[Freesurfer] Differences in FLAIR assisted pial segmentation from FS6.0 to FS7.1

External Email - Use Caution Dear FreeSurfer experts, We have processed UKB data with FLAIR assisted pial segmentation using FS7.1. The results differs quite a lot from using FLAIR assisted pial segmentation in FS6.0. For details please see the reported issue on the freesurfer

Re: [Freesurfer] Differences in FLAIR assisted pial segmentation from FS6.0 to FS7.1

External Email - Use Caution We have seen surface placement issues with FreeSurfer 7.X on HCP data as well, which is why we’ve continued to recommend folks use FreeSurfer 6.X with the HCP Pipelines for now. Overall, we’ve found that getting the surface placement right is often

[Freesurfer] Hippocampus subfield segmentation

External Email - Use Caution Hello FS experts, I have performed hippocampus subfield segmentation on my T1 scans. I also gathered the volume from all my analyzed subjects through the following command - quantifyHippocampalSubfields.sh T1 hippotest.txt Now I want to perform sta

Re: [Freesurfer] Hippocampus subfield segmentation

Dear Ishi, At this point, you have a bunch of volumes for each subjects (in hippo test.txt), not maps. You can analyze them with your favorite statistical software ;-) Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On J

Re: [Freesurfer] Hippocampus subfield segmentation

External Email - Use Caution Hello, Thank you for the quick response. Yes, I have kind of done that. But just wanted a little more clarification if I should use GLM further. Thanks for the info. On Thu, Jun 24, 2021 at 7:41 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mg

Re: [Freesurfer] nu correction

My understanding is that you compute the ratio on the uncorrected images because the ratio will be free from bias (part of the motivation for doing it) On 6/14/2021 1:23 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, I would like to create myelin maps calcula

Re: [Freesurfer] Running FreeSurfer with fmriprep

It looks like the data are fairly low quality. This will require some manual intervention (control points, fixing topologogical errors, etc). See our wiki on manual interventions On 6/15/2021 10:52 AM, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Here is what I am refer

Re: [Freesurfer] Longitudinal processing

If you are going to compare the volume across subject, then it does need to be corrected with eTIV On 6/15/2021 8:06 AM, AJ wrote: External Email - Use Caution Hi, After running longitudinal processing and creating base and long runs, When looking at volumes of various structures ov

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

Don't use --grf with surfaces On 6/15/2021 7:24 PM, Paul, Jhelum wrote: External Email - Use Caution Hello, I also have the same error. I have been looking into all the tutorials available for Freesurfer v7 and trying to search why, mri_glmfit-sim   --glmdir lh.age_gender_volume.gl

Re: [Freesurfer] Extracting stats from surface overlay

You can do it in two ways. - First, you can just apply mri_segstats with the --annot option to get the mean NODDI values using the ?h.aparc.stats file, then compute the LI on the ROIs - Second, you can compute the map of the LI values (just added this here https://surfer.nmr.mgh.harvard.edu/fsw

Re: [Freesurfer] analyzing fmriprep data in fsfast

Sorry, it is too hard to try to read your code to figure out what is  going on. Is is possible that you are passing surface data into the volume  (mni305) analysis? On 6/16/2021 11:51 AM, Pedersen, Walker Scott wrote: I am trying to use fsfast to analyze task-based functional data output by fm

Re: [Freesurfer] The specific steps of the mri_surf2surf command

Is there a question that you have? On 6/17/2021 7:45 AM, 1248742467 wrote: External Email - Use Caution Hello, Fs I am not familiar with the exact steps of sampling a pre-segment file into the FSAVERAGE5 space. In other words, I am not very familiar with the exact steps of the mri_su

Re: [Freesurfer] T2 T1 registration with mri_robust_register

Try mri_coreg. You can run it with multiple cores with --threads N On 6/17/2021 8:48 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I would like to co-register T2 to T1 robustly, both images have a resolution of 0.65mm3. Firstly, I tried bbregister with the '-

Re: [Freesurfer] mri_convert help w/ GE Genesis files

Have you tried dcm2niix? It's pretty robust On 6/17/2021 6:59 PM, Christopher Mcnorgan wrote: External Email - Use Caution External Email - Use Caution Hi all, I’ve been provided with some data collected on a 1.5T GE scanner from an old published study. The paper doesn’t ind

Re: [Freesurfer] Demeaning for Longitudinal Analyses

1. You need to be careful here demeaning. When you set up a linear model, you have two parameters: the intercept and the slope. Without demeaning, the intercept is defined to be where the line intercepts the y axis at x=0 (in this case age=0, birth). When you demean age, you do the test at x=me

