 >>>>> 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 >>>>>> >>>>>> 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 >>>>>> wrote: >>>>>> >>>>>>Hi Isaiah >>>>>> >>>>>>recon-all -i -s -sd >>>>>to put subject in> -all >>>>>> >>>>>>should do the trick. should be a *single* >>>>>>
Re: [Freesurfer] Freesurfer Start Up
Thanks Sent from my iPhone > On Jul 31, 2014, at 10:47 AM, "Bruce Fischl" > 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" >>> 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" >>>>> 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 >>>>>>> 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 >>>>>>>> >>>>>>>> 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: F
Re: [Freesurfer] Freesurfer Start Up
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 mailto:fis...@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" mailto:fis...@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" mailto:fis...@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 mailto:fis...@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 mailto:isaiah.c.smith...@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 wrote: Hi Isaiah recon-all -i -s -sd -all should do the trick. should be a *single* file in the right dicom series, or a .nii f
[Freesurfer] Freesurfer and MNE
I have the MRI data, but I am confused as to how to proceed with the mne_setup_mri for the brain, skull and scalp volume conduction models because the brain and T1 are the defaults. Do I need to add some other slices? And does the subject data need to be placed in /freesurfer/subjects for it to be read by MNE? Isaiah ___ 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] Flaws in my segmentation
Hello, There is some flaw in my segmentation that is not allowing me to change produce a mesh in MNE. How do I fix the segmentation in freesurfer so that skull surfaces do not overlap? Isaiah (Error Shown Below) Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = 8.85217e-16 * 4*PI). Could't create the geometry ___ 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] Output Time
Hello Experts, I was wondering if there is a way to short time of recon-all; I see that by using some of the parameters, one can get rid of different outputs. For mne forward models and inverses is there a recommended list of necessary and unnecessary outputs? Isaiah Smith ___ 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.
