Re: [Freesurfer] Delay

SubCortGrayVol on Mac is 208022 and 296990 on VM, for the same patient.Does the processing time have something to with the results,it varies a lot. On 29 January 2013 19:33, Nick Schmansky wrote: > Chikku, > > Can you send us your recon-all.log and recon-all.cmd files? I'd like to > inve

Re: [Freesurfer] Problem with glmfit: matrix is ill-conditioned

Hi Doug, It is indeed correct that columns 1 and 17 are highly correlated. However, for another version of the fsgd file, where the corresponding class and covariate values where identical but with other covariates (so leading to the same columns 1 and 17, other columns are different), all went

Re: [Freesurfer] beta

Hi Bruce, What do you mean: no support anymore or no new development? Cheers, Ed On 30 Jan 2013, at 13:41, Jacobs H (NP) wrote: > Message: 7 > Date: Mon, 21 Jan 2013 19:19:25 -0500 (EST) > From: Bruce Fischl > Subject: Re: [Freesurfer] beta > To: Colin Reveley > Cc: Joshua Lee , freesurfer@nm

Re: [Freesurfer] beta

Hi Ed I mean that the grant funding FreeSurfer maintainance didn't get renewed. We certainly will continue support and development, but it does have a substantial negative impact on the engineering we can do, such as getting rid of the 1mm restrictions. cheers Bruce On Wed, 30 Jan 2013, E

Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not have an FDR option). Are you using the FDR in QDEC? If so, it will display the voxel-wise threshold that realizes the FDR threshold. You can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where thresho

Re: [Freesurfer] bug repport mri_convert in freesurfer 5.1 segment fault on fedora 19

Knut, thanks for testing the other two builds and for filing the report. i noticed they had you run valgrind. if you want, i've put a debug build of mri_convert here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ running it in valgrind i think would output sou

Re: [Freesurfer] beta

This news is most unfortunate. We all appreciate the Freesurfer team's work. Freesurfer, and project's like these, provide a substantial multiplier effect to the productivity of the neuroscience community. There should be more funding for these types of neuroscience research infrastructure. - Joshu

Re: [Freesurfer] beta

thanks Joshua I wish study sections agreed with you. We will probably put in another support grant in the next year when I work up the energy to write one (they are quite dull). I'll probably request support letters at that time. cheers Bruce On Wed, 30 Jan 2013, Joshua Lee wrote: This

[Freesurfer] tracula batch processing

Hello Experts, Unfortunately I am currently only able to run  tracula on a personal computer, System Version:    Mac OS X 10.6.7 (10J869)   Kernel Version:    Darwin 10.7.0. I have no problem running a single subject on the dmrirc_single subject configuration file. When I try to run several sub

Re: [Freesurfer] tracula batch processing

Hi Cat - What's the "runlist" variable set to in the configuration file? a.y On Wed, 30 Jan 2013, Cat Chong wrote: Hello Experts, Unfortunately I am currently only able to run  tracula on a personal computer, System Version:    Mac OS X 10.6.7 (10J869)   Kernel Version:    Darwin 10.7.0. I

[Freesurfer] question about MRF

Dear freesurfer experts, I have questions about the MRF in Freesurfer: (1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown in fig.8 in paper: Whole Brain Segmentation: Aut

Re: [Freesurfer] mris_pmake

Hi Andrew -- First the good news: Indeed, there is a much simpler (and quicker way): mris_pmake --subj --hemi --surface --mpmProg autodijk --mpmArgs vertexPolar:0 --mpmOverlay euclidean If called with hemi=lh and surface=smoothwm, it will create an output overlay called lh.autodijk.crv.

Re: [Freesurfer] beta

thanks Fidel we will certainly take you up on it in the next submission Bruce On Wed, 30 Jan 2013, Fidel Vila wrote: > Sorry to hear about this. If there is anything it can be done at a > "FS-virtual-community" level that could support the funding request, I'd be > supportive of it. > > Fidel

Re: [Freesurfer] question about MRF

Hi Zhennan there is an option to mri_ca_label to read in a prior segmentation and iterate the MRF minimization, but unless your labels and conventions are identical to our's it's unlikely to work. You can use mri_ca_train to build the MRF and likelihoods and such if you want. cheers Bruce On

[Freesurfer] tracula longitudinal

Hello Experts, Please forgive another question. I have run 59 people through the recon-all freesurfer longitudinal stream with 2 timepoints (tp1id, tp2id). I want to run these subjects through "tracula" next, since the same people also received repeated Tensor imaging. To process everybody t

Re: [Freesurfer] Delay

oh, that's way too big a difference. Something is wrong On Wed, 30 Jan 2013, Varghese Chikku wrote: SubCortGrayVol  on Mac is 208022 and 296990 on VM, for the  same patient.Does  the processing time  have  something to with the  results,it varies  a  lot. On 29 January 2013 19:33, Nick Schman

Re: [Freesurfer] ERROR: aparcstats2table

The options for these 3: GausCurv FoldInd CurvInd do not exist when I use the -h Thanks, Catherine On 1/29/13, Douglas N Greve wrote: > yes, use the -m or --meas flags. If you run it with -h, you will get > help and examples > doug > On 01/29/2013 04:12 PM, Nucleos P wrote: >> Hello again! >> >>

Re: [Freesurfer] tracula longitudinal

Hi Catherine - Yes, for now treat each time point as a different subject for trac-all purposes. (You can pass the time points' recon-all directories either before or after longitudinal processing.) However, there may also be a longitudinal version of tracula coming soon - but you didn't hear