[Freesurfer] Open Letter to NIH Director Francis Collins

Dear Everyone, Please note the following NIH petition regarding the impending classification of basic science research as clinical trials: https://ipetitions.com/petition/open-letter-nih-collins Regards, Thomas ___ Freesurfer mailing list

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Thank you Dr Bruce, It seems that FS5.3 doesn't output this file. I just checked many recons processed using FS5.3 without FLAIR and the file "aparc.DKTatlas+aseg.mgz" is missing in all these recons. I see aseg.mgz, aseg+aparc.mgz and wmparc.mgz > Original Message > Subject:

Re: [Freesurfer] acceptable values for white matter on the T1.mgz volume

Hi Antonio yes, 100 is fine. If it gets much below 90 I would start to get concerned as then it will overlap a lot with GM. Tweaking the intensity correction is ok, but you have to be careful not to have it leak into the gray matter. cheers Bruce On Thu, 31 Aug 2017, Antonio wrote: > Dear FS

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Hi John the atlas isn't flair-based (and is done before the flair processing). I thought we always generated both (plus Christophe's for 3 total), so I'm a bit confused cheers Bruce On Thu, 31 Aug 2017, John Anderson wrote: Hi Emma, Thank you for your response.  I am running my recons using

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Hi John, I don't believe this atlas is FLAIR based. Could you please attach a recon-all log for one of these subjects? Thank you, Emma From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of John Anderson

[Freesurfer] acceptable values for white matter on the T1.mgz volume

Dear FS community, I have a question regarding T1.mgz normalization values. Is there an established range of acceptable values for white matter around 110? For example, I'm getting values around 100 or so in some areas of low SNR (around the anterior temporal lobe region). Notwithstanding, the

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Hi Emma, Thank you for your response. I am running my recons using V5.3 and V6.0 In the data base I have ~200 T1 images and for some I have FLAIR images. When I run recon all with the flag FLAIR I get the file "aparc.DKTatlas+aseg.mgz" in FS5.3 and FS6.0 If I run recon-all without the flag FLAIR

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Hi John, Which version of FreeSurfer are you running? Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Contrast matrix for PVR

Hi experts, I have a follow up question: In case I wanted to add another covariate in contrast matrix e.g. in addition to age and gender if I want to add BMI as another covariate in calculating correlation between volume and LGI (as mentioned in previous email), could you please confirm if

[Freesurfer] individual mri_segstats waveforms for vertices or face in label

Though one workaround might be to subdivide a label many, many times using mris_divide_parcellation, I was wondering if it is possible to obtain a per-vertex (or even per-face) fMRI waveform for a label. In other words, rather than compute the average waveform across all vertices, as with

[Freesurfer] rh.white and rh.pial surface manual edit

Hello FreeSurfer experts, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sharing

Re: [Freesurfer] motion estimates

Perfect! Thank you a bunch! From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Thursday, August 31, 2017 10:19:36 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] motion estimates

just the brain. For the spine you probably want to do it manually. freeview can help with this - draw ROIs in the gray and white matter, then look at the difference between the means (squared) divided by the sum of the variance On Thu, 31 Aug 2017, James Welsh wrote: Thank you Dr Bruce for

Re: [Freesurfer] motion estimates

Thank you Dr Bruce for the info! Is this command works on T1 images acquired from the spine or just the brain? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent:

Re: [Freesurfer] preproc-sess

1) bbregister ("Accurate and robust brain image alignment using...") 2) We don't typically resample - most analyses are done in native space by default cheers Bruce On Thu, 31 Aug 2017, Jiahe Zhang wrote: > Dear Freesurfer experts, > I have two questions regarding preproc-sess: > > 1) What is

Re: [Freesurfer] motion estimates

Hi James after running recon-all you can use mri_cnr to measure CNR (which is usually more interesting than SNR). Motion is harder. Martin investigated this at some point, but I'm not sure where he left it cheers Bruce On Thu, 31 Aug 2017, James Welsh wrote: Dear Freesurfer experts, I

Re: [Freesurfer] aparc.stats files from FreeSurfer 6.0

a) yes b) yes, of course. We are always trying to improve things, so the new versions are almost always a little different cheers Bruce On Thu, 31 Aug 2017, Mehta, Chintan wrote: Dear FreeSurfer Users, I have run recon-all on data using both FreeSurfer versions 5.3.0 and 6.0. FS v6.0

Re: [Freesurfer] Freesurfer Preliminary Questions

Hi Bruce, Do you have any suggestions as to how to determine the correct directory and pathway to use? Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.lede...@labiomed.org From:

Re: [Freesurfer] aparc.DKTatlas+aseg.mgz

Dear experts, looking into the output of Freesurfer in this page https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles I see that there should be a file named "aparc.DKTatlas+aseg.mgz". Is this atlas can be generated with the presence of FLAIR images. When i run recon-all without FLAIR

[Freesurfer] preproc-sess

Dear Freesurfer experts, I have two questions regarding preproc-sess: 1) What is the default algorithm that does the functional-anatomical registration? And is there any way to change the default to other types of registration methods? 2) If I do not want to normalize to template, i.e. I want

[Freesurfer] motion estimates

Dear Freesurfer experts, I want to inquire if there are any tools in freesurfer that can help to evaluate T1 quality regarding motion and SNR. Thanks! James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] aparc.stats files from FreeSurfer 6.0

Dear FreeSurfer Users, I have run recon-all on data using both FreeSurfer versions 5.3.0 and 6.0. FS v6.0 generated files named lh.aparc.pial.stats and lh.aparc.stats, whereas FS v5.3.0 created only lh.aparc.stats. I wanted to verify two things: (a) Is it right that surface areas in

Re: [Freesurfer] How to estimate the Intracranial area?

Hi Zhiliang the space inside the skull is a volume, so I'm not sure any measure of area would make sense. cheers Bruce On Thu, 31 Aug 2017, Zhiliang Long wrote: Dear FS experts:      I'am writting to ask for help about intracranial area. I can find the information of intracranial volume

[Freesurfer] Combining Echo Frames Error

Dear Freesurfer experts, Here are the commands I entered, and errors I received: recon-all -subjid Test01 -i /Testing/T1_MEMPRAGE_4/IM-0002-0206.dcm -autorecon1 #@# MotionCor Thu Aug 31 09:00:15 EDT 2017 Found 1 runs /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001.mgz Checking for