[Freesurfer] seek help

2017-10-20 Thread 辛雨萌
Dear FreeSurfer Experts, I'm a beginner in cognitive neuronscience and so new to the FreeSurfer. Recently I got some datas from AFNI, and in the documents I only found some surfaces that had been created by FreeSurfer. However, the documents only include some resting state volumes without t

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

2017-10-20 Thread Christopher Markiewicz
Hi Martin, I've tracked down the issue. It turns out that the difference is that the VolGeoms are determined by the sform, while ANTs uses the qform. Syncing the qform to the sform resolves the issue. Chris From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

2017-10-20 Thread Sean Froudist Walsh
That would be great Melanie, thank you very much. And thanks to Bruce and Satra for the quick responses. How will I be able to find the processed files? Will it be announced somehow? Best wishes, Sean ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

Re: [Freesurfer] asking for literature

2017-10-20 Thread Matt Glasser
Also we used T2w scans in the HCP Pipelines Paper and have Figure 14 showing the effects of using T2w scan vs not using one. Peace, Matt. On 10/20/17, 10:00 AM, "Bruce Fischl" wrote: >Hi Jiook > >this paper: > >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/ > >discusses the basic algori

Re: [Freesurfer] FreeSurfer connection with another modality

2017-10-20 Thread Josh Abusnaineh
Thank you. I will try that! Sincerely,   Josh Snaineh TechCare Computers, Inc 1-310-202-0922 1-866-FIX-PC4U 1-866-349-7248 2805 S. Robertson Blvd Los Angeles, CA 90034 j...@mytechcare.com http://www.mytechcare.com/ Your Total Computer Solution -Original Message- From: freesurfer-boun...@n

Re: [Freesurfer] FreeSurfer connection with another modality

2017-10-20 Thread Bruce Fischl
you can just convert to nifti, can't you? Then read them into Osirix? On Fri, 20 Oct 2017, Josh Abusnaineh wrote: Thank you for getting back to me. We have a software called Osirix and I’m wondering if there is a way to push images from FreeSurfer to Osirix software and vice versa? Hope th

Re: [Freesurfer] FreeSurfer connection with another modality

2017-10-20 Thread Douglas Greve
Not in FS. Osirix is a dicom program, so you would need to convert them to dicom first, and we don't have a way to do this. On 10/20/17 4:15 PM, Josh Abusnaineh wrote: Thank you for getting back to me. We have a software called Osirix and I’m wondering if there is a way to push images from F

Re: [Freesurfer] subcortical analysis in native space

2017-10-20 Thread Douglas Greve
That looks ok. I would try applying some spatial smoothing to see if you can get something that looks reasonable On 10/20/17 12:14 PM, Jiahe Zhang wrote: Hi Freesurfer experts, I would like to do a resting state analysis not in mni305, but in subject's native subcortical space. Here is the c

Re: [Freesurfer] FreeSurfer connection with another modality

2017-10-20 Thread Josh Abusnaineh
Thank you for getting back to me. We have a software called Osirix and I'm wondering if there is a way to push images from FreeSurfer to Osirix software and vice versa? Hope this helps Sincerely, Josh Snaineh TechCare Computers, Inc 1-310-202-0922 1-866-FIX-PC4U 1-866-349-7248 2805 S. Robertso

Re: [Freesurfer] FreeSurfer connection with another modality

2017-10-20 Thread Douglas Greve
Hi Josh, I have no idea what you mean. Can you elaborate? doug On 10/20/17 1:30 PM, Josh Abusnaineh wrote: Hello FreeSurfer Developers, The Installation and test part is complete! I was just wondering if FreeSurfer has a way to send/retrieve images from another station using AE_Title/port

[Freesurfer] FreeSurfer connection with another modality

2017-10-20 Thread Josh Abusnaineh
Hello FreeSurfer Developers, The Installation and test part is complete! I was just wondering if FreeSurfer has a way to send/retrieve images from another station using AE_Title/port and IP. Please let me know. Thank you. Sincerely, Josh Snaineh TechCare Computers, Inc 1-310-202-0922 1-866-F

[Freesurfer] subcortical analysis in native space

2017-10-20 Thread Jiahe Zhang
Hi Freesurfer experts, I would like to do a resting state analysis not in mni305, but in subject's native subcortical space. Here is the command I wrote: mkanalysis-sess -analysis seed.native -native -fwhm 0 -notask -taskreg seed.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -nuisreg mcprextreg 2 -

Re: [Freesurfer] asking for literature

2017-10-20 Thread Bruce Fischl
Hi Jiook this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/ discusses the basic algorithm (it is based on T2* but is pretty much the same for T2) cheers Bruce On Fri, 20 Oct 2017, Jiook Cha wrote: Hello, Could anybody please point me to a paper/asbtract showing meaningful

[Freesurfer] asking for literature

2017-10-20 Thread Jiook Cha
Hello, Could anybody please point me to a paper/asbtract showing meaningful improvement of pial surface segmentation using additional T2 or Flair images in the recon-all procedure? Thanks, Jiook ᐧ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

[Freesurfer] mri_surf2surf failure in FS6.0

2017-10-20 Thread Dongnandi
Dear Freesurfer experts, I have a binary brainmask made in volumetric space and trying to transfer it into surface space, first I use mri_vol2surf to transfer the mask into fsaverage space, then run mri_surf2surf (fs 6.0) to down sample it to fsaverage5 space. After vol2surf, some values