Re: [Freesurfer] Reenviar: xhemi registration problem

Nick,Is not the one from the distribution, is the one on the FS-xhemi wikihttp://surfer.nmr.mgh.harvard.edu/fswiki/XhemiIf I use the one from my the fs v5.1 distribution, will it work as the one on the wiki???Thanks,GabrielEl 31/01/13, Nick Schmansky escribió:Gabriel,Where did you get the mri_con

Re: [Freesurfer] 回复: about ROI to SPSS

Dear experts I has obtained two ROIs (corrected FDR) difference between AA and GG regressing out the effect of age and gender using the QDEC, following extract the average surface area of two ROIs to analysis using SPSS, in which I used the univariate analysis of variance to find the differ

Re: [Freesurfer] Reenviar: xhemi registration problem

Gabriel, I think you will need the newer builds. Doug will need to update his links though to use Centos 4 binaries, which have an older glibc. (doug, you can get them from /space/freesurfer/centos4.0_x86_64). Alternatively, you could use our v5.2 beta, from here, which has everything you need:

[Freesurfer] longitudinal processing

Dear Freesurfer experts, I just tried creating the -base for longitudinal processing on two time points using recon-all -base -tp -tp ... -all After doing this, I received no error messages and a third folder named after the template name I had given it it was present in the subjects direct

[Freesurfer] Qdec

Freesurfer, I ran a group comparison using qdec and got my results showing the differences in the thickness between the groups. I want to take these results I see in the viewer and convert them to nifti format so I can use them in another software called MANGO. Which files do I need to conver

[Freesurfer] (no subject)

Dear Freesurfer Experts, Are the fsaverage files necessary for qdec analysis? Regards ___ 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 on

Re: [Freesurfer] question about MRF

Dear Bruce, Thank you for your help and the great work on Freesurfer! Best, Zhennan Zhennan Yan Department of Computer Science Rutgers University On 1/31/2013 1:43 PM, Bruce Fischl wrote: > 1. 40 subjects, 10 young, 10 middle ages, 10 elderly (healthy) and 10 > with AD. > > 2. Many small thing

Re: [Freesurfer] question about MRF

thanks Zhennan good luck and let us know if we can help Bruce On Fri, 1 Feb 2013, Zhennan Yan wrote: > Dear Bruce, > > Thank you for your help and the great work on Freesurfer! > > Best, > Zhennan > > Zhennan Yan > Department of Computer Science > Rutgers University > > On 1/31/2013 1:43 PM, Bru

Re: [Freesurfer] Reenviar: xhemi registration problem

Thanks Nick,Doug, will it be possible to update the mri_convert (I don't know if any of the other scripts has the same problem), as Nick said?I will like to not change my FS version, since I have some in-house scrips made for the v5.1 and the v5.2 is still a beta version.Thanks again,Gabriel.El 01/

Re: [Freesurfer] Error from mri_concat while using QDEC

Hi Doug Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a "\" at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. A

Re: [Freesurfer] Inaccurate transformation

Hi Doug I'm sorry it's fs_read_regdat.m a matlab script I found in the mail archive which converts the register.dat file into ras2ras transformation matrix.I want to use thess surfaces to extract vector normals in the diffusion space. Hope it's clear now Thanks! Shani On Thu, Jan 31, 2013 at 10:3

[Freesurfer] mrisReadTriangleFile failed

Experts, Having an issue with this error. It's complaining about rh.pial not matching rh.white, indicates there's no such file or directory and that mrisReadTriangleFile failed, and then proceeds to load without rh.pial. I tried loading rh.pial manually, but upon loading it immediately removes

Re: [Freesurfer] mrisReadTriangleFile failed

Hi Jon that means that one of the surfaces is out of date, usually because you edited and reran but not to completion. Try running recon-all -s -make all cheers Bruce p.s. ignore the "can't find file" thing. It really means it tried to read it, but found it wasn't the same topology as the ot

Re: [Freesurfer] mrisReadTriangleFile failed

OK, good deal! The first time I ran recon-all it exited with errors. That must be the issue. thanks, jon > >> Hi Jon >> >> that means that one of the surfaces is out of date, usually because you >> edited and reran but not to completion. Try running >> >> recon-all -s -make all >> >> cheer

Re: [Freesurfer] (no subject)

yes, unless you make your own average doug On 02/01/2013 09:42 AM, Linn Mittlestein wrote: > Dear Freesurfer Experts, > > Are the fsaverage files necessary for qdec analysis? > > Regards > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Qdec

