Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-11 Thread SHAHIN NASR
Sorry that I keep on asking questions but I want to know if using a model can significantly increase the chance of getting a significant response. As far as I see for the positive peak, when I use a model (e.g. gamma model or spmhrf), I see a more significant response compared to when I use

[Freesurfer] Surfaces to *native* space

2013-04-11 Thread Oscar Esteban
Dear all, I think my issue is quite related to this one (if not duplicated, sorry in that case): https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.html As Shani, I used bbregister to coregister diffusion images to anatomical: bbregister --s OE0_T1 --mov

[Freesurfer] mgz to dicom

2013-04-11 Thread Varghese Chikku
Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ 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 only for

[Freesurfer] DTI: problems with (high) FA values

2013-04-11 Thread Rotem Saar
Hi Douge, In your last reply to my email (that contained questions regarding some really high FA values - see recent emails below), u asked me to write u the first value in register.dat.mincost - I'm copying the line I have: 0.280554 140.210312 156.795241 11.152485 Does this takes us one step

Re: [Freesurfer] mgz to dicom

2013-04-11 Thread Bruce Fischl
Sorry, we don't write dicom usually, just read it Bruce On Apr 11, 2013, at 8:27 AM, Varghese Chikku chik...@tcd.ie wrote: Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ Freesurfer mailing list

Re: [Freesurfer] merging dti data

2013-04-11 Thread Jon Wieser
Those commands were given to me by Anastasia. they work fine for merging two whole brain datasets. jon - Original Message - From: Douglas Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, April 10, 2013 10:13:05 PM Subject: Re: [Freesurfer] merging dti

[Freesurfer] Transform SMOOTHWM to DTI B0

2013-04-11 Thread Daniel Haehn
Hi all, I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space. I found http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but this describes transforming the B0 to T1 space and then match the surfaces. I don't want to change the DTI B0 image. What is the best

Re: [Freesurfer] Transform SMOOTHWM to DTI B0

2013-04-11 Thread Satrajit Ghosh
hi dan, if you use bbregister to match the DTI b0 to freesurfer space, then you can transform the surface back (no guarantees on the tesselations though i think). the only additional component here would be a tkr transform that's based on the conformed space. i might even have some python code

Re: [Freesurfer] Transform SMOOTHWM to DTI B0

2013-04-11 Thread Shantanu Ghosh
Hi Satra, I have been trying to do that too. Do you have it as Nipy code? Thanks. Shantanu On Thu, April 11, 2013 10:53 am, Satrajit Ghosh wrote: hi dan, if you use bbregister to match the DTI b0 to freesurfer space, then you can transform the surface back (no guarantees on the tesselations

Re: [Freesurfer] merging dti data

2013-04-11 Thread Douglas Greve
yes, they work for whole brain, but not if you have two brain halves. You might be able to do something in matlab. I assume the gradient direction order was the same for both slabs? doug On 4/11/13 10:36 AM, Jon Wieser wrote: Those commands were given to me by Anastasia. they work fine for

[Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Lucille Deroche
Hi,  My name is Lucille and I'm really new  with Freesurfer : My questions are very basic, sorry. I just start a project in segmentation of cerebrum.   For converting a surface in volume. I would like to use mri_surf2vol but for that I need a  volume registration file . For creating that file, I

Re: [Freesurfer] merging dti data

2013-04-11 Thread Jon Wieser
the gradients were the same for each slab. What is the difficulty with runnning the merged brain halves in tracula? I have another to do it that I am going to try. I made AFNI Brik's of the two slabs, and merged them together into one AFNI brik with the AFNI command 3dZcat. I made a nifti

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Bruce Fischl
Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi,  My name is Lucille and I'm really new  with Freesurfer : My questions are very

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Lucille Deroche
Hi Bruce,   In fact, have 2 differents  surfaces  of pial surface. I would like to save my surfaces in volume to be able to calculate the dice score between the two.  Cheers  Lucille De : Bruce Fischl fis...@nmr.mgh.harvard.edu À : Lucille Deroche

Re: [Freesurfer] tracula FS 5.2

2013-04-11 Thread Antonenko, Daria
Hi Anastasia, I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has 8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this computer. Daria - Daria Antonenko, Dipl.-Psych. Charité - Universitätsmedizin

Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

2013-04-11 Thread Douglas N Greve
Yes, assuming a shape will give you much more power, at least for the individual subject. doug On 04/11/2013 02:55 AM, SHAHIN NASR wrote: Sorry that I keep on asking questions but I want to know if using a model can significantly increase the chance of getting a significant response.

