[Freesurfer] Fwd: Re: One Group (One Factor), Two Covariates

Thanks.what do I do if I would like to maintain the effect of "main" in the points 2 and 3.Best regardsStefano --- Begin Message --- On 2/2/18 7:47 AM, std...@virgilio.it wrote: Hi list, in reference to One Group (One Factor), Two Covariates https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

I have run: 1) mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas thickness --out rh.GROUP1.thickness.00.mgh mri_surf2surf --hemi rh --s fsaverage --sval rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval rh.GROUP1.thickness.10B.mgh 2) mri_glmfit --y ces.nii.gz --wls cesvar

Re: [Freesurfer] One Group (One Factor), Two Covariates

I would like to find where the functional connectivity is correlated to VARIABLE 1 regressing out the VARIABLE 2. How I should set my contrast.mtx? Thanks Stefano > Il 3 febbraio 2018 alle 19.57 Douglas Greve ha > scritto: > > > > > On 2/2/18 7:47 AM, std...@virgilio.it mailto:std..

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

This is not expected. You would need to provide more details (recon-all.log) for anyone to be able to help you. It might be also worth googling the specific error message before hand - it could be that someone else run into this before. Best, Chris On Sat, Feb 3, 2018 at 7:55 PM, Dianne Patterso

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

Hello Dr. Greve, The analysis.info file is below. I should also say that, when I am trying to create new analysis and contrast files, while creating the .config file for contrast, th system gives the same error saying that it cannot enter the file. # FSBUILD freesurfer-Linux-centos6_x86_64-stab

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

This looks like a memory issue to me as indicated bu those two lines: /opt/freesurfer/bin/reconbatchjobs: line 81: 4014 Killed exec $JOB >> $LOG 2>&1 /opt/freesurfer/bin/reconbatchjobs: line 81: 4017 Killed exec $JOB >> $LOG 2>&1 You can adjust how much memory of your host machine will be acces

Re: [Freesurfer] [bids-discussion] freesurfer bids container fails to find license file

Thanks so much! Docker had 2 GB of ram, now it has 10...we'll see if that makes it happy. -Dianne On Sun, Feb 4, 2018 at 10:52 AM, Chris Gorgolewski < krzysztof.gorgolew...@gmail.com> wrote: > This looks like a memory issue to me as indicated bu those two lines: > > /opt/freesurfer/bin/reconbatc

[Freesurfer] Removing labels after extending parcellation into white matter

Hi Freesurfer experts, I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at