Re: [Freesurfer] longitudinal analyses after lesion segmentation

Hi Kathleen, if you map one image to the other, this introduces interpolation artefacts, which will bias your analysis (any type of analysis, so this is already a problem in the lesion segmentation part). Technically you run longitudinal freesurfer on these images but (similar to the lesion ana

Re: [Freesurfer] Longitudinal processing and paralllel flag

Hi Erik, usually we parallelize the number of subjects, rather than the individual pipelines. That gives us the best performance. Best, Martin On Thu, 2018-12-06 at 11:07 +, Erik O'Hanlon wrote: > External Email - Use Caution > Hi FS experts, > > I'm running a longitudinal

Re: [Freesurfer] Longitudinal Stream - LONG step

It says "Could not find file ..". I wonder which one it is looking for. Did you try to completely delete this long subject dir and re-run from scratch? Do other time points with this base go through? If not, you could re- run the base also. Also when you open orig of all time points (from the l

Re: [Freesurfer] Longitudinal processing - LAS and RAS orientation baseline vs follow-up

Hi Elena, FreeSurfer put inputs in RAS coordinates (during the conform step at the very beginning), so it will take care of this. But only if the correct information is available from the input image header. If that header was corrupted earlier, it is impossilbe to know what coordinates the input

Re: [Freesurfer] Longitudinal stream : LME and limits of model

Hi Matthieu, no, sorry. Maybe you can find a local biostatistician who knows. A slope estimate with less time points is more uncertain than one with more time points (obviously). Also a slope estimate with time points on a line is more certain than one with time points values all over the place

Re: [Freesurfer] GPU/supercomputer adaptation of freesurfer?

External Email - Use Caution Hi Richard, That is a very good point. I knew it was being deprecated and there was talk of OpenCL but I have not been keeping up. Multicore systems were getting the most benefit from newer releases. Certainly, to run the existing CUDA code involved ma

Re: [Freesurfer] Segmentation Query

Hi Fariha The number of regions is based on the anatomy. You can combine them if you like. The volume to use is probably the aparc+aseg.mgz, which is easily convertible to .nii with mri_convert. Also, you should use freeview not tkmedit (tkmedit has been deprecated for many years) cheers B

Re: [Freesurfer] eTIV vs. ICV

Hi Jim it is an estimate of everything inside skull. cheers Bruce On Thu, 13 Dec 2018, Alexopoulos, Dimitrios wrote: External Email - Use Caution The eTIV from FS 6.0  has been used by many as a normalization measure for regional volumetric analyses. I know it is not a tr

[Freesurfer] Inferior colliculus and Brainstem-cochlear-nucleus

External Email - Use Caution Dear comittee, I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can freesurfer distinguish it from other brainstem structures in segmentation? I have found these references in the LUT "7100 Brainstem-inferior-colliculus and 7101 Brai

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

what is your input data format? On Fri, 14 Dec 2018, Geha, Paul wrote: Dear Bruce, Thank you for your reply. However, we are obtaining an odd result with FreeSurfer when we examine the volume of the left and right accumbens. In the UK BioBank data >20K subjects freesurfer segmentations the

Re: [Freesurfer] Inferior colliculus and Brainstem-cochlear-nucleus

Hi Chama sorry, not yet cheers Bruce On Fri, 14 Dec 2018, Chama Belkhiria wrote: External Email - Use Caution Dear comittee, I need ROIs of Inferior Colliculus and  Brainstem-cochlear-nucleus. Can freesurfer distinguish it from other brainstem structures in segmentation? I hav

Re: [Freesurfer] Inferior colliculus and Brainstem-cochlear-nucleus

We don't have ways to automatically segment those (yet). They were optimistically added to the LUT a few years ago:) On 12/14/18 10:49 AM, Chama Belkhiria wrote: External Email - Use Caution Dear comittee, I need ROIs of Inferior Colliculus and Brainstem-cochlear-nucleus. Can freesurfe

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

when you bring it up in freeview does it properly show left and right? If it ever went through analyze as a format you will have lost the information that lets us distinguish left from right cheers Bruce On Fri, 14 Dec 2018, Geha, Paul wrote: It is NIFTI format.   —— Paul Ge

Re: [Freesurfer] Error in running make_average_subject

can you include the full terminal output? On 12/13/18 7:45 AM, Emanuel Alvaredo wrote: External Email - Use Caution Hello Bruce, thanks for your anwer. Sure. The command is make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon Baez_Recon Bonilla_Recon The outpu

Re: [Freesurfer] Extracting both the GM and WM ROIs

External Email - Use Caution Hello, Does the fsaverage subject have a wmparc.mgz file? Thank you, Da-Yea -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesda

Re: [Freesurfer] Extracting both the GM and WM ROIs

No, but each individual subject does. On 12/14/18 11:04 AM, Song, Da-Yea wrote: > External Email - Use Caution > > Hello, > > Does the fsaverage subject have a wmparc.mgz file? > > Thank you, > Da-Yea > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto

Re: [Freesurfer] NormMean information

It could be anything related to the T1-weighting, so T1 itself or PD. It is possible for the T2* to affect it, but usually the echo time is too short for it to make much of a difference. I could imagine some other indirect effects because of the normalization itself. The normMean was not added f

[Freesurfer] FreeSurfer Stats files: format of 'Measure' lines

External Email - Use Caution Dear FreeSurfer experts, I'm parsing data from FreeSurfer stats files, e.g., /stats/lh.aparc.stats and aseg.stats. My question: when parsing measure lines, which combination of fields are guaranteed to uniquely identify a measure? Here are two exam

[Freesurfer] Power analysis

External Email - Use Caution I performed a two tailed t-test analysis using stats data and after the analysis, results were corrected for multiple comparisons using FDR. Now, I want to perform a power analysis and I have some doubts: 1. Gammavar is the variance or the standard d

Re: [Freesurfer] Program installation - fmriprep

Hi, Please see below my issue with a freesurfer license when I try to run fmriprep. Kind regards, Zeynab Alshelh, PhD | Postdoctoral Research Fellow Neuroinflammation and Pain Imaging Laboratory A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thir

[Freesurfer] mri_segstats reporting more decimals

External Email - Use Caution Hi Freesurfers, Is there an option to write out more decimals when using the mri_segstats command? I'm extracting mean diffusivity values and would need at least 5 decimals to make sense of them. Thanks for your help! Cheers Stephanie The informa

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed} {Disarmed}

External Email - Use Caution Hi Doug & Bruce, Thanks again to both of your for your help! I ended up using label2vol to extend the parcels into the wm and register them to DTI space. Using mri_segstats with an FA_skeletonised mask and the dti_FA.nii.gz image, I get reasonable W

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed} {Disarmed}

External Email - Use Caution My bad, I found that the output file from label2vol, vol250-?h.nii.gz, is not oriented correctly when I view it in fsleyes... Trying fslorient2std left vol250-?h.nii.gz totally un-impressed with the same orientation as before. Fslswapdim also doesn't

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

External Email - Use Caution Thank you Bruce for your reply and the helpful information. Our data never went through Analyze format (we converted the data from dcm > NIFTI using mricron). FreeView reads the data appropriately (confirmed by attaching a Vitamin D pill to one of our s