Re: [Freesurfer] MNI305 to MNI152 coordinates

2013-11-14 Thread Anita van Loenhoud
It worked, thanks. I tried to invert it but the coordinates didn't fully correspond; I must have made an error. Thanks for helping me out! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] Error when using --mask flag in mri_glmfit

2013-11-14 Thread Suzanne Oosterwijk
Hi Doug, Thanks for the code, this works. Nevertheless, I am a bit unsure about whether the masks that are used as input into this command are correct. I like to check all the stages of the process and when I open the mask.mgh file within the appropriate glm folder, the segmentation is totally off

[Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?

2013-11-14 Thread cabe
Hello, I have a question regarding nifti (.nii) input files. I have .nii image files, which are aligned to AC-PC with SPM. The actual (original) data in this file is not changed, but the transformation matrix is saved in the .nii file. When displaying the freesurfer reconstructed results with tkm

Re: [Freesurfer] Linux recon-all error

2013-11-14 Thread Alan Francis
Hi Krista: You may want to update tcsh. You can do this by using SUDO and 'yum update'. best, Alan On Thu, Nov 14, 2013 at 10:42 AM, krista kelly wrote: > Hello, > > I'm running freesurfer's recon-all using Linux and the past few subjects > I've run, recon-all has exited with errors. I've ran

[Freesurfer] Linux recon-all error

2013-11-14 Thread krista kelly
Hello, I'm running freesurfer's recon-all using Linux and the past few subjects I've run, recon-all has exited with errors. I've ran a few subjects so far with no problems, and now all of a sudden there's an issue and I can't figure out why. I have been able to run these "problem' subjects using

[Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Martijn Steenwijk
Dear all, There seem to be some serious issues with the T2pial / FLAIRpial processing options provided in the latest versions of FreeSurfer. First of all, although not clearly documented, T2pial / FLAIRpial processing does require the FSLDIR to be set (in order to use bbregister with --init-fsl).

Re: [Freesurfer] Re global lgi values

2013-11-14 Thread Anna Jonsson
Thank you. Can I then use aparcstats2table --subjects --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command? On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve wrote: > yes and yes > > > On 1

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Matt Glasser
To fix the second problem, why not reorient the T2w image so the image axes are oriented in the way that FreeSurfer expects? Peace, Matt. From: Martijn Steenwijk Date: Thursday, November 14, 2013 8:13 AM To: freesurfer Cc: Veronica Popescu , Hugo Vrenken Subject: [Freesurfer] T2pial/FLAI

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Bruce Fischl
Hi Martijn we can print warning and errors if FSLDIR is not set, but the registration errros seem to be mostly a flirt issue, no? Have you posted on the FSL list? Bruce On Thu, 14 Nov 2013, Martijn Steenwijk wrote: Dear all, There seem to be some serious issues with the T2pial / FLAIRpia

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Martijn Steenwijk
Hi Matt, Bruce, The problems are indeed a flirt issue, but given that it's programmed with --init-fsl there is not much flexibility. However, from a FS point of view, it might be a better and more robust approach to first register FLAIRraw.mgz to raw.mgz, and then concatenate the resulting regist

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Matt Glasser
I think you can do it with mri_convert ­rl. I don't think it makes sense to expect FLIRT to get the registration right reliably if the axes are off (in the HCP Pipelines we definitely don't expect this and make sure all images are RPI before processing them). Peace, Matt. From: Martijn Steenwi

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Bruce Fischl
Hi Matt hopefully Doug will chime in, but I don't see why that is the case. We preserve all the RAS information when we "conform", so the info should be there for flirt cheers Bruce On Thu, 14 Nov 2013, Matt Glasser wrote: I think you can do it with mri_convert ?rl.  I don't think it make

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Matt Glasser
So the T2w image is already having the axes realigned to RAS with mri_convert in FreeSurfer prior to running -init-fsl? If that is the case, FLIRT should work well enough assuming the input orientation information in the T2w and T1w NIFTI headers was accurate. I suppose you could also restrict th