Re: [Freesurfer] Seeing "Include the flag -cw256 with recon-all!" for HCP 7T data

Can you send the recon-all.log file? On 6/18/2021 10:54 AM, Soichi Hayashi wrote: External Email - Use Caution Hello. I am having a problem running freesurfer on a HCP 7T data and I am wondering if someone from this mail list could help me out. I am trying to run freesurfer (v7.1.1)

Re: [Freesurfer] Running FreeSurfer with fmriprep

External Email - Use Caution Hi Douglas, Whay do you exactly mean by low quality data? As far as I have been told, is high. I would like to know so I cam discuss it further with the engineers as we are at the very beggining of the acquisition. Kind regards, Rosie El jue., 24 ju

Re: [Freesurfer] Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats

External Email - Use Caution Hello, I was wondering if anyone has an answer to my question. Cheers On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude wrote: > Hello All, > > I was wondering if the Right/Left-Cerebral-White-Matter in the > aparc+aseg.mgz contains WM hypointensitie

Re: [Freesurfer] Visualization of specific ROIs

In Freeview, hit the "View/Edit" button. The resulting interface will allow you to hide/show any combination of labels. You can hit the "All" button to turn them all off and then just add the ones you want. On 6/24/2021 12:11 PM, Jennifer James, MD wrote: External Email - Use Caution

Re: [Freesurfer] Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats

it should not have hypointensities (as long as they are labeled as such) On 6/24/2021 12:07 PM, miracle ozzoude wrote: External Email - Use Caution Hello, I was wondering if anyone has an answer to my question. Cheers On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude

Re: [Freesurfer] Running FreeSurfer with fmriprep

It just looked noisy to me, but then again the images were pretty small On 6/24/2021 12:00 PM, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Hi Douglas, Whay do you exactly mean by low quality data? As far as I have been told, is high. I would like to know so I cam discu

[Freesurfer] Fwd: Yeo atlas for children!

External Email - Use Caution Hi all, I am reposting my concerns below. I would really appreciate any help. -- Forwarded message - From: Martin Juneja Date: Fri, Jun 18, 2021 at 6:16 PM Subject: Yeo atlas for children! To: Freesurfer support list Dear experts,

Re: [Freesurfer] Is hypointensities part of lh/rh cerebral white matter from aparc+aseg.mgz using mri_segstats

External Email - Use Caution Great. thanks Doug. I appreciate it On Thu, Jun 24, 2021 at 12:07 PM miracle ozzoude wrote: > Hello, > I was wondering if anyone has an answer to my question. > > Cheers > > On Wed, Jun 23, 2021 at 5:42 PM miracle ozzoude > wrote: > >> Hello All, >>

[Freesurfer] Cortical thicknees normalization values

External Email - Use Caution Hi freesurfer user. I have been working with some cortical thickness values of a control group to test some changes related to cognitive training. However, I have been hesitating about whether I have to normalize the cortical thickness values (as h

Re: [Freesurfer] Running FreeSurfer with fmriprep

External Email - Use Caution Hi Douglas, Could I share one T1 with you so you can closely inspect it and give me your opinion? Kind regards, Rosie El jue., 24 jun. 2021 18:22, Douglas N. Greve escribió: > It just looked noisy to me, but then again the images were pretty small

Re: [Freesurfer] Longitudinal processing

External Email - Use Caution Many thanks. Best regards On Thu, Jun 24, 2021, 10:07 Douglas N. Greve wrote: > If you are going to compare the volume across subject, then it does need > to be corrected with eTIV > > On 6/15/2021 8:06 AM, AJ wrote: > > External Email - Use

[Freesurfer] Saving ROIs on freeview

External Email - Use Caution Hello, I am attempting to edit ROIs using Freeview, but when I save the label files, none of my edits are being saved. I am using a Mac. When I tried troubleshooting on a different computer (PC), I was able to save changes using the same methods. Could

Re: [Freesurfer] Saving ROIs on freeview

Can you try the latest build of freeview for macOS? You can download it from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Jun 24, 2021, at 6:09 PM, Tina Thomas mailto:tinathoma...@gmail.com>> wrote: External Email - Use Caution Hello, I am attempting to

Re: [Freesurfer] Fwd: Yeo atlas for children!

External Email - Use Caution Hi Martin, With regards to adolescents versus adults, there's obviously differences between the two age groups. In our experience, when we re-estimate parcellations from this study (https://secure-web.cisco.com/1TF7OmC5fKijUUx5uZkr1n5IUfkGr1RFX7MO-Emd