[Freesurfer] unsubscribe

External Email - Use Caution Dear Sir， I am wonder how to unsubscribe the mails like ， my mailbox is almost full and i can not recieve mails from my workmates Shaoxun Yuan, PhD Candidate State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

External Email - Use Caution Dear Sir， I am wonder how to unsubscribe the mails likes ， my mailbox is almost full and i can not recieve mails from my workmates Shaoxun Yuan, PhD Candidate State Key Laboratory of Bioelectronics School of Biological Science and Medical

[Freesurfer] Exporting mean curvature indices

External Email - Use Caution Hi Freesurfer experts, I am interested in estimating mean curvature index for each of the 7 networks (Yeo7 atlas) for my data of healthy controls. I am able to estimate this subjectwise, and the output stats file for each subject looks like following:

Re: [Freesurfer] preproc-sess mask issue

That is possible. I can't remember which version started using register.dof6.lta. But if they are not there in 5.3, then they will be regenerated. On 1/16/19 1:06 PM, Dowling, Kevin Francis wrote: > Hi Doug, > Thanks so much for your note, that makes complete sense! > To confirm, if I just

Re: [Freesurfer] Talairach Transform failure

when you say it does not load, do you mean that the moveable is blank/black? The terminal output indicates that it is being loaded. It is probably the case that the registration is so far off that it is out of the field of view On 1/16/19 11:30 AM, Daniel Ferreira wrote: > > External

Re: [Freesurfer] Large cluster size significant clusters

You can do the analysis in a particular region with masking (--mask input to mri_glmfit). You can also load the uncorrected overlay into freeview and adjust the threshold until you get  a cluster distribution you like, then use that threshold in mri_glmfit-sim On 1/16/19 4:44 PM, Azeez,

Re: [Freesurfer] convert surface-based label to volumetric space...mri_label2vol?

External Email - Use Caution Dr. Greve, Thank you for your swift reply. I will give this a try. I appreciate it. Have a nice evening. Best, Stephanie On Tue, Jan 15, 2019 at 4:50 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > There should already be two volumes

Re: [Freesurfer] Large cluster size significant clusters

External Email - Use Caution Hello I have tried using a greater threshold,(original 0.05) now 0.001 sill the result persist. Is there a way to threshold over a specific region? Total Cortical Surface Area *65416.6 (mm^2)* # FixMNI = 0 # ClusterNo Max VtxMax Size(mm^2) MNIX

Re: [Freesurfer] using tkregister2 to check registration to custom atlas

External Email - Use Caution Just had a chance to try the command. Thanks, it worked! I was struggling to also have the surface projections in the same space, but found a way to do that. For anyone else who might need this: tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz

Re: [Freesurfer] preproc-sess mask issue

Hi Doug, Thanks so much for your note, that makes complete sense! To confirm, if I just delete the session/bold/masks and session/bold/RRR/masks and re-ran my preproc-sess command (-update) in v 6.0 new masks would be generated but my registration, stc, motion correction, (normalization?),

Re: [Freesurfer] Talairach Transform failure

External Email - Use Caution Hi Greve, Thanks for your quick reply. I mean that tkregister2 loads the target volume (I think the original T1 it is) but it does not load the moveable volume as stated in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview: "You

Re: [Freesurfer] mni --> RAS T1

Hi Don, have you checked out this web page? http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 1/15/19 7:11 AM, Krieger, Donald N. wrote: External Email - Use Caution Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1 coordinates, I.e. something

Re: [Freesurfer] using tkregister2 to check registration to custom atlas

Not sure what you are trying to do, but if you want to check the tal reg of a typical analysis, you can run tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz --targ $SUBJECTS_DIR/subject/mri/orig.mgz --ixfm $SUBJECTS_DIR/subject/mri/transforms/talairach.xfm -outxfm

Re: [Freesurfer] Talairach Transform failure

What do you mean that the tal volume does not load as a mov volume? Can you send the terminal output from tkregister2? On 1/16/19 10:01 AM, Daniel Ferreira wrote: External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking

Re: [Freesurfer] using tkregister2 to check registration to custom atlas

External Email - Use Caution Hi, I just wanted to follow up on this post. Is there a way to load the command below, but with a different atlas? tkregister2 --s 180523_HTP02168_ANAT5_init2base --fstal --surfs Again, I have tried other options but am unable to the get the surfs in

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

External Email - Use Caution Hi Rachel, Sorry I missed your previous email. Would you mind uploading your subject(s), so I can take a look? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London

[Freesurfer] Talairach Transform failure

External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking through the archives but can not figure out the solution myself. I was wondering if you would have any suggestion on how to fix the issue described further down?

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

External Email - Use Caution Any guidance on this error is appreciated. I am still receiving the same output stated earlier. Rachel Phillips From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Rachel Phillips Sent: Monday, January 7,

Re: [Freesurfer] Running TRACULA

External Email - Use Caution Hi Anastasia, In the past days, we have obtained the original T1s from the original study and we are running Freesurfer in all of the subjects in order to run TRACULA correctly so we can avoid all the problems you mention. TRACULA is running in some