Re: [Freesurfer] mri_aparc2aseg issue

2013-04-11 Thread Douglas N Greve
Hi Paul, try using this color table, something like tkmedit HS_001 orig.mgz -seg aug_aparc+aseg.mgz paul.ctab doug On 04/08/2013 10:02 AM, Paul Beach wrote: Hi Freesurfers, I'm currently trying to take manually made ROIs (label files) that have been incorporated into new annotation files

[Freesurfer] LME and clusterwise correction

2013-04-11 Thread Benjamín Garzón
Hi, I am doing a longitudinal analysis using the LME toolbox, and I would like to perform a clusterwise correction for multiple comparisons. Would it be correct to use mri_surfcluster on the resulting maps, or do you suggest any alternative otherwise ? I can only find functions implementing

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Douglas N Greve
Hi Lucile, don't use autoreg-sess (that is an old program and was for fMRI). Use mri_surf2vol with --identity subjectname instead of --reg doug On 04/11/2013 11:45 AM, Lucille Deroche wrote: Hi Bruce, In fact, have 2 differents surfaces of pial surface. I would like to save my surfaces

Re: [Freesurfer] DTI: problems with (high) FA values

2013-04-11 Thread Douglas N Greve
That is a good value, so the regis not the problem. If you upload your dt_recon folder as well as your recon-all folder for that subject I'll take a look. doug On 04/11/2013 10:02 AM, Rotem Saar wrote: Hi Douge, In your last reply to my email (that contained questions regarding some really

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

2013-04-11 Thread Yang, Daniel
Hi PPJ and all, I found that the 5.2 – 5.1 difference is primarily seen in the cortical thickness, and much less so in the aseg.volume. Here, I picked right-amygdala volume as an example of aseg.volume and rh_bankssts_thickness as an example of rh.aparc.thickness. While the correlation

[Freesurfer] Fwd: Sample size estimation from LME models

2013-04-11 Thread nicolas guizard
Hi, I am new to Freesurfer and the Linear Mixed Effects (LME) Models packages. And I would like to compute sample size from volumetric measures for 2 groups. I followed the longitudinal example provided in the wiki (

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

2013-04-11 Thread Yang, Daniel
Thanks Nick! I have uploaded the relevant files to you. Thanks, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 4/10/13 1:19 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Daniel, We're repeating our

[Freesurfer] final skull-stripped file?

2013-04-11 Thread Marco Loggia, PhD
Dear all, what is the 'best' skull stripped file produced by freesurfer? From what I see, it would seem to be 'brainmask'. However this file -if I understand correctly- is produced in the very first stages of recon-all, and therefore does not take advantage of the detailed reconstruction of

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Michael Harms
Try: mri_surf2vol --surf pial --mkmask --hemi lh --identity subjid --template subjid/mri/norm.mgz --o subjid/mri/pial_in_vol.mgz FWIW, I'm not sure if sampling two surfaces to the volume, and then computing a dice coefficient is really the best way to compare two surfaces. I would instead

Re: [Freesurfer] merging dti data

2013-04-11 Thread Jon Wieser
Hi Doug I can motion correct the briks with 3dvolreg Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, April 11, 2013 11:22:13 AM Subject: Re: [Freesurfer] merging dti data

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Bruce Fischl
yes, I agree. Two surfaces could be extremely close and have 0 dice. I don't think it would be as informative as Hausdorff or RMS as Mike suggests Bruce On Thu, 11 Apr 2013, Michael Harms wrote: Try: mri_surf2vol --surf pial --mkmask --hemi lh --identity subjid --template

Re: [Freesurfer] final skull-stripped file?

2013-04-11 Thread Douglas N Greve
Hi Marco, the aparc+aseg.mgz is probably going to be the best one (it is what I use:). When you binarize it, you can dilate it by a voxel as well with: mri_binarize --i aparc+aseg.mgz --min 0.5 --dilate 1 --o yourmask.mgz doug On 04/11/2013 03:31 PM, Marco Loggia, PhD wrote: Dear all,

Re: [Freesurfer] Fwd: Sample size estimation from LME models

2013-04-11 Thread jorge luis
Hi Nicolas The common random effects design matrix expression  means that all subjects in your prospective study are expected in advance to have the same random effects design matrix (Zi). If you assume a linear trajectory over time and a two-year study with repeated measurements every six

Re: [Freesurfer] bblabel values for DLPFC

2013-04-11 Thread Anupa AV
Dear Doug, I used bblabel for making coronal cut. The definition is given below. bblabel Applies a bounding box to a label. The bounding box is specified by six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label points within this box are copied to the output. If a min is not