[Freesurfer] optseq with dependent stim types in a single trial

Hello, I am using optseq to optimize a new task. I have been playing around with the examples they have on the documentation. What I can't find is information on how to set up the trial structure when 1 trial is comprised of 3 different stimuli types: (choice 3sec --> effort (hard or easy) 3 sec

Re: [Freesurfer] changing qdec path?

use export SUBJECTS_DIR=/mnt/data2 On 11/15/2017 05:48 PM, 박경일 wrote: > Hi, Dr Greve > I tried following command > > setenv SUBJECTS_DIR /mnt/data2 (data2 is a mounted disk) > > the result is > > bash: setenv: command not found > what is wrong? > > Kyung > > > > > 2017-11-16 4:57 GMT+09:00

Re: [Freesurfer] changing qdec path?

Hi, Dr Greve I tried following command setenv SUBJECTS_DIR /mnt/data2 (data2 is a mounted disk) the result is bash: setenv: command not found what is wrong? Kyung 2017-11-16 4:57 GMT+09:00 Douglas N Greve : > You can just > > setenv SUBJECTS_DIR

[Freesurfer] Using aparcstats2table for LGI

Dear Experts, I have extracted mean LGI values for each ROI using mri_segstats --annot SUBJ rh aparc --i $SUBJECTS_DIR/SUBJ/surf/rh.pial_lgi --sum lh.aparc.pial_lgi.stats For the next step, I am attempting to combine them into one table, and am trying to use the aparcstats2table function. Does

Re: [Freesurfer] "error parsing license file, expected 4 values" with amygdala segmentation

Hi Andrew, Looks like only 3 lines. I'll see if I can locate a back up. Thanks, Carl On Wed, Nov 15, 2017 at 3:06 PM, Hoopes, Andrew wrote: > Hi Carl, > > How many lines of text exist in your license file? > > Andrew > > On Nov 9, 2017, at 8:18 AM, Carl Anderson

Re: [Freesurfer] "error parsing license file, expected 4 values" with amygdala segmentation

Hi Carl, How many lines of text exist in your license file? Andrew On Nov 9, 2017, at 8:18 AM, Carl Anderson > wrote: Hi Everyone, I'm running freesurfer-Darwin-OSX-dev-20171107-ec5ce3a I seem to get the line "error parsing license file, expected

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

Sorry for the delay. First run mni152reg for each subject (should take only a few min, but needs FSL I think). Then run mri_label2vol --aparc+aseg --temp MNI152_2mm.nii.gz --reg $SUBJECTS_DIR/subject/mri/transforms/reg.mni152.2mm.lta --o aparc+aseg.subject.mni152_2mm.nii.gz On 11/14/2017

Re: [Freesurfer] changing qdec path?

You can just setenv SUBJECTS_DIR /path/to/your/big/disk On 11/15/2017 04:06 AM, 박경일 wrote: > Dear experts, > Based on my knowledge, all image folders should be within subject_dir > for qdec process. > But, my data are so huge to be included in this directory in my > default setting. > Do

Re: [Freesurfer] ERROR: fast_sexavg3() failed\n

Can you send the log files for those subjects? You will find them in the log folder of the project folder. You will see one for preproc and one for selxavg3 On 11/15/2017 11:04 AM, Christina Pressl wrote: > /Hi Freesurferteam, / > /For some of my subjects I get an error when I try to perform

Re: [Freesurfer] surface based fMRI gorup analysis from spm

Thank you very much, now it is working! The backslash was there but there was no space just after the .dat I report below the final commands that I have used in case somebody else might find it useful. Thanks again! mris_preproc --target fsaverage --hemi lh \ --iv

[Freesurfer] ERROR: fast_sexavg3() failed\n

Hi Freesurferteam, For some of my subjects I get an error when I try to perform my analyses, because the mcprextreg file is missing. It is not apparent to my why this file is missing for some of my subjects, while it is there for all the other subjects. Also, there is one subject for which

[Freesurfer] changing qdec path?

Dear experts, Based on my knowledge, all image folders should be within subject_dir for qdec process. But, my data are so huge to be included in this directory in my default setting. Do you have any idea to change qdec path by which qdec can import image files in external hard drive or other