[Freesurfer] (no subject)
External Email - Use Caution Hi experts I use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram. When i use mri_cvs_register as: mri_cvs_register --mov subjid --mni or mri_cvs_register --mov subjid --template subjid in both cases it stops in step 2 by diffrent errors. I asked zollei this problem and she sujest that it is ram problem. My question is: If it is true. How many ram this command needs? Thanks Nader Phd student in medical engineering Alzheimer research project ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
External Email - Use Caution Thanks alot lilla. Nader On Tue, 29 Oct 2019, 19:37 Lilla Zollei > Our default setting to run mrri_cvs_register on our cluster is to use > 35gb. > Lilla > > On Tue, 29 Oct 2019, Nader Razmara wrote: > > > > > Hi expertsI use freesurfer vm 5.3 on oracle vb 6 with 8 GB ram. > > When i use mri_cvs_register as: > > mri_cvs_register --mov subjid --mni or > > mri_cvs_register --mov subjid --template subjid in both cases it stops > in step 2 by diffrent errors. I asked zollei this problem and she sujest > that it is ram problem. > > My question is: > > If it is true. How many ram this command needs? > > Thanks > > Nader > > Phd student in medical engineering > > Alzheimer research project > > > > > >___ > 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] registration
External Email - Use Caution Instead of mri_cvs_register Which type of registration is more accurate or coparative to this. Best Regards Nader ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_cvs_register: no such file or directory
External Email - Use Caution Hi Check your subject and template address directory. On Sat, 16 Nov 2019, 01:05 Vinny K External Email - Use Caution > > Hi, > > I'm using the development version of FreeSurfer and am attempting to > register two subjects using mri_cvs_register. > > This is the command I ran: > > mri_cvs_register --mov subjb/ --template subja/ > > Below was the outputted message: > > The outdir: > /home/vinny/Tools/freesurfer/subjects/subjb//cvs > > Log file is > /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log > > /home/vinny/Tools/freesurfer/subjects/subjb//cvs/subjb/_to_subja/.mri_cvs_register.1911151623.log: > No such file or directory. > > Thanks, > > Vinny > ___ > 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
Re: [Freesurfer] Save output as attach file
External Email - Use Caution Thanks a lot. As yuo see in attach i have opened an aseg.mgz which i have made with recon-all. In freeview i thicked lookup table and outline. As you see this is appearance of what i did. Now i want to save this as a new mgz file which when i opened it with other image softwares i have this apearanse. Is it possibe? Best regards Nader Neuroimaging phd student On 21 Dec 2019 18:36, "Bruce Fischl" wrote: sorry, can you clarify what you mean? Isn't the attachment already a saved output of freeview? I don't understand what you are trying to do cheers Bruce On Sat, 21 Dec 2019, Nader Razmara wrote: > > External Email - Use Caution > > Dear I want to save output of freeview as attach file. Which is a > segmentation after thick colourmap ad lookptable and thick outline. > Best regards > > >___ 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
Re: [Freesurfer] Save output as attach file
External Email - Use Caution Dear Bruce Thats correct. Regards Nader On 21 Dec 2019 18:49, "Bruce Fischl" wrote: oh, you want to save a volume that has just the borders of each structure labeled? I'm not sure we have anything that can do that. Ruopeng: can freeview? cheers Bruce On Sat, 21 Dec 2019, Nader Razmara wrote: > > External Email - Use Caution > > Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i have > made with recon-all. In freeview i thicked lookup table and outline. As you > see this is appearance of what i did. Now i want to save this as a new mgz > file which when i opened it with other image softwares i have this > apearanse. > Is it possibe? > Best regards > Nader > Neuroimaging phd student > > On 21 Dec 2019 18:36, "Bruce Fischl" wrote: > sorry, can you clarify what you mean? Isn't the attachment > already a > saved output of freeview? I don't understand what you are trying > to do > > cheers > Bruce > On > Sat, 21 Dec 2019, Nader Razmara wrote: > > > > > External Email - Use Caution > > > > Dear I want to save output of freeview as attach file. Which > is a > > segmentation after thick colourmap ad lookptable and thick > outline. > > Best regards > > > > > >___ > 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
Re: [Freesurfer] Save output as attach file
External Email - Use Caution Hi Roupeng Can i hope you do it soon. It is an important part of my phd thesis. Best regards and best wishes Nader On 23 Dec 2019 19:24, "Ruopeng Wang" wrote: Hi Nader, Freeview can't do that currently. But I will add an option for it. Best, Ruopeng On 12/21/19 10:19 AM, Bruce Fischl wrote: > oh, you want to save a volume that has just the borders of each > structure labeled? I'm not sure we have anything that can do that. > Ruopeng: can freeview? > > cheers > Bruce > > > On Sat, 21 Dec 2019, Nader Razmara wrote: > >> >> External Email - Use Caution >> >> Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i have >> made with recon-all. In freeview i thicked lookup table and outline. >> As you >> see this is appearance of what i did. Now i want to save this as a >> new mgz >> file which when i opened it with other image softwares i have this >> apearanse. >> Is it possibe? >> Best regards >> Nader >> Neuroimaging phd student >> >> On 21 Dec 2019 18:36, "Bruce Fischl" wrote: >> sorry, can you clarify what you mean? Isn't the attachment >> already a >> saved output of freeview? I don't understand what you are trying >> to do >> >> cheers >> Bruce >> On >> Sat, 21 Dec 2019, Nader Razmara wrote: >> >> > >> > External Email - Use Caution >> > >> > Dear I want to save output of freeview as attach file. Which >> is a >> > segmentation after thick colourmap ad lookptable and thick >> outline. >> > Best regards >> > >> > >> >___ >> 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
