Re: [Freesurfer] bbregister + mri_vol2vol different results

Hello Experts, Just to follow up on my previous posting, here is the information from the headrs of the different nifti files after the steps performed. * First, the header of the mean original nifti after realignment: qto_xyz:1 -1.099422 0.024665 0.025745 65.286888 qto_xyz:2 -0.02

Re: [Freesurfer] FS Version 6 Long Processing

Hi Allison, seems like autorecon2-pial has been removed from FreeSurfer (also in the cross sectional stream). I don't know when, why and what would be the equivalent command, but someone on the list will know. About brainmask edits, they are described here: https://surfer.nmr.mgh.harvard.ed

[Freesurfer] qcache ERROR on longitudinal image processing with FreeSurfer v6.0

Hello everyone, I'm using the new version of FreeSurfer processing with longitudinal image processing. And at the step -base after a recon-all processing i would like to make a qcache processing but it doesn't work... "cannot find [...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment lo

Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness

Hi Douglas Greve, Yes, I'm getting the same result as mentioned below. Regards, Janani - Did you get exact

Re: [Freesurfer] Pediatric Atlas/Template

Hi Jess, Yes, there are. But currently we are focusing on the 0-2yrs age range. Your age range of interest will come after that. Lilla On Thu, 13 Jul 2017, Jessica Reynolds wrote: I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with child

Re: [Freesurfer] Freesurfer pipeline for infant

Hi Gianluca, For your younger ages, this is the wiki that I would check: https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits We will look into the stats file. Best, Lilla On Tue, 11 Jul 2017, Gianluca Sforza wrote: Hi Lilla,is there a range of age I should possibly take more car

[Freesurfer] SPMPainting

I am confused that how to align the brain.img with my functional data in spm... https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting Best wishes! 1. Convert the brain.mgz volume to analyze: mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img 2. Align brain.img with your functional d

Re: [Freesurfer] SPMPainting

I am confused that how to align the brain.img with my functional data in spm... https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting Best wishes! 1. Convert the brain.mgz volume to analyze: mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img 2. Align brain.img with your functional d

Re: [Freesurfer] bbregister + mri_vol2vol different results

Hello again, I've found my mistake! Instead of using the brainmask from reconall for the target, I used the brain from the fsl ouput of BET. This is a mistake, since the two brains aren't aligned. I've corrected the mistake and now it works. Regards, Glad On 07/13/2017 11:02 PM, Paul Glad Mihai

Re: [Freesurfer] SPMPainting

use bbregister On 7/17/17 10:35 AM, Geng Shuang wrote: I am confused that how to align the brain.img with my functional data in spm... https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting Best wishes! 1. Convert the brain.mgz volu

Re: [Freesurfer] FS Version 6 Long Processing

Hi Martin I believe it has been replaced with -autorecon-pial (since some of the pial surface generation has moved to autorecon3) cheers Bruce On Mon, 17 Jul 2017, Martin Reuter wrote: Hi Allison, seems like autorecon2-pial has been removed from FreeSurfer (also in the cross sectional s

Re: [Freesurfer] bbregister + mri_vol2vol different results

glad it worked out Bruce On Mon, 17 Jul 2017, Paul Glad Mihai wrote: > Hello again, > > I've found my mistake! Instead of using the brainmask from reconall for > the target, I used the brain from the fsl ouput of BET. This is a > mistake, since the two brains aren't aligned. I've corrected the mis

Re: [Freesurfer] Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview

Hi Ursula, Since FS 6.0, freeview stopped displaying index 0 in the annotation look up table which is usually reserved as "unknown 0 0 0 0", so that it doesn't show a black region on the surface. Would it be possible for you change your indices starting from 1? I will also update freeview so t

Re: [Freesurfer] qcache ERROR on longitudinal image processing with FreeSurfer v6.0

you can run pctsurfcon --s subject On 07/17/2017 06:32 AM, Lisa Delalande wrote: > Hello everyone, > > I'm using the new version of FreeSurfer processing with longitudinal > image processing. And at the step -base after a recon-all processing i > would like to make a qcache processing but it d

Re: [Freesurfer] Fw: spmregister

Can you try tkregister --mov perfusion_calib.nii.gz --reg reg.dat On 07/14/2017 06:56 PM, John Anderson wrote: > > Hi Doug, > > It is the same command left by spmregister > freeview orig.mgz pcals.nii > > Just i excluded the flag -f /surf/?h.orig > > what is your freeview command? > > > > On 07/

Re: [Freesurfer] TalAviQA and mris_jacobian

cc'ing Avi who is the best person to shed light on TalAviQA. Not sure about the jacobian answer On 07/15/2017 03:25 PM, Helfand, Alexander I wrote: > Hi FreeSurfer Team, > > I was hoping I might be able to get some information about TalAviQA. I have > read that this number is a spatial correlat

[Freesurfer] dev -FLAIRpial bug?

Hi FS Devs, We're running some reconstructions of 7T MPRAGEs with the -FLAIRpial flag turned on using the Martinos install of the dev version. Recently we encountered the error in the attached recon-all log in which it appears that recon-all is trying to use the aseg.mgz before it has been crea

[Freesurfer] Monte-Carlo in LME

Dear FS experts, I was wondering if someone had performed multiple comparisons (ie monte-carlo) with the LME analyses. I have found a thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) where Doug recommends to run a GLM fit with the same data and then overwrite