Re: [Freesurfer] T2pial/FLAIRpial processing issues

2013-11-14 Thread Douglas N Greve
It should not make a difference. We compute an initial registration based on the header and pass that to FLIRT. Can you verify that this initial registration is correct? You can do that with tkregister2 --mov FLAIRraw.mgz --targ orig.mgz --regheader --reg junk If that looks ok, then it is poss

Re: [Freesurfer] Re global lgi values

2013-11-14 Thread Douglas N Greve
I think it would be --parc aparc.pial_lgi doug On 11/14/2013 11:27 AM, Anna Jonsson wrote: > Thank you. Can I then use > aparcstats2table --subjects --hemi lh --meas thickness --parc > lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in > 1 tablefile or should

Re: [Freesurfer] qdec

2013-11-14 Thread Douglas N Greve
The non-gui verion is to run mri_glmfit from the command line:) doug On 11/13/2013 05:23 PM, dgw wrote: > Hello, > > I sent the message below yesterday. I can confirm that I am also having > problems visualizing with qdec using the standard nmr center install over nx. > Everytime I click genera

Re: [Freesurfer] Error when using --mask flag in mri_glmfit

2013-11-14 Thread Douglas N Greve
What is your tkmedit command used to view the segmentation? doug On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > Thanks for the code, this works. Nevertheless, I am a bit unsure about > whether the masks that are used as input into this command are > correct. I like to check all

Re: [Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?

2013-11-14 Thread Douglas N Greve
There are two matrices in the nifti file (qform and sform). By default we use the qform. The qform is 6 dof and so is probably not appropriate for your talairach transform. Bottom line is that the sform is probably being ignored. doug On 11/14/2013 07:18 AM, c...@uos.de wrote: > Hello, > > I

Re: [Freesurfer] Seg fault with mri_segstats?

2013-11-14 Thread Douglas N Greve
Hmmm, I can't replicate this error. This is 5.3 I assume? doug On 11/12/2013 06:02 PM, Michael Waskom wrote: > sorry, unclear why the original email wasn't included in the reply. > copied here: > > > I'm running into a strange seg fault when trying to use mri_segstats > (it's actually ocurrin

Re: [Freesurfer] Is transformation matrix in .nii (nifti) header applied by FS?

2013-11-14 Thread Douglas N Greve
you will see some differences due to reslicing and interpolation. These differences should be somewhat random, so they might be difficult to detect in a group analysis. But in general, you should treat all your data the same. On 11/14/2013 03:40 PM, c...@uos.de wrote: > thanks, that was alre

[Freesurfer] are there any previous studies on the robustness of freesurfer default parameters as used in cortical thickness computation?

2013-11-14 Thread Mark Alexiuk
Hi, My interest is in cortical thickness measurements for longitudinal Alzheimer data, namely the ADNI dataset. My understanding is that recon-all can be used to generate cortical thicknesses. I am trying to understand how the default parameter values used in recon-all were arrived at. Are th

[Freesurfer] Order of edits for longitudinal data

2013-11-14 Thread Rongxiang Tang
Dear All, I was would like to double check the order of edits for longitudinal data. I did edits for my cross-sectional data, and for my base data, I did the following: 1. skull strips edits (if necessary) 2. control points edits 3. white matter edits 4. pial edits 5.brain final surfs edits. I

[Freesurfer] freesurfer5.3 version In CentOS5

2013-11-14 Thread Rujing Zha
Dear all, In CentOS5,which freesurfer5.3 version(centos4 or centos6?) can be compatible? Thanks! All the best. 2013-11-15 Rujing Zha___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Export T1 volume and a set of points in the same space

2013-11-14 Thread Octavian Lie
Dear All, I need to export a T1.mgz and N points (Nx3 coordinates .mat file) of the same volume in SPM12b. N are actually intracranial electrodes. For this, I save T1.mgz as .nii prior to import into SPM. Should I use volume index, volume RAS or surface RAS coordinates for N? What other transform