[Freesurfer] A Help Request for Random Parcellation

External Email - Use Caution Dear Dr.Bruce Fischle; Thank you very much for all help you have given me so far,I would like to know if it is possible to access the algorithms(or any specific parts of them) that run FreeSurfer and I also would like to know if I can do a random pa

[Freesurfer] Fwd: vertex MNI305

External Email - Use Caution Hi there Still waiting for an answer to this! Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology -- Forwarded message -- From: Trisanna Sprung-Much Date: Thu, Jul 26, 2018 at 7:35 PM

Re: [Freesurfer] A Help Request for Random Parcellation

Hi Maedeh sure, all our code is open source and you are welcome to download it. As for a random parcellation, I guess you could use mris_make_face_parcellation then randomize the parcel numbers. cheers Bruce On Tue, 31 Jul 2018, Maedeh Khalilian wrote: External Email - Use Cautio

Re: [Freesurfer] Fwd: vertex MNI305

Hi Trisanna sorry, I think this came during Doug's vacation. I believe that those coords in fsaverage are MNI ones, but he can confirm cheers Bruce On Tue, 31 Jul 2018, Trisanna Sprung-Much wrote: External Email - Use Caution Hi there Still waiting for an answer to this!

Re: [Freesurfer] Surface editing: recon-all exited with errors

Hi Eli yes, please send the recon-all.log thanks Bruce On Mon, 30 Jul 2018, Rockers, Elijah D. wrote: External Email - Use Caution Hello. I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortic

Re: [Freesurfer] Fwd: vertex MNI305

External Email - Use Caution thanks Bruce! I will wait for Doug's response. Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Jul 31, 2018 at 10:41 AM, Bruce Fischl wrote: > Hi Trisanna > > sorry, I think this came during Doug

[Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits

External Email - Use Caution Dear FreeSurfer Developers, I posted this question last week, but did not receive a response. Please let me know if I can provide any additional information. We are using your longitudinal processing pipeline (version 6.0) for our study (n=140, 3 ti

Re: [Freesurfer] fcseed-config

Your problem solved? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-

Re: [Freesurfer] Surface editing: recon-all exited with errors

did you run recon-all -s -make all ? I don't see it in the log On Tue, 31 Jul 2018, Rockers, Elijah D. wrote: External Email - Use Caution Oh, yep, sorry about that. I copy the list on this e-mail, and attach the log. I think the list blocks attachments, but if anyone w

Re: [Freesurfer] Surface editing: recon-all exited with errors

h, maybe -make all has changed (or my memory of what it does is incorrect). I'll find someone else here to help you out cheers Bruce On Tue, 31 Jul 2018, Bruce Fischl wrote: did you run recon-all -s -make all ? I don't see it in the log On Tue, 31 Jul 2018, Rockers, Elijah D. wrote:

Re: [Freesurfer] Surface editing: recon-all exited with errors

External Email - Use Caution Yeah, we have an XNAT instance which can automatically run "recon-all -all" on new incoming images. Then I download the subject Freesurfer folder from that database, and edit the surfaces (following the tutorial on the freesurfer site), then I run r

Re: [Freesurfer] Surface editing: recon-all exited with errors

Hi Eli, the -make all flag contains a bug in the 6.0 release. This can be fixed if you download this script - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/recon-all.makefile - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile Let me know if yo

[Freesurfer] Mixed Block Event-related Design Optseq Question

External Email - Use Caution Hello experts, We would like to use the optseq 2 to optimize a mixed block and event-related design. Is it possible to use optseq for a mixed design? We are specifically not sure how to specify block duration. What commands shall I use in order to do

[Freesurfer] mri_cvs_register using fsaverage

I need to transfer one of our patient's electrodes locations (depth electrodes, they aren't located on the cortical surface) to MNI305 space. For that, I'm trying to use mri_cvs_register to register the patient to fsaverage. I'm using to the following command: mri_cvs_register --mov subjid --te

[Freesurfer] Postdoctoral Fellowship for Child Brain Connectome and Genetics

External Email - Use Caution Postdoctoral Fellowship for Child Brain Connectome and Genetics Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort longitudinal study over the world. The GUSTO mothers were recruited during pregnancy between

[Freesurfer] Postdoctoral Fellowship for Child Brain Connectome and Genetics

External Email - Use Caution Postdoctoral Fellowship for Child Brain Connectome and Genetics Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort longitudinal study over the world. The GUSTO mothers were recruited during pregnancy between

[Freesurfer] Postdoctoral Fellowship for Child Brain Connectome and Genetics

External Email - Use Caution Postdoctoral Fellowship for Child Brain Connectome and Genetics Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most comprehensive birth cohort longitudinal study over the world. The GUSTO mothers were recruited during pregnancy between

[Freesurfer] Sag T1 3D post-contrast

External Email - Use Caution Has anyone else tried to do recon-all with Sagittal 3D T1 post-contrast volumes? We're getting hung in recon-all at the Talairach registration step, and I wonder if the vascular enhancement at the pial surface might be throwing the algorithm off. Abo