[Freesurfer] Needing advises for results in my study.

External Email - Use Caution Hi. Recently, I analyzed patients who have taken 1.5T MRI ; (Because they had to go in MRI room with some metal materials) and normal controls who took 3.0T MRI. And, after recon and preprocessing of each group of patients and controls in freesurfer v6

Re: [Freesurfer] Help with LGI

External Email - Use Caution Dear Tim, 1) Here is the output after I type matlab: - Matlab does open, and the following appears on terminal: shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory pwd: error retrieving cu

Re: [Freesurfer] mri_cvs_register for fMRI

External Email - Use Caution Thank you very much both of you for your answers. The co-registration looks fine to me. Apologies for causing confusion, [realignedFunctional.nii] is the functional volume which has previously been ST-corrected and realigned (motion corrected). (Th

Re: [Freesurfer] mri_cvs_register for fMRI

Also, use the .lta output of bbregister instead of the .dat output On 8/5/2020 11:46 AM, Zollei, Lilla,Ph.D. wrote: Hi Peter, Have you checked the output from bbregister? Did the registration look accurate? Also, the --mov volume should be the functional volume (not the realigned one) Best, L

Re: [Freesurfer] mri_cvs_register for fMRI

Hi Peter, Have you checked the output from bbregister? Did the registration look accurate? Also, the --mov volume should be the functional volume (not the realigned one) Best, Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Sperrer Sent:

Re: [Freesurfer] mri_cvs_register for fMRI

External Email - Use Caution Dear Lilla, Thank you for your quick response. Now I tried using bbregister --s [SUBJECT] --mov [realignedFunctional.nii] --init-coreg --reg register.dat --bold and then again mri_vol2vol --mov [realignedFunctional.nii] --o [CVSrealignedFun

Re: [Freesurfer] Questions about speed up the longitudinal processing

Rather than -parrallel, use -threads to indicate the number of processors to use On 8/5/20 10:47 AM, Yang Molly wrote: External Email - Use Caution Hi list, I tried to run some longitudinal data with two time points with the latest version Freesurfer (7.1.0) on the Ubantu 16 system.

[Freesurfer] Questions about speed up the longitudinal processing

External Email - Use Caution Hi list, I tried to run some longitudinal data with two time points with the latest version Freesurfer (7.1.0) on the Ubantu 16 system. "recon-all -base" with two time points need 5 hours to complete on my PC, and recon-all -long need 2 hours. I try to

Re: [Freesurfer] mri_cvs_register for fMRI

If you have a registration LTA file (eg, from bbregister), the you can run something like set gcam = $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z set dstreg = $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta mri_vol2vol --gcam input.nii.gz  reg $gcam $ds

Re: [Freesurfer] Quetion about thalamic nuclei segmentation in freesurfer v7

Dear HR, You can run the FS7 substructures on data reconned with 6.0. It's not ideal in the sense that the results are a bit harder to reproduce, but definitely doable (as long as you report it in the papers your write!). The results will indeed be slightly different than if you ran the whole th

Re: [Freesurfer] The input for Petsurfer

External Email - Use Caution Thank you for your response. On Mon, Jul 27, 2020 at 7:19 PM Douglas N. Greve wrote: > Sorry, no, not with PETsurfer > > On 7/26/2020 1:05 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Thank you for the quick response. > >

Re: [Freesurfer] bad interpreter: No such file or directory error

External Email - Use Caution I appreciate your answer! On Thu, Jul 30, 2020 at 8:18 PM fsbuild wrote: > Hello Hengameh, > > You probably need to install tcsh (and or csh). > > I would try, > > $ sudo apt-get install csh tcsh > > - R. > > On Jul 30, 2020, at 09:19, Hengameh Marzb

Re: [Freesurfer] mri_cvs_register for fMRI

Hi Peter, Running the currently existing command, implicitly assumes that your fMRI data is in the same spatial coordinate space (with the same resolution) as the norm that you used for mri_cvs_register. You will need to use the --reg flag to input the fmri-2-structural transform. Best, Lilla __

[Freesurfer] mri_cvs_register for fMRI

External Email - Use Caution Dear FreeSurfer experts, My goal is to morph fMRI (data in voxel space) for best possible intersubject GM-overlap. I am using /mri_cvs_register/ as it seemed like a perfect tool for this. I have already run /recon-all /on the anatomical scan (160x2

Re: [Freesurfer] Help with LGI

External Email - Use Caution Looks like something is wrong with the Matlab installation. It would be good to know: 1) What happens if you type 'matlab' in your shell? 2) What happens if you type '/Applications/MATLAB_R2020a/bin/matlab' in your shell? Best, Tim > On August 4,