Re: [Freesurfer] midbrain mask
I have feared that. Sorry for asking, but do you have an atlas in mind for my purpose? Cheers Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 15. April 2015 19:04 An: Freesurfer support list Betreff: Re: [Freesurfer] midbrain mask oh, if you have no anatomical images then we can't help you Bruce On Wed, 15 Apr 2015, André Schmidt wrote: > Thanks Bruce. I'll try this. > > The problem is I have no anatomical images for my subjects. What can I use as > input volume in mri_extract_label? > > I want use this mask to extract time series afterwards. > > Thanks again. > > Best wishes > Andre > > > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce > Fischl [fis...@nmr.mgh.harvard.edu] > Gesendet: Mittwoch, 15. April 2015 18:18 > An: Freesurfer support list > Betreff: Re: [Freesurfer] midbrain mask > > p.s. sorry, maybe not brainstem, maybe "ventral diencephalon" > On Wed, 15 > Apr 2015, André Schmidt wrote: > >> Dear FS experts, >> Can you please guide me how to create a binary mask of the left midbrain >> (VTA, SN)? >> >> Thanks for your help >> Andre >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] midbrain mask
not if you don't have any anatomical images Bruce On Thu, 16 Apr 2015, André Schmidt wrote: I have feared that. Sorry for asking, but do you have an atlas in mind for my purpose? Cheers Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 15. April 2015 19:04 An: Freesurfer support list Betreff: Re: [Freesurfer] midbrain mask oh, if you have no anatomical images then we can't help you Bruce On Wed, 15 Apr 2015, André Schmidt wrote: Thanks Bruce. I'll try this. The problem is I have no anatomical images for my subjects. What can I use as input volume in mri_extract_label? I want use this mask to extract time series afterwards. Thanks again. Best wishes Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 15. April 2015 18:18 An: Freesurfer support list Betreff: Re: [Freesurfer] midbrain mask p.s. sorry, maybe not brainstem, maybe "ventral diencephalon" On Wed, 15 Apr 2015, André Schmidt wrote: Dear FS experts, Can you please guide me how to create a binary mask of the left midbrain (VTA, SN)? Thanks for your help Andre ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Advice - best method, longitudinal vs. cross-sectional
Hello All, I have pre-processed a subject that has T1 scans at 3 time points using the freesurfer cross-sectional and longitudinal methods. The results show a lot of variability. I have attached the plots. Any advice would be much appreciated. Thanks, Pradeep On Wed, Apr 15, 2015 at 5:26 PM, Pradeep wrote: > Hello All, > > I have pre-processed a subject that has T1 scans at 3 time using the > freesurfer cross-sectional and longitudinal methods. The results show a lot > of variability. I have attached the plots. Any advice would be much > appreciated. > > Thanks, > Pradeep > > On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu > wrote: > >> Thank you very much for your answer Bruce ! >> >> have a nice evening, >> >> Alex. >> >> >> Le 3 juin 14 7:6, Bruce Fischl a écrit : >> > Hi Alex >> > >> > I would think that longitudinal analysis is still the way to go as we >> try >> > to improve both reliability and sensitivity using the fact that we have >> > multiple scans/subject. >> > >> > cheers >> > Bruce >> > On Tue, 3 Jun 2014, Alexandru Hanganu wrote: >> > >> >> Hello Everyone, >> >> >> >> could someone please give us an advice about which method you consider >> is >> >> the best for our study ? >> >> >> >> we have two groups with MRI at Time 1. Each group received medication. >> After >> >> this we performed another MRI at Time 2 after 2 weeks. >> >> >> >> The best method for this study is a longitudinal one or a >> cross-sectional >> >> GLM ? >> >> >> >> We consider that the distance between the time points is too small, >> and the >> >> longitudinal method is not the best choice. Hence, this study should be >> >> treated as a cross-sectional one. In this case we think about >> performing a >> >> simple GLM with the contrasts: >> >> 0.5 0.5 0.5 0.5 >> >> or 1 -1 -1 1 >> >> >> >> for the groups: >> >> 1) grp 1 time 1 >> >> 2) grp 1 time 2 >> >> 3) grp 2 time 1 >> >> 4) grp 2 time 2 >> >> >> >> we are searching to see whether medication had any impact on the >> cortical >> >> morphology in each group and between the groups. >> >> >> >> Thank you ! >> >> Best regards, >> >> Alex. >> >> >> >> >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > The information in this e-mail is intended only for the person to whom >> it is >> > addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> > contains patient information, please contact the Partners Compliance >> HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> > but does not contain patient information, please contact the sender and >> properly >> > dispose of the e-mail. >> > >> > >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Installing FreeSurfer on Fedora 21
