[Freesurfer] Running DICOMS versus FreeSurfer5.3 Output

External Email - Use Caution Dear FreeSurfer Developers If we want to rerun FreeSurfer dev 6.1 on an old dataset, is it better to rerun with the original DICOMS or to rerun over the 5.3 output? Would that even work? Thanks very much. Kind regards, FREDA SCHEFFLER Research Ass

[Freesurfer] Physiological Noise Regression from rsMRI

Hi all, I am currently developing a pipeline to remove physiological noise (respiratory and cardiac) from rsMRI images. I am at the point where I have created the regressors using fast_retroicor.m from the physiological data logs. When I add the columns of the regressors up and plot the result

[Freesurfer] Problems setting the directory

External Email - Use Caution Dear Free Surfer team, Surely this is a basic question but I am having a trouble setting the subjects_dir in my terminal and, as a result, any of the commands work. This is how I have my Free Surfer configurated in my computer: freesurfer-Li

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

External Email - Use Caution Thank you for the response. Which smoothing option would you recommend, there is one in mris_preproc, but there is also mris_smooth. Thanks You On Wed, Oct 17, 2018 at 1:56 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > You cannot use Q

[Freesurfer] Computing relative cortical measures maps instead of absolute cortical measures maps

External Email - Use Caution Hi, I am referring to a paper of Vuoksimaa et al. 2016. The authors used relative instead of absolute cortical measures (cortical thickness and surface area) to compute individual vertex-cognitive ability correlations throughout the cortex. To

Re: [Freesurfer] Problems setting the directory

Hi Rosalia you either need to give recon-all an input file (or more than one) with the -i switch, or create the subject directory tree under SUBJECTS_DIR for that subject, and put a file named 001.mgz in the mri/orig subdir. Note you can also specify SUBJECTS_DIR explicitly on the recon-all co

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Hi Bruce, Thank you very much for answering my questions. This is how I have organized my subject_dir for one subject so you can see better. It is still not working. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls FOLDERS S_01

Re: [Freesurfer] Problems setting the directory

Hi Rosalia can you send us the full command line, screen output and recon-all.log? In the arrangement you show below it would be: recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i -all cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Hi Bruce, There is not recon-all.log. The full command line is: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ *recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1* *ERROR

Re: [Freesurfer] Problems setting the directory

Hi Rosalia -i must point to a file that you want to import, usually a single dicom file in the correct (e.g. mprage) series. cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi Bruce, There is not recon-all.log. The full comman

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Yes, you are right. I saw the error. I have been running one of the participants and here it is the report.log. Also, because these kind of participants are special, I used some bet parameters to run the skull-stripping. This is the main reason why I di

Re: [Freesurfer] Problems setting the directory

yes, you can do that. If you run recon-all through the skill stripping, then replace the brainmask.mgz with yours generated by bet, we should detect that and retain it for further processing cheers Bruce On Thu, 18 Oct 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Cautio

[Freesurfer] errors running mri_glmfit

External Email - Use Caution Hello I keep getting the same error and am not sure how to address the issue. I have attached the design matrix and the FSGD file and contrast file of interest Thanks for the help ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Re: [Freesurfer] Problems setting the directory

External Email - Use Caution Thank you a lot Bruce. Just one more question. If I would like to run all the participants. where should I include the subject.list? Regards, Rosalia On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl wrote: > yes, you can do that. If you run recon-all thr

Re: [Freesurfer] Problems setting the directory

Hi Rosalia that you would do outside of FreeSurfer, probably with a shell script. I typically make a scripts dir under SUBJECTS_DIR and put a file names subjects.csh that creates an env variable listing the subjects and setting the SUBJECTS_DIR, then write scripts that source it and run things

[Freesurfer] Mapping a custom measure to the pial surface of fsaverage

External Email - Use Caution Dear FreeSurfer experts, I have created a custom measure on the pial surface of a number of subjects, and I would like to map the data to the fsaverage subject. (By custom measure I mean something like 'area' or 'curv', i.e., one scalar value per sur

[Freesurfer] How to export the image and label

External Email - Use Caution Dear FreeSurfer Team : I used the freeSurfer brainstem structure to segment the brainstem from the MRI successfully. But I have several questions as followed: 1. I want to export this data in dcm file with all the ROI information, what should I do? 2.