Re: [Freesurfer] New to Freesurfer; cortical thickness
you have to run them separately On Fri, 27 May 2016, Marja Caverlé wrote: Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl wrote: the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote: Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl wrote: Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one
Re: [Freesurfer] New to Freesurfer; cortical thickness
whatever then environment variable SUBJECTS_DIR points to On Fri, 27 May 2016, Marja Caverlé wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl wrote: the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote: Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl wrote: Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar
Re: [Freesurfer] New to Freesurfer; cortical thickness
If you don't give it a -s option, the program will not run and there will not be any output On 5/26/16 10:43 AM, Marja Caverlé wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote: the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote: Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet. Thank you guys. Best, Marja
Re: [Freesurfer] New to Freesurfer; cortical thickness
Thanks Douglas! On Fri, May 27, 2016 at 1:02 AM, Douglas Greve wrote: > run them separately > > On 5/26/16 11:01 AM, Marja Caverlé wrote: > > Thanks! It runs now. But that still leaves me with the question whether I > can do all the patients in one run or that I have to run them separately. > > Best, > > Marja > > On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé > wrote: > >> Thanks Bruce, >> >> 001 was indeed the subject id, but I did not know it needed -s. >> If I don't specify the output directory, where will it be put? >> >> Best, >> >> Marja >> >> On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> >>> the subject id is something you make up. What is 001 in your example? >>> Maybe it is the subject ID? If so, preface it with -s. You probably also >>> want to specify the location of your output directory with -sd >> where you will put each subject> >>> >>> cheers >>> Bruce >>> >>> >>> On Fri, 27 May 2016, Marja Caverlé wrote: >>> >>> Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu> wrote: Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue
Re: [Freesurfer] New to Freesurfer; cortical thickness
run them separately On 5/26/16 11:01 AM, Marja Caverlé wrote: Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé mailto:marja.cave...@gmail.com>> wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote: the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote: Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does n
Re: [Freesurfer] New to Freesurfer; cortical thickness
Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé wrote: > Thanks Bruce, > > 001 was indeed the subject id, but I did not know it needed -s. > If I don't specify the output directory, where will it be put? > > Best, > > Marja > > On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl > wrote: > >> the subject id is something you make up. What is 001 in your example? >> Maybe it is the subject ID? If so, preface it with -s. You probably also >> want to specify the location of your output directory with -sd > where you will put each subject> >> >> cheers >> Bruce >> >> >> On Fri, 27 May 2016, Marja Caverlé wrote: >> >> Hi Bruce, >>> >>> Thank you for your response. I tried it many times and I kept getting the >>> same error like at the bottom of this email. >>> Why do you put the -s in there? and what exactly is the subject ID? FYI, >>> I >>> was already in the folder where the .nii.gz is located. And by your >>> answer >>> I assume I can do it only one patient at a time? >>> >>> Thanks, >>> >>> Marja >>> >>> --- >>> Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz >>> -all >>> >>> ERROR: Flag -001 unrecognized. >>> >>> -001 -i AD_TM001.nii.gz -all >>> >>> Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri >>> Feb >>> 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 >>> >>> >>> recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 >>> >>> >>> For more details, see the log file >>> >>> To report a problem, see >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin >>> --- >>> >>> >>> On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> Hi Marja >>> >>> can you send us the actual command and screen output you ran? It >>> should be something like: >>> >>> recon-all -all -s -i >>> >>> Depending on your hardware it will take hours to finish, but it >>> will do pretty much everything (segmentation, surface >>> reconstruction, template registration, thickness measurement, >>> parcellation, etc...) >>> >>>cheers >>> Bruce >>> >>> On Thu, 26 May 2016, Marja Caverlé wrote: >>> >>> Hi All, >>> >>> I am new to Freesurfer and I would like to use it >>> for a project I am working >>> on right now. For this project I have two patient >>> groups of which I have >>> structural MRI scans and a lot of other measures. I >>> hope to get cortical >>> thickness numbers from the scans and compare these >>> with the other measures. >>> >>> Anyway, I am trying to get something done in >>> Freesurfer and it does not >>> really seem to work. I assume I have to do a >>> recon-all -all, but when I try >>> this, I get an error saying that the flag is >>> unrecognised. It probably is a >>> small error, easy to solve, but I already get stuck >>> on it since I am totally >>> new to Freesurfer. >>> >>> Could anyone help me out? >>> Some of my questions are; >>> >>> - Am I correct that recon-all -all already >>> coregisters the scans to >>> template? >>> - What will be the outcome? Will I get pictures, or >>> a table with numbers, >>> and if it is a table, which area's are specified? I >>> have a list of ROIs, but >>> how do I let Freesurfer know I am interested in >>> those areas? >>> - Can I do recon-all -all on a folder with all my >>> patients, or do I have to >>> do it one by one? (There not that much, >>> approximately 12 scans) >>> - Can I do recon-all -all on .nii.gz files? The >>> originals are DICOM, but the >>> problem is that there is just one large DICOM >>> folder, which does not specify >>> which files are part of which scan. I have converted >>> them to .nii.gz since I >>> am a bit familiar with FSL, but I do not know >>> whether this actually works in >>> Freesurfer. >>> - Why do I get the unrecognised flag error? >>> >>> I apologise for these questions, they are probably >>> very easy to answer, but >>> I just don't have a clue yet. >>> >>> Thank you guys. >>> >>> Best, >>> >>> Marja >>> >>> >>> >>> >>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The inform
Re: [Freesurfer] New to Freesurfer; cortical thickness
Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl wrote: > the subject id is something you make up. What is 001 in your example? > Maybe it is the subject ID? If so, preface it with -s. You probably also > want to specify the location of your output directory with -sd where you will put each subject> > > cheers > Bruce > > > On Fri, 27 May 2016, Marja Caverlé wrote: > > Hi Bruce, >> >> Thank you for your response. I tried it many times and I kept getting the >> same error like at the bottom of this email. >> Why do you put the -s in there? and what exactly is the subject ID? FYI, I >> was already in the folder where the .nii.gz is located. And by your >> answer >> I assume I can do it only one patient at a time? >> >> Thanks, >> >> Marja >> >> --- >> Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz >> -all >> >> ERROR: Flag -001 unrecognized. >> >> -001 -i AD_TM001.nii.gz -all >> >> Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri >> Feb >> 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 >> >> >> recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 >> >> >> For more details, see the log file >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin >> --- >> >> >> On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Marja >> >> can you send us the actual command and screen output you ran? It >> should be something like: >> >> recon-all -all -s -i >> >> Depending on your hardware it will take hours to finish, but it >> will do pretty much everything (segmentation, surface >> reconstruction, template registration, thickness measurement, >> parcellation, etc...) >> >>cheers >> Bruce >> >> On Thu, 26 May 2016, Marja Caverlé wrote: >> >> Hi All, >> >> I am new to Freesurfer and I would like to use it >> for a project I am working >> on right now. For this project I have two patient >> groups of which I have >> structural MRI scans and a lot of other measures. I >> hope to get cortical >> thickness numbers from the scans and compare these >> with the other measures. >> >> Anyway, I am trying to get something done in >> Freesurfer and it does not >> really seem to work. I assume I have to do a >> recon-all -all, but when I try >> this, I get an error saying that the flag is >> unrecognised. It probably is a >> small error, easy to solve, but I already get stuck >> on it since I am totally >> new to Freesurfer. >> >> Could anyone help me out? >> Some of my questions are; >> >> - Am I correct that recon-all -all already >> coregisters the scans to >> template? >> - What will be the outcome? Will I get pictures, or >> a table with numbers, >> and if it is a table, which area's are specified? I >> have a list of ROIs, but >> how do I let Freesurfer know I am interested in >> those areas? >> - Can I do recon-all -all on a folder with all my >> patients, or do I have to >> do it one by one? (There not that much, >> approximately 12 scans) >> - Can I do recon-all -all on .nii.gz files? The >> originals are DICOM, but the >> problem is that there is just one large DICOM >> folder, which does not specify >> which files are part of which scan. I have converted >> them to .nii.gz since I >> am a bit familiar with FSL, but I do not know >> whether this actually works in >> Freesurfer. >> - Why do I get the unrecognised flag error? >> >> I apologise for these questions, they are probably >> very easy to answer, but >> I just don't have a clue yet. >> >> Thank you guys. >> >> Best, >> >> Marja >> >> >> >> >> >> >> >> ___ >> 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 co
Re: [Freesurfer] New to Freesurfer; cortical thickness
the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd where you will put each subject> cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote: Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl wrote: Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet. Thank you guys. Best, Marja ___ 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 dis
Re: [Freesurfer] New to Freesurfer; cortical thickness
Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time? Thanks, Marja --- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all ERROR: Flag -001 unrecognized. -001 -i AD_TM001.nii.gz -all Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin --- On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl wrote: > Hi Marja > > can you send us the actual command and screen output you ran? It should be > something like: > > recon-all -all -s -i > > Depending on your hardware it will take hours to finish, but it will do > pretty much everything (segmentation, surface reconstruction, template > registration, thickness measurement, parcellation, etc...) > > cheers > Bruce > > > On Thu, 26 May 2016, Marja Caverlé wrote: > > Hi All, >> >> I am new to Freesurfer and I would like to use it for a project I am >> working >> on right now. For this project I have two patient groups of which I have >> structural MRI scans and a lot of other measures. I hope to get cortical >> thickness numbers from the scans and compare these with the other >> measures. >> >> Anyway, I am trying to get something done in Freesurfer and it does not >> really seem to work. I assume I have to do a recon-all -all, but when I >> try >> this, I get an error saying that the flag is unrecognised. It probably is >> a >> small error, easy to solve, but I already get stuck on it since I am >> totally >> new to Freesurfer. >> >> Could anyone help me out? >> Some of my questions are; >> >> - Am I correct that recon-all -all already coregisters the scans to >> template? >> - What will be the outcome? Will I get pictures, or a table with numbers, >> and if it is a table, which area's are specified? I have a list of ROIs, >> but >> how do I let Freesurfer know I am interested in those areas? >> - Can I do recon-all -all on a folder with all my patients, or do I have >> to >> do it one by one? (There not that much, approximately 12 scans) >> - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but >> the >> problem is that there is just one large DICOM folder, which does not >> specify >> which files are part of which scan. I have converted them to .nii.gz >> since I >> am a bit familiar with FSL, but I do not know whether this actually works >> in >> Freesurfer. >> - Why do I get the unrecognised flag error? >> >> I apologise for these questions, they are probably very easy to answer, >> but >> I just don't have a clue yet. >> >> Thank you guys. >> >> Best, >> >> Marja >> >> >> >> >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] New to Freesurfer; cortical thickness
Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...) cheers Bruce On Thu, 26 May 2016, Marja Caverlé wrote: Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet. Thank you guys. Best, Marja ___ 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] New to Freesurfer; cortical thickness
Hi All, I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures. Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer. Could anyone help me out? Some of my questions are; - Am I correct that recon-all -all already coregisters the scans to template? - What will be the outcome? Will I get pictures, or a table with numbers, and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas? - Can I do recon-all -all on a folder with all my patients, or do I have to do it one by one? (There not that much, approximately 12 scans) - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer. - Why do I get the unrecognised flag error? I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet. Thank you guys. Best, Marja ___ 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.