Zeke and others, I wanted to let you know that installing it on the local hard drive gets around the issues. I sincerely appreciate your help and thank you very much for the time taken in helping out. Many thanks, Ranjan > -Original Message- > From: zkauf...@nmr.mgh.harvard.edu > Sent: Wed, 15 Apr 2015 13:52:03 -0400 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 > > Ranjan, > > I installed Fedora21 onto a laptop. I then download and installed > freesurfer and, after installing a few basic packages (tcsh > libXcrnSaver), I was able to open freeview without any errors. > > Which means the "library not found" issue you are encountering has > something to do with your local environment. Either the filesystems you > are mounting or the extraction errors you encounter when untarring. As > Daniel suggests, you may want to confine this to your local disk. > > -Zeke > > > On 04/15/2015 10:03 AM, dgw wrote: >> Ranjan, >> >> You may want to try installing it on a local hard disk. Do you have >> any scratch space you can use on the computer? >> >> HTH, >> D >> >> On Tue, Apr 14, 2015 at 5:09 PM, Ranjan Maitra >> wrote: >>> Nick, >>> >>> Thanks! It does match in the gzipped tarball: >>> >>> ~$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz >>> 6642289df823ebc27de52af57e9b3989 >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz >>> >>> ~$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar >>> 8cf47fbcd0a675f7832986ee87c2d00f >>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar >>> >>> I don't think that this matters, but the filesystem is an Inselon OneFS >>> filesystem and is mounted on to my machine via a cifs mount. >>> >>> Many thanks, >>> Ranjan >>> >>> >>> >>> >>> -Original Message- From: ni...@nmr.mgh.harvard.edu Sent: Tue, 14 Apr 2015 16:26:50 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 Ranjan, after downloading, confirm the integrity of the tarball by running md5sum on it. you should get the following sum: 6642289df823ebc27de52af57e9b3989 also, make sure you have at least 4.2GB of space prior to download. some older partitions have a 4GB max size (probably not the case, but thought i'd mention it). Nick On Tue, 2015-04-14 at 12:06 -0800, Ranjan Maitra wrote: > Zeke, > > Thanks! > >> >> We support centos6 platform but we are currently unaware of any >> linux >> distributions in which freeview can not open. I dont not have >> immediate >> access to a Fedora21 system but I will attempt to install one and >> investigate this further. Please allow a day or so for a response. > > Thank you very much! > >> >> Lastly, it would make me feel a lot better if you could extract the >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz without >> getting >> any errors. Its possible something is getting corrupted along the >> way >> which is somehow responsible for this issue. > > I agree with you, but I have tried downloading and unpacking several > times, to no avail. Always the same error/message. (I use wget, but I > don't see why that should be a problem.) I can not see how to get > around > this. Do you have any other suggestions as to how to get around this? > > Many thanks, > Ranjan > > > > >> On 04/14/2015 03:15 PM, Ranjan Maitra wrote: >>> Zeke, >>> >>> Thanks again! >>> -Original Message- From: zkauf...@nmr.mgh.harvard.edu Sent: Tue, 14 Apr 2015 15:12:06 -0400 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21 Ranjan, Ok, the binaries appear work. So at the present moments the issue appears to only be with libvtkverdict.so.5.6.0 1) What happens if, right before you type the freeview command, you set the LD_LIBRARY_PATH environment variable as follows: (if bash) $> export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 $> freeview >>> >>> I tried this, to no avail: >>> >>> ~$ export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 >>> ~$ freeview >>> freeview.bin: error while loading shared libraries: >>> libvtkverdict.so.5.6: cannot open shared object file: No such file >>> or >>> directory >>> >>> (if csh) $> setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 $> freeview 2) What is the output when you perform an 'md5sum' on libvtkverdict.so.5.6.0
[Freesurfer] Is the linux centos package compiled with openmp enabled?
Hi, I've installed FreeSurfer from a binary package freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz., does that package was compiled witn ---enable-openmp? Thank you. Kind regards, - j ___ 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.
