[Freesurfer] mri_glmfit skipping .mtx files

Dear freesurfer mailing list, Is there a limit to the number of .mtx files you can feed to mri_glmfit? I am running an anlysis with 25 different .mtx files, and when the analysis runs it just skips the 22nd and 23rd .mtx file. This means these contrasts are also missing from the glmdir. Do you

[Freesurfer] Label to Nii Conversion

I have a label file on the surface, but want to be able to use it to extract surface data that is already in nifti format (dimensions: [2737 1 6]). Is there a way to convert a label to nifti? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurolo

Re: [Freesurfer] epidewarp?

Use --fsm shiftmap.nii.gz (ie, it needs an extension) On 04/01/2015 05:02 PM, Marco Loggia, PhD wrote: > Hi Doug, > > I just noticed that when I run epidewarp, it gives me a strange " 'if: > Expression Syntax' " error message, even if I have no if-statements in > my script (see below for an exam

[Freesurfer] epidewarp?

Hi Doug, I just noticed that when I run epidewarp, it gives me a strange " 'if: Expression Syntax' " error message, even if I have no if-statements in my script (see below for an example of usage). Note that I use the full path for epidewarp because I am using FSL 5.0.7. Is this a bug? Thanks

Re: [Freesurfer] hello freesurfer developer~

You're dicom file is jpeg compressed which FS version 5.3 does not handle. Get the two files from below ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdjpeg.fs ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert Copy into $FREESURFER_HOME/bin (make a backu

Re: [Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?

Hi Falko, I'm not sure what you mean by extract the visual areas as an ROI. Do you want the mean over the ROI? Or each of the time courses? Is your input data a surface or a volume? On 04/01/2015 11:25 AM, Kaule, Falko wrote: > Dear all, > having phasemaps, generated with AFNI, I would like to e

Re: [Freesurfer] -per-run analysis in native space

The two have different dimensions. One has 256^3, the other 160^3 doug On 04/01/2015 12:31 PM, sha...@nmr.mgh.harvard.edu wrote: > I emailed them! > >> I can't tell from that message. Can you copy mask.nii.gz and >> rho1mn.nii.gz somewhere I can access? >> >> On 04/01/2015 12:14 PM, SHAHIN NASR

Re: [Freesurfer] -per-run analysis in native space

I can't tell from that message. Can you copy mask.nii.gz and rho1mn.nii.gz somewhere I can access? On 04/01/2015 12:14 PM, SHAHIN NASR wrote: > Hi Doug, > Selxavg3-sess started without any problem but then I faced the > below error. Do you know what is the problem? > > Global In-Mask Mean =

Re: [Freesurfer] -per-run analysis in native space

Hi Doug, Selxavg3-sess started without any problem but then I faced the below error. Do you know what is the problem? Global In-Mask Mean = 1316.7 (8.68411) Rescale Target = 100 RescaleFactor = 0.0759477 OLS Residual Pass run 1t= 0.0 Saving rho1 run 2t=144.1 Saving rho1 run 3

Re: [Freesurfer] Accounting for lesions misclassified as non-brain matter

I tried editing the apar.2009a.aseg vpolume using 77 to fill in the lesions, ran this code: recon-all -s ${subject} -autorecon2-cp this did not make any difference. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of

Re: [Freesurfer] Longitudinal - varying geometries

Thanks, Martin. It is unfortunate to hear such news, but they are of course accurate. Hopefully this affects a small subset of subjects, and I will be able to add a covariate to it. Regards, Pedro Rosa. On Wednesday, April 1, 2015 at 12:30 PM, Martin Reuter wrote: > Hi Pedro, > > there is re

Re: [Freesurfer] Longitudinal - varying geometries

Hi Pedro, there is really no way to fix it. Especially if all you subjects changed acquisition. If it is only a small subset, you can then include a co-variable to account for this in your stats. You should then also test whether one group has more of these cases than the other, or if it is d

[Freesurfer] How extract visual areas from non-freesurfer generated Phasemaps?

Dear all, having phasemaps, generated with AFNI, I would like to extract the visual areas as ROI from a surface view (infalted, flatmap or sth. like this). > Steps I've tried: As I'm already familar with freeview and a bit with tksurfer I tried to use them to do that. After reading through the f

Re: [Freesurfer] Longitudinal - varying geometries

Hi Martin, Thank you for your answer. Is there a way to fix it? Can reslicing help? Or to try compenate for it in the processing or statistics? Regards -- Pedro Rosa > On Apr 1, 2015, at 12:13, Martin Reuter wrote: > > Hi Pedro, > > yes, there was a bug (well, not really a bug but the check w

Re: [Freesurfer] Longitudinal - varying geometries

Hi Pedro, yes, there was a bug (well, not really a bug but the check was oversensitive). It was testing too many image parameters, some of them could be problematic (e.g. different voxel sizes across time), and some not. Looking at your attached files, you can see that the voxel sizes differ

[Freesurfer] freesurfer pipeline for sub mm voxel resolution

Hi All, I am working with some 7T data with 0.7 mm isotropic voxels and wanted to know if free surfer pipeline (version 5.3) can work these images ? I also have FLAIR images and wanted to know if I can use the two to create myelin maps ? Please suggest. Thanks Ri ___

Re: [Freesurfer] Fw: longitudinal statistics LGI

Hi Jorge, Which direction does this contrast show? con > pat is redis or vice versa? I mean how can one interpret the result? Best regards, Amirhossein Manzouri On Sat, Mar 28, 2015 at 3:46 PM, jorge luis wrote: > Hi Amirhossein > > You need another column in your design matrix to encode the

[Freesurfer] Longitudinal - varying geometries

Dear FreeSurfers, I have read in the Mailing list (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html and others) other users asking questioning in regard of a Warning from FreeSurfer 5.3 longitudinal pipeline (-base step): \n**