Re: [Freesurfer] Save output as attach file
External Email - Use Caution Dear Ruopeng Thanks a lot for what you did. But I have installed and work with freesurfer Disk image 5.3 not freesurfer V6. Can i do this procedure to update freeview on it or i must install v6. Best regards and best wishes. Nader On Tue, 24 Dec 2019, 19:09 Ruopeng Wang Hi Nadar, > > I’ve added a new volume filter called “Boundary” in menu Tools -> Volume > Filters. You can apply it to your volume and then save volume as. Here is > an instruction on how to update to the latest freeview: > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > > Best, > Ruopeng > > > On Dec 23, 2019, at 10:59 AM, Nader Razmara wrote: > > External Email - Use Caution > > Hi Roupeng > Can i hope you do it soon. > It is an important part of my phd thesis. > Best regards and best wishes > Nader > > On 23 Dec 2019 19:24, "Ruopeng Wang" wrote: > > Hi Nader, > > Freeview can't do that currently. But I will add an option for it. > > Best, > Ruopeng > > > On 12/21/19 10:19 AM, Bruce Fischl wrote: > > oh, you want to save a volume that has just the borders of each > > structure labeled? I'm not sure we have anything that can do that. > > Ruopeng: can freeview? > > > > cheers > > Bruce > > > > > > On Sat, 21 Dec 2019, Nader Razmara wrote: > > > >> > >> External Email - Use Caution > >> > >> Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i have > >> made with recon-all. In freeview i thicked lookup table and outline. > >> As you > >> see this is appearance of what i did. Now i want to save this as a > >> new mgz > >> file which when i opened it with other image softwares i have this > >> apearanse. > >> Is it possibe? > >> Best regards > >> Nader > >> Neuroimaging phd student > >> > >> On 21 Dec 2019 18:36, "Bruce Fischl" > wrote: > >> sorry, can you clarify what you mean? Isn't the attachment > >> already a > >> saved output of freeview? I don't understand what you are trying > >> to do > >> > >> cheers > >> Bruce > >> On > >> Sat, 21 Dec 2019, Nader Razmara wrote: > >> > >> > > >> > External Email - Use Caution > >> > > >> > Dear I want to save output of freeview as attach file. Which > >> is a > >> > segmentation after thick colourmap ad lookptable and thick > >> outline. > >> > Best regards > >> > > >> > > >> >___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Save output as attach file
External Email - Use Caution Dear Ruopeng Thanks a lot. Thanks a lot. Best Regards and wishes Nader On Tue, 24 Dec 2019, 21:27 Ruopeng Wang You can go ahead and try it. > > Ruopeng > > On Dec 24, 2019, at 12:09 PM, Nader Razmara wrote: > > External Email - Use Caution > > Dear Ruopeng > Thanks a lot for what you did. > But I have installed and work with freesurfer Disk image 5.3 not > freesurfer V6. > Can i do this procedure to update freeview on it or i must install v6. > Best regards and best wishes. > Nader > > > On Tue, 24 Dec 2019, 19:09 Ruopeng Wang >> Hi Nadar, >> >> I’ve added a new volume filter called “Boundary” in menu Tools -> Volume >> Filters. You can apply it to your volume and then save volume as. Here is >> an instruction on how to update to the latest freeview: >> https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview >> >> Best, >> Ruopeng >> >> >> On Dec 23, 2019, at 10:59 AM, Nader Razmara wrote: >> >> External Email - Use Caution >> >> Hi Roupeng >> Can i hope you do it soon. >> It is an important part of my phd thesis. >> Best regards and best wishes >> Nader >> >> On 23 Dec 2019 19:24, "Ruopeng Wang" wrote: >> >> Hi Nader, >> >> Freeview can't do that currently. But I will add an option for it. >> >> Best, >> Ruopeng >> >> >> On 12/21/19 10:19 AM, Bruce Fischl wrote: >> > oh, you want to save a volume that has just the borders of each >> > structure labeled? I'm not sure we have anything that can do that. >> > Ruopeng: can freeview? >> > >> > cheers >> > Bruce >> > >> > >> > On Sat, 21 Dec 2019, Nader Razmara wrote: >> > >> >> >> >> External Email - Use Caution >> >> >> >> Thanks a lot.As yuo see in attach i have opened an aseg.mgz which i >> have >> >> made with recon-all. In freeview i thicked lookup table and outline. >> >> As you >> >> see this is appearance of what i did. Now i want to save this as a >> >> new mgz >> >> file which when i opened it with other image softwares i have this >> >> apearanse. >> >> Is it possibe? >> >> Best regards >> >> Nader >> >> Neuroimaging phd student >> >> >> >> On 21 Dec 2019 18:36, "Bruce Fischl" >> wrote: >> >> sorry, can you clarify what you mean? Isn't the attachment >> >> already a >> >> saved output of freeview? I don't understand what you are trying >> >> to do >> >> >> >> cheers >> >> Bruce >> >> On >> >> Sat, 21 Dec 2019, Nader Razmara wrote: >> >> >> >> > >> >> > External Email - Use Caution >> >> > >> >> > Dear I want to save output of freeview as attach file. Which >> >> is a >> >> > segmentation after thick colourmap ad lookptable and thick >> >> outline. >> >> > Best regards >> >> > >> >> > >> >> >___ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
