Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: tracula and recon-all

Hi Stefano - You need to download the file dmri_5.1_snow_leopard.tar.gz from the wiki page, unzip it, and copy ALL the files that come out into the same directory where you copied the trac-all update. The trac-all update doesn't solve the memory issue, for that you need the executables in

Re: [Freesurfer] Difficult results from our PD data

Hi Bruce, I checked the surface of every subject with tksurfer, inaccuracy's were founded in 13 of 140 subjects. These subjects were manually edited with control points and pial edits. Then i start recon-all on the subjects with edits again. After these procedure tksurfer showed a correct

Re: [Freesurfer] Qdec

I never received a reply, so I am reposting my message below. Any help would be greatly appreciated. Thanks in advance, Crystal On 2/4/13 10:35 AM, Franklin, Crystal G frankl...@uthscsa.edu wrote: So I ran mri_surf2vol --help and I am still a little confused on what to run. Where do I

Re: [Freesurfer] nu_estimate_np_and_em error during recon-all

Tudor, Sorry to hear its not working. There is a plan B: scrap our VirtualBox instance entirely and instead install FSL's VMWare (from their website). This has a 64b Centos, so upon successful installation of it, you would download our 64b centos freesurfer distribution. Nick On Wed,

Re: [Freesurfer] Memory Consumption of GPU-assisted Freesurfer?

The environment variable 'FREESURFER_CUDA_DEVICE' defines the device number of the GPU device. Although I dont think you will see much benefit in splitting the surface processing across two gpus, as the CUDA surface code is not as optimal as the volume-based mri_ca_register code for parallel

Re: [Freesurfer] invalid=766 recon-all

None of the text in bold is of concern. It appears that mri_ca_register was running, which can take many hours to complete. Nick On Mon, 2013-02-04 at 22:55 +0100, std...@virgilio.it wrote: Hi list, I'm running : recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject

Re: [Freesurfer] Qdec

something like mri_surf2vol --surfval sig.mgh --hemi lh --identity fsaverage --o sig.lh.vol.nii.gz doug On 02/06/2013 09:50 AM, Franklin, Crystal G wrote: I never received a reply, so I am reposting my message below. Any help would be greatly appreciated. Thanks in advance, Crystal On

[Freesurfer] Xhemi questions

Dear Doug and FreeSurfer experts,Thnak you so much for all your lasts responses!.I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions:given the command for interhemispheric comparisons:mri_glmfit --y lh.lh-rh.thickness.sm05.mgh

[Freesurfer] Problem with flip4fsl

Hi FreeSurfer community, I am trying to run 'trac-all -corr -c config file' on the tutorial data, specifically for the single subject: Diff001. To start from 'scratch', I've deleted all but the './scripts' and the './orig' directories in the Diff001 parent folder. When I run the following

[Freesurfer] Troubleshooting the preproc

Hi FreeSurfer community, I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for *Diff001* as the subject, specifically), running *trac-all -corr -c config dmrirc*. I am running the commands in * subjectID/scripts/trac-all.cmd* one by one because

Re: [Freesurfer] Difficult results from our PD data

Hi Stan, the VBM results may be picking up changes in GM volume. These volume changes may be driven by differences in surface area and would not necessarily show up in a thickness analysis. Maybe the surface area is increasing with performance but the thickness is decreasing. You can do a

Re: [Freesurfer] aparc2aseg for an averaged subject

Hi Paul, try this cd $SUBJECTS_DIR/youraveragesubjectname mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon youraveragesubjectname doug On 02/04/2013 02:40 PM, Paul Beach wrote: Hi Doug, Your suggestion to remove the

Re: [Freesurfer] FDR threshold on functional data

Hi Susan, try right clicking in the display window to remove the marks from the label. doug On 02/04/2013 03:08 PM, Susan Alice McLaughlin wrote: Hi, I am looking at functional group surface data analyzed with mri_glmfit in tksurfer (using Freesurfer 4.1). I would like to threshold using

[Freesurfer] Multi-voxel pattern analysis

Hi, I am very new to FreeSurfer, but would like to start using it for my research. In particular, I would like to know if I could do MVPA with FreeSurfer? Thanks. Luísa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Multi-voxel pattern analysis

Hi Luisa yes, Mert Sabuncu and Koen Van Leemput have developed a MVPA algorithm called RvoxM that I believe is state-of-the-art in terms of classification accuracy. Perhaps they can point you in the right direction? cheers Bruce On Thu, 7 Feb 2013, Luísa Pinto wrote: Hi, I am very new to

Re: [Freesurfer] mrisReadTriangleFile failed

Just had a cluster of computers lock up, unfortunately resulting in several freesurfer jobs terminating prior to completion. It's possible I may have a ton of this same error come tomorrow. Two questions 1) is there a way to tell if a surface is out of date without starting up tkmedit? 2)