[Freesurfer] Reliability of labeling procedure in the same scan
Hi all, Without noticing I run recon-all twice on the same scan of the same subject and we noticed there are some differences, at least in the hippocampal volume estimation. Is it normal? If it is, why is it so? Thank you so much for your help This is a great community! ___ 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] differences between OS recon all output, longitudinal data
Oks, thank you! Last question! And using CUDA this time... would the results also differ? 2016-11-15 16:18 GMT+01:00 Z K <zkauf...@nmr.mgh.harvard.edu>: > > > On 11/15/2016 07:21 AM, anonymous anonymous wrote: > >> Thank you so much for the extense answer! >> >> It happens that the person who analysed the first measure (of this >> longitudinal dataset) used two different OS (he did it in a Virtual >> machine on windows and a mac OS X) to speed up this step. That data has >> already been used in some studies. >> >> >> ¿So my question now would be how much does that really affect to the >> results? >> > > It is impossible to know for sure without processing the results on the > same OS. My guess is quite small, generally we see results differ on the > order of 5% or less, but still potentially enough to introduce bias. > > > > >> >> >> >> >> >> >> Hi >>> >>> I am using recon-all in some longitudinal data on a ubuntu 16.04, and >>> using >>> the development version of freesurfer as I was told here, because the >>> other >>> current version doesnt work on ubuntu 16.04. >>> >>> The problem is that the first scans were probablly processed using >>> virtualbox in a windows and an older version of freesurfer. >>> >>> >>> i think I already know the answer, that I can't do this if I dont want to >>> bias my results. Can I? >>> >> >> Yup. You know the answer ;) However, I did discover a way to make >> freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install >> an older version of perl : >> >> 1) install perlbrew: >> >> $> sudo apt-get install perlbrew >> >> 2) use perlbrew to install perl version 5.20.3: >> >> $> perlbrew install perl-5.20.3 >> >> 3) You must change the '/bin/perl' file to a link which points to the >> version of perl installed by perlbrew. (This technique is not the >> standard practice but it is the only way to get the mni tools to use the >> older version of perl): >> >> $> cd /bin >> $> sudo mv perl perl.orig (can always set back later) >> $> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl >> >> >> >>> But I'm using a better computer now and I use the one with windows for >>> other analyses, so I wanted to know if I could install Virtual box on my >>> ubuntu 16.04 computer, and install the same version of linux used to >>> process the first measure. Should I also need to use the same version of >>> freesurfer? >>> >> >> >> You could do that, but The Virtual Box version is not really good for >> processing a large number of subjects because of the limited amount of >> disk space on the virtual image. Its really meant more as a teaching tool >> for users with Windows machines. >> >> >>> f the computer's specs are dfferent, does it matter? And if I assign >>> different cpu and ram on my virtual machine? >>> >> >> Different specs are fine. Its the OS, OS version, and version of >> freesurfer that should stay the same. >> >> >> >>> Thank you! >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> <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] differences between OS recon all output, longitudinal data
Thank you so much for the extense answer! It happens that the person who analysed the first measure (of this longitudinal dataset) used two different OS (he did it in a Virtual machine on windows and a mac OS X) to speed up this step. That data has already been used in some studies. ¿So my question now would be how much does that really affect to the results? > Hi > > I am using recon-all in some longitudinal data on a ubuntu 16.04, and > using > the development version of freesurfer as I was told here, because the > other > current version doesnt work on ubuntu 16.04. > > The problem is that the first scans were probablly processed using > virtualbox in a windows and an older version of freesurfer. > > > i think I already know the answer, that I can't do this if I dont want to > bias my results. Can I? Yup. You know the answer ;) However, I did discover a way to make freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install an older version of perl : 1) install perlbrew: $> sudo apt-get install perlbrew 2) use perlbrew to install perl version 5.20.3: $> perlbrew install perl-5.20.3 3) You must change the '/bin/perl' file to a link which points to the version of perl installed by perlbrew. (This technique is not the standard practice but it is the only way to get the mni tools to use the older version of perl): $> cd /bin $> sudo mv perl perl.orig (can always set back later) $> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl > > But I'm using a better computer now and I use the one with windows for > other analyses, so I wanted to know if I could install Virtual box on my > ubuntu 16.04 computer, and install the same version of linux used to > process the first measure. Should I also need to use the same version of > freesurfer? You could do that, but The Virtual Box version is not really good for processing a large number of subjects because of the limited amount of disk space on the virtual image. Its really meant more as a teaching tool for users with Windows machines. > > f the computer's specs are dfferent, does it matter? And if I assign > different cpu and ram on my virtual machine? Different specs are fine. Its the OS, OS version, and version of freesurfer that should stay the same. > > Thank you! > ___ > 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] differences between OS recon all output, longitudinal data
Hi I am using recon-all in some longitudinal data on a ubuntu 16.04, and using the development version of freesurfer as I was told here, because the other current version doesnt work on ubuntu 16.04. The problem is that the first scans were probablly processed using virtualbox in a windows and an older version of freesurfer. i think I already know the answer, that I can't do this if I dont want to bias my results. Can I? But I'm using a better computer now and I use the one with windows for other analyses, so I wanted to know if I could install Virtual box on my ubuntu 16.04 computer, and install the same version of linux used to process the first measure. Should I also need to use the same version of freesurfer? f the computer's specs are dfferent, does it matter? And if I assign different cpu and ram on my virtual machine? Thank you! ___ 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] CUDA 8.0 and error on recon-all nu_correct
Hi all, I'm new to freesurfer and I'm having some issues. 1) First of all I tried recon-all in one subject but I got an error on nu_correct. This is what the log says: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct I searched through the mail list and I found that it may be because my data is in an external hard drive... (the hard drive is in FAT32). But it's not because the data is in the external hard drive. I copied a folder to my computer and I got the same problem. Could it be the data? 2) Then I tried to install CUDA 8.0 ... I don't know if succesfully because the command cudadetect shows the following: cudadetect.bin: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Reading as well I'm afraid that freesurfer may not be able to use versions of CUDA that are +5? I have an NVIDIA Geforce GTX 950 and using NVIDIA binary driver version 370.28. 3) I think after the installation of CUDA using a .deb I got the paths messed up and now I can't even use recon-all on my hard drive. When I type recon-all on any other external hard drive or folder, it does show the information though. I dont know if it's a permissions problem (I also had a blackout earlier...) but the hard disk's files and folders seem to have all permissions and the ownership is root:root. I can't remount it now because I'm running some things using fsl... Please any help would be really appreciated. I've spent a lt of hours struggling with all these. I'm on a ubuntu 16.04 by the way. Thaankius ___ 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.
