Re: [Freesurfer] Segmentation of MR-PET structurals

Hi Gabriel, I don't have experience with the MR-PET yet. Why do you think there is a problem? Try running wm-anat-snr on this subject. In general, you don't want to be smoothing/denoising the anatomical doug On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote: Hi, I've started

Re: [Freesurfer] qdec differences in FS 5.0 vs 5.3

Hi Maria, can you elaborate on exactly what you have done? Is the data the same and you are only changing the version of QDEC? What is the nature of the difference? Can you send pics or stats? doug On 6/18/13 6:06 AM, Maria Kharitonova wrote: Hi, I'm learning how to use QDEC and was

Re: [Freesurfer] problem downloading Xhemi files

try now On 6/18/13 9:37 PM, amirhossein manzouri wrote: I have version 5.1 so please recreate the links! BR On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Amir, if you are using 5.2 or 5.3, then you should already

Re: [Freesurfer] MRIread.m and hippocampal subfields

Hi Marcos, it is weird that the posterior*.mgz does not have that info. Maybe Koen or Eugenio know why. In the mean time, you can use mri_convert to change/set the parameters, eg mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0 doug On 6/18/13 2:50 PM, Marcos Martins da Silva

Re: [Freesurfer] problem downloading Xhemi files

I use curl to download in MAC with the links you mentioned and it is not there! amir% curl -O ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg % Total% Received % Xferd Average Speed TimeTime Time Current Dload Upload Total

[Freesurfer] TRACULA - tract volume and length

Dear DTI experts, I am trying to understand how to interpret tract length volume measurements that TRACULA provides. For example, let’s say a clinical population differs from a control group in mean FA of a particular tract, and tract length volume are comparable across the 2 groups. I think

Re: [Freesurfer] Reviewer not satisfied

read_curv.m should do the trick On Wed, 19 Jun 2013, Jürgen Hänggi wrote: Dear Bruce Yes, the .max and the .min files were produced, but how to access the values in it. Is there a possibility to import these files into MATLAB? Thanks in advance Cheers Jürgen On [DATE], Bruce Fischl

Re: [Freesurfer] MRIread.m and hippocampal subfields

I knew you would have a clean solution. :-) Thank you, Doug. Em Ter, 2013-06-18 às 23:45 -0700, Douglas Greve escreveu: Hi Marcos, it is weird that the posterior*.mgz does not have that info. Maybe Koen or Eugenio know why. In the mean time, you can use mri_convert to change/set the

[Freesurfer] error in lme_mass_fit using matlab tools

Dear Freesurfer experts, I have a question about fitting linear mixed models to mass-univariate data using the lme tools in matlab. I am currently trying to compute the initial vertex-wise temporal covariance estimates by [lhTh0lhRe] = lme_mass_fit_EMinit(X,[2],ni,lhcortex,3] However, I

[Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'

Dear FS team, I tried to run this command asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile aseg_stats.txt But got this error,permission denied, SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to

[Freesurfer] Interior white matter surfaces

Dear FreeSurfer Experts, I am attempting to construct surfaces that are 1, 2, 3, and 4 mm interior from the GM/WM boundary (?h.white). So going gradually deeper into white matter from the GM/WM boundary. I have successfully used mris_fill to fill the ?h.white surface and mri_morphology to

[Freesurfer] recon-all error MRIthickenThinWMStrands

Hi ERROR: MRIthickenThinWMStrands: invalid x,y,z! Numerical result out of range Any tips? S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

Re: [Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'

Hi Chikku, I think this is a permissions issue. Check that you have write permissions to where you are trying to write the stats table. -Louis On Wed, 19 Jun 2013, Varghese Chikku wrote: Dear FS team, I  tried to  run this  command asegstats2table --subjects bert ernie fred margaret --meas

Re: [Freesurfer] Interior white matter surfaces

Hi Jason you could try using mris_expand with a negative # of millimeters. At 4mm you will lose a lot of the gyri and the procedure will probably fail, but for smaller amounts it should work (and is what we've done in the past). You can also use mris_distance_transform to compute the distance

Re: [Freesurfer] Segmentation of MR-PET structurals

Hi Gabriel can you give us details of your acquisition? Why is it so noisy? Bruce On Wed, 19 Jun 2013, Gabriel Obregon wrote: Hi Douglas, The brainmask volumes are extremely grainy (similar to the raw structurals), i.e., dark voxels throughout the WM and high-intensity voxels across the

Re: [Freesurfer] recon-all error MRIthickenThinWMStrands

nope, never seen that error. Probably from mri_segment. If you send me the input volume I'll take a look (check the recon-all.log and see what command was running when that happened). Also, definitely check it before sending to make sure it's reasonable On Wed, 19 Jun 2013, Sudhin A. Shah

Re: [Freesurfer] MRIread.m and hippocampal subfields

Hi, Doug Hi, all This single BASH script line works like a charm for all posterior.mgz files in a once and keeps the original names (must be in yoursubject/mri folder). for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0 -flip_angle 0 -i $f -o $f; done You can also use in a more

[Freesurfer] check orientation

Dear Freesurfer experts, is there a command in Freesurfer to check for correct orientation (LAS vs. PSR) of T1 images (similar to fslhd in FSL)? Thank you very much! Brigitte ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] check orientation

Hi Brigette, not sure how you could do this except visually. Bring the images up and verify that the directions that we specify are correct (although of course this isn't possible for L/R unless you have some type of external fiducial marker like a vitamin E tablet) cheers Bruce On Wed, 19

[Freesurfer] export the ROIs in 'Desikan-Killiany' cortical atlas

Hi FreeSurfer expert, I am interested in a particular region of the Desikan-Killiany atlas and I'd like to use it as an ROI image mask in my fMRI analysis. Could you please suggest how I can do that? From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see that the DK

Re: [Freesurfer] problem bbregister onto longitudinal pipeline

Hi Daniel, bbregister is completely independent of the longitudinal stream, so if it fails, it has other reasons (e.g. bad initial alignment). You could try to switch the initial alignment to some other methods. Best, Martin On Jun 14, 2013, at 3:25 AM, Daniel Garcia

Re: [Freesurfer] error --qdec long

Hi Catherine, probably you are not using 5.3. otherwise it should recognize the --qdec-long flag. You can open mris_preproc and take a look (it is a text file), there should be a qdec-long if you search it. Best, Martin On Jun 17, 2013, at 12:04 PM, Catherine Bois c.b...@sms.ed.ac.uk wrote:

Re: [Freesurfer] Longitudinal processing

Hi Linn, do you mean the brain mask in the cross sectional runs gets worse after you run the longitudinal steps (base and long)? That is not really possible, as these steps don't touch the cross data (only read from it). If you mean that the brain mask in the long looks worse than in the cross