Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

Mike, Hi, a new mris_convert I’ve posted to the ftp site corrects this problem. It will now store the volume geometry info into two giiCoordSys structs, which an updated freeview will be able to read. mris_convert is here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos

Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF

Hi Kristina, Sorry, I misread your email slightly. I don't believe it is possible to get total CSF without some additional non-T1-weighted scans. The closest you can get is adding up all the ventricular volumes. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg26258.html http

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

Hi Nick, That works PERFECTLY! Thank you so much, it has been a big help! I hope I may ask you another question: I am actually trying to convert each freesurfer-label (from aparc.annot) into separate surfaces (not gifti-labels) So ideally I would convert lh.precentral.label > lh.precentral.gii.

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

Hi Bastian do you mean a surface that is only a piece of th original surface? You can use label2patch for that, but I'm not sure if we can convert patches to gifti. You should ask the FSL crew about label2surf though - we can't help with that. cheers Bruce On Thu, 29 May 2014, Bastian Cheng

[Freesurfer] asegstats2table Longitudinal data.

FS experts, The aim of this mail is about some errors I had encountered when I try to generate a table from some *.stats files obtained after a longitudinal analysis. After running the command : *long_stats_slopes --qdec ./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas v

Re: [Freesurfer] Longitudinal design

Hi Tudor, I don't think there is a way to speed things up. Let me know if you find a case where the template is blurry or has ghosts. It should not happen, but if it does it indicates a bad registratration, you'd have to run the mri_robust_template command with different parameters manually th

Re: [Freesurfer] asegstats2table Longitudinal data.

Hi Victor, I am also not sure, but why not use the flags --stack-rate and --stack-pc1 in the long_stats_slopes. It should do the trick. Best, Martin On 05/29/2014 11:47 AM, Victor Montal Blancafort wrote: FS experts, The aim of this mail is about some errors I had encountered when I try

Re: [Freesurfer] URGENT: Error in analyse

Yes! It worked! Thank you so much for all your help! Best Regards, Saloni On 28 May 2014 23:31, Douglas N Greve wrote: > > Daniel found your problem as he mentioned in his previous email (see > below). Change the qdec table to have the name of the subject be > 54987500_output. > > Also, I

Re: [Freesurfer] Longitudinal design

Tudor, in your virtual machine, make sure the 3D rendering option, or 'use hardware rendering' (or something like that) is enabled. this would be on the Windows VM config side of things. otherwise it will do software rendering which is painfully slow. Nick > Hi Tudor, > > I don't think there

[Freesurfer] Tracula with multi-shell data

Dear Anastasia et al. I have data DTI that has multiple b-values. I worked around this by skipping '-tensor', and sym linking 'mean_fsumsamples.nii.gz' to 'dtifit_FA.nii.gz'. However, at the end of 'trac-path', there is an error thrown. Specifically when 'dmri_pathstats' is called, because it

[Freesurfer] Surface Label to Nifti File

I'm trying to convert a surface label to a nifti file to use with functional surface data that is already in nifti format. The ultimate goal is to be able to use the converted surface label as a seed in gPPI analyses that is run in MATLAB. I've been able to use volume based seeds for the MNI305 su

[Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

Hi Due to aberrantly high for a few of the subjects, I ran recon-all -autorecon2-wm -randomness -autorecon3 –hemi ?h before, calculating the localGI index. However, I intended to use these data in a longitudinal stream. These subject that were reprocessed using recon-all -autorecon2-wm -ra

Re: [Freesurfer] FDR correction in Matlab

Hi help lme_mass_FDR and help /lme_mass_FDR2/ For help with input and output? Knut J On 05/26/2014 11:24 AM, Nandita Vijayakumar wrote: Hi FS team, I was wondering if you could help me with FDR correction for linear mixed models within Matlab. I have run FDR2 correction using the follo

Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

Hi Knut, Basically as you reprocessed totally your surfaces, yes it is safer to reprocess the longitudinal stream to make sure that everything is coherent. As for the smoothing, lGI is already inherently very smoothed, so you definitely have to take a lower FWHM than for thickness. When you ru

Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

Hi Marie Thank you for your reply. I have one additional question. Is there any difference in results when using Matlab 2012a compared to Matlab 2013b for localGI? Best regards, Knut J On 05/29/2014 11:05 PM, Marie Schaer wrote: > Hi Knut, > > Basically as you reprocessed totally your surfa

Re: [Freesurfer] Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing

Hi Knut, No, there is no difference in the results. At some point we had an issue with Matlab 2013, which was solved in the last FreeSurfer version. This issue makes the lGI crash, but as soon as it is solved the computation gets to the end with similar results independently on the Matlab vers