Re: [Freesurfer] Flattening the surface

Hi Bruce, I sent you a message a while ago but have’t received your reply. I generated a mgh file using mri_vol2surf, and thus mapped the texture that I want to project onto both the inflated and the flattened surfaces. I wonder whether it is possible to reversely map the vertices on the vectori

Re: [Freesurfer] Covariates for cortical Thickness and LGI

Hi Doug, Thanks for the follow up. Do you recommend using a covariate such as mean thickness or is a covariate not necessary for cortical thickness analysis? Thanks, Ajay On Thu, Sep 8, 2016 at 2:00 PM, Ajay Kurani wrote: > Hi Freesurfer Experts, >I am comparing a control group and 2 pa

[Freesurfer] recon-all/ mri_convert (preprocessing dicom file error)

Hello, I am trying to preprocess couple of dicom images (146 dicom image) and I constantly get this error. "dan% *recon-all -all -i IM-0065-0001.dcm -s fsdir (recon-all script)* Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO:

[Freesurfer] issues with GUI {Disarmed}

Dear freesurfers, I encounter problems with the GUI, for example I can't change the "Design name" from "Untitled" to a custom title. I get following error when I start qdec with .tcsh from the terminal, which might be related: pci id for fd 4: 80ee:beef, driver (null) libGL error: core dri or d

Re: [Freesurfer] Covariates for cortical Thickness and LGI

thickness does not scale with ICV (surface area does). Not sure about LGI On 09/08/2016 03:00 PM, Ajay Kurani wrote: > Hi Freesurfer Experts, >I am comparing a control group and 2 patient groups (HC vs Group1, > HC vs Group2, Group1 vs Group2). I am interested in seeing what is > the most

Re: [Freesurfer] FreeSurfer registration tool in ASL image

I don't think robust register will work as that assumes that the modalites are the same. You can try using mri_coreg, which you can find here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg On 09/08/2016 03:51 PM, Frank Robert wrote: > Hello FreeSurfer expert > > I wa

Re: [Freesurfer] Spmregister issues

I have no idea. An RA wrote the guts of spmregister about 10 years ago. You might try using mri_coreg in the dev environemnt. Don't know how to convert an spm mat into FSL. On 09/08/2016 04:02 PM, Albrecht, Daniel S. wrote: > Hello, > > I've been using spmregister in order to coregister a stat

Re: [Freesurfer] Can't Load More Than Four Unique Overlays on TKSurfer From Command Line

Yea, this bug has been there for a while. We are trying to get people to use freeview instead as tksurfer will not be developed further. You can try using tksurferfv (see below). This is a script that takes tksurfer arguments and creates a freeview command line. Not sure it will work in 5.3, bu

[Freesurfer] Can't Load More Than Four Unique Overlays on TKSurfer From Command Line

Hello, I am trying to load five overlays on TKSurfer from the command line (actual command attached). The problem is this: if I try to load five different overlays, the fifth one will show up on Freesurfer as being identical to the first one (for instance, in this example, the "all-slope" overlay

[Freesurfer] Spmregister issues

Hello, I've been using spmregister in order to coregister a static PET image to an MPRAGE, typically with good results. A representative run is as follows: spmregister --mov $file.nii --s $subj --reg SUV_lin_T1.dat --fsvol orig We then convert *.dat to *.mat with tkregister2, and apply the *.ma

[Freesurfer] Covariates for cortical Thickness and LGI

Hi Freesurfer Experts, I am comparing a control group and 2 patient groups (HC vs Group1, HC vs Group2, Group1 vs Group2). I am interested in seeing what is the most appropriate covariate to use for both a cortical thickness analysis and LGI analysis. I do not expect major changes in brain sha

[Freesurfer] Re Re: Extracting aseg.stats data

That seemed to work, thank you! Tamara ___ 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 the person to whom it is addressed. If yo

Re: [Freesurfer] White matter surface don't change after editing

Hi Cong you could try using expert options to modify the mris_make_surfaces parameters. It looks like you white surface is too far out. Try increasing min_border_white and/or increasing max_gray. If you can't get it working feel free to upload the entire subject dir and we will take a look c

Re: [Freesurfer] extract JUST pial surface for brain-printing purposes - what can I skip?

sorry, no. You pretty much need to do everything Bruce On Wed, 7 Sep 2016, djpet...@u.washington.edu wrote: > Hi Freesurfer list, > > Say I was interested ONLY in extracting the pial surface for the purpose of > getting a 3D print of a brain. Are there any time-intensive steps that can I > s