QDEC will create an output folder. In that folder, there will be a folder for each contrast. In the contrast folder, there will be a sig.mgh file. this has the -log10(p) significance values. You can convert this to nifti with mri_convert, but it will still be on the surface. If you need it in

Re: [Freesurfer] Reenviar: xhemi registration problem

I have put new versions here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemi-reg Note that all of the xhemi stuff is technically 5.2, but with these patches, it works with 5.1 doug On 02/01/2013 11:09 AM, Gabriel Gonzalez Escamilla wrote: > Thanks Nick, > > Doug, will it b

Re: [Freesurfer] Inaccurate transformation

Hi Shani, I don't know anything about that program and can't vouch for it (which probably means that I wrote it:). Anyway, the way that I would do it would be to compute a new matrix: K = M*inv(T)*R where R is the register.dat and T is the vox2tkrRAS and M is the vox2scannerRAS of the DTI. Thes

[Freesurfer] slice timing correction and motion correction order

Can you tell me the order of the slice timing and motion correction steps in preproc-sess (freesurfer v 4.5)? From the wiki it looks like motion correction is done first (For MC the input will be f and the output will be fmc For STC the input will be fmc and the output will be fmcstc". However, w

Re: [Freesurfer] slice timing correction and motion correction order

Yes, it does MC then STC. This is a chronic problem that has never been solved. If you do STC first and there is significant motion, then the STC will be wrong. They really need to be done simultaneously. However, if you use an ascending or descending slice acq (instead of interleaved), then th

Re: [Freesurfer] Reenviar: xhemi registration problem

Thanks a lot!!I've download all the files, and I will try to use them tomorrow morning.Gabriel.El 01/02/13, Douglas N Greve escribió:I have put new versions here:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemi-regNote that all of the xhemi stuff is technically 5.2, but with th

Re: [Freesurfer] Qdec

Which options should I use when running mri_surf2vol? Crystal On 2/1/13 1:08 PM, "Douglas N Greve" wrote: > >QDEC will create an output folder. In that folder, there will be a >folder for each contrast. In the contrast folder, there will be a >sig.mgh file. this has the -log10(p) significance v

Re: [Freesurfer] question about MRF

Dear Bruce, I have mapped my labels to the Freesurfer labels. But when I tried the "mri_ca_label -R init_label.mgz norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca new_label.mgz", I got a "Segmentation fault" after "0 singular and 1812 ill-conditioned covariance

Re: [Freesurfer] Qdec

You can run it with --help to get more info, let me know if you have questions after that On 02/01/2013 05:08 PM, Franklin, Crystal G wrote: > Which options should I use when running mri_surf2vol? > > Crystal > > On 2/1/13 1:08 PM, "Douglas N Greve" wrote: > >> QDEC will create an output folder.

Re: [Freesurfer] question about MRF

that might be the problem. Specify nearest nbr resampling with -rt nearest on the mri_convert cmd line cheers Bruce On Fri, 1 Feb 2013, Zhennan Yan wrote: > Dear Bruce, > > I have mapped my labels to the Freesurfer labels. But when I tried the > "mri_ca_label -R init_label.mgz norm.mgz transfo

[Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

Hi Folks, Just wanted to share our experience with running FS 5.2-beta on Amazon Web Services (AWS). Basically, AWS has multiple instance types ( http://aws.amazon.com/ec2/instance-types/) and we were trying to figure out the most cost-effective approach. We ran two subjects through FS 5.2-beta o

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

Hi Mehul, Thank you for sharing this. Could you include how this would compare to a GPU AWS instance with FreeSurfer's GPU switch? Cheers, -Morgan On Feb 1, 2013, at 6:54 PM, Mehul Sampat wrote: > Hi Folks, > > Just wanted to share our experience with running FS 5.2-beta on Amazon Web > S

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

Hi Mehul did you specify the # of open mp threads on the recon-all cmd line? cheers Bruce On Fri, 1 Feb 2013, Mehul Sampat wrote: Hi Folks,  Just wanted to share our experience with running FS 5.2-beta on Amazon Web Services (AWS).  Basically, AWS has multiple instance types (http://aws.amazo

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

Hi Bruce, No I did not specify the # of open mp threads on the recon-all cmd line. These run times were obtained by running one subject per core. for example cc2.8xlarge has 8 cores and so we ran 8 subjects at once; Thanks for the info about the # of open mp threads options; I will look into it.