[Freesurfer] two postdoctoral positions at Florida International University, Miami, open immediately

2016-09-13 Thread Anthony Dick
Dear colleagues--Please share widely, we are looking to hire immediately. Thanks! The S.E.L.F Regulation Laboratory (http://self-regulationlab.fiu.edu/; PI Dr. Paulo Graziano, PhD) in collaboration with the Developmental Cognitive Neuroscience Laboratory (http://dcn.fiu.edu; PI Dr. Anthony

Re: [Freesurfer] convert FSFAST files to gifti format

2016-09-13 Thread Sabin Khadka
Hi Doug- I did try mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz fmcpr.lh.gifit-file.gii I still get freadFloat: frear failed error. Cheers, Sabin Khadka On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve

Re: [Freesurfer] Pial surface vs. aparc+aseg

2016-09-13 Thread Douglas N Greve
No, the surface is not valid in those regions as they are not cortex On 09/12/2016 07:18 PM, Nosal, Eryka [PSY] wrote: > > Hi, > > I’m very new to Freesurfer, and I am trying to get subject-specific > masks from the output of recon all that I can use on my functional > data. I was going to

Re: [Freesurfer] convert FSFAST files to gifti format

2016-09-13 Thread Douglas N Greve
what is your mris_convert command line? You need to include vertex position information (eg, -o lh.white) On 09/12/2016 03:32 PM, Sabin Khadka wrote: > Hi all, > > Is there a way to convert FSFAST files > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti > format? I've tried

Re: [Freesurfer] Some volumes not loading (corrupted?)

2016-09-13 Thread Douglas N Greve
Did you run out of disk space? The recon could have been aborted during the middle of the write (but unlikely). If the edits were in the brainmask, then there is not much you can do. If the edits were not in the brainmask, you can just rerun starting at the brainmask and the edits will be

Re: [Freesurfer] cannot read white surface

2016-09-13 Thread Douglas N Greve
Can you send the full terminal output? On 09/13/2016 01:26 PM, Claudia Dacquino wrote: > Hi freesurfers, > I'm trying to create an average subject for GLM analysis from my > group, using > > make_average_subject --out newtemplate > > and I got this error: > > Reading surface >

[Freesurfer] QA tools

2016-09-13 Thread John Anderson
Hello, FS experts, I am trying to use QA tool:  I ran the following command  recon_checker -snaps-only -s-file subjects.txt   The script output the following: X11 connection rejected because of wrong authentication. GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0

[Freesurfer] Some volumes not loading (corrupted?)

2016-09-13 Thread Rachel Romeo
Hi all, After doing some manual edits to the wm and pial masks, I recently had a recon fail with the following error: mghRead(/subject_177/mri/brainmask.mgz, -1): read error Invalid argument mri_em_register: could not open mask volume brainmask.mgz. When trying to load either the

[Freesurfer] cannot read white surface

2016-09-13 Thread Claudia Dacquino
Hi freesurfers, I'm trying to create an average subject for GLM analysis from my group, using make_average_subject --out newtemplate and I got this error: Reading surface /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white No such file or directory ERROR: could not read

[Freesurfer] cannot read white surface

2016-09-13 Thread Claudia Dacquino
Hi freesurfers, I'm trying to create an average subject for GLM analysis from my group, using make_average_subject --out newtemplate and I got this error: Reading surface /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white No such file or directory ERROR: could not read