Re: [Freesurfer] XL defect in recon-all

External Email - Use Caution Hi I found this tutorial helpful https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview I was able to correct a defect of similar size (18k+ vertices) corresponding to a “huge periventricular heterotopia” according to clinic

Re: [Freesurfer] Tuning WM threshold

Hi Paul yes, the -mprage flag could definitely cause what you are seeing. It assume higher CNR and lower SNR in the images (hence bigger class separation between gray and white), and if used on SPGR it could definitely erode boundaries like this. cheers Bruce On Fri, 31 Jan 2020, Wright, Pau

Re: [Freesurfer] XL defect in recon-all

Hi Devika these types of huge defects usually mean something dramatic has gone wrong with e.g. the skull stripping. Even if it completes it is unlikely to generate accurate surfaces. Check the ?h.inflated.nofix and ?h.orig.nofix over the wm.mgz and you will likely find the issue quicky cheers

Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

External Email - Use Caution Hi Bruce, Thank you for your help! I removed the IsRunning.lh+rh script as well and reran the recon. Everything seems to have worked! -Laurel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl

Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

glad to hear it Bruce On Fri, 31 Jan 2020, Laurel Quinlan wrote: External Email - Use Caution Hi Bruce, Thank you for your help! I removed the IsRunning.lh+rh script as well and reran the recon. Everything seems to have worked! -Laurel ___

[Freesurfer] Pial surface not including parts of cortex

External Email - Use Caution Dear Freesurfer experts, I was wondering if I could get some help with a problem that I keep experiencing. For some of the patients, their gray matter is not properly included in the pial surface. I have tried tkmregister and using control points but n

Re: [Freesurfer] Pial surface not including parts of cortex

Hi Monica sure, if you tar and gzip the entire subject dir and ftp it to us, then send us a description that includes the voxel coords of where you think things should be more accurate we will take a look cheers Bruce On Fri, 31 Jan 2020, Monica Bondy wrote: External Email - Use

Re: [Freesurfer] Pial surface not including parts of cortex

External Email - Use Caution Thank you so much! I just sent the gzipped subject directory *subjectdir.gz. * My main concern is that a lot of the lateral gray matter isn't included. Here are some Talairach coordinates that illustrate the areas I'm concerned about: (-67 -27 -9) (-65

[Freesurfer] Software support

External Email - Use Caution Hi, I was wondering if there is a version available for Windows OS or is this available for Mac and Linux only? Thank you, - Ricardo J. Rodríguez ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] Software support

Not native to windows. If you have windows 10, you can install an ubuntu shell and run FS from that On 1/31/2020 12:43 PM, Ricardo J Rodriguez Colon wrote: External Email - Use Caution Hi, I was wondering if there is a version available for Windows OS or is this available for Mac and

Re: [Freesurfer] Software support

External Email - Use Caution Alright, I'll look into that. Thank you! - Ricardo J. El vie., 31 ene. 2020 a las 14:23, Douglas N. Greve () escribió: > Not native to windows. If you have windows 10, you can install an ubuntu > shell and run FS from that > > On 1/31/2020 12:43 PM,

[Freesurfer] Question longitudinal study about treatment effect with change of scanner and head coil?

External Email - Use Caution Dear experts, I am reviewing a study that proposes a longitudinal study in patients across several years on the effect of medical treatment in terms of fcMRI and DTI-connectivity measures. However, in several but not all patients, the scanner was upgr

Re: [Freesurfer] Extract specific LGI and Volume values

Sorry, I do not have the previous emails, can you repost with previous emails in the message? On 1/28/2020 7:35 PM, Tien Pham wrote: External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI diff

Re: [Freesurfer] Question longitudinal study about treatment effect with change of scanner and head coil?

Hi Markus - If you were to find longitudinal changes in this study, you would have no way of knowing if they are changes in the brain or changes in the instrument used to measure the brain. a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Markus Gs

Re: [Freesurfer] Cortical segmentation error

It is hard to say from that image because of the aseg, but it looks like the white surface is not extending far enough and so the pial surface starts too far away to get all the way out. You might need some control points in the WM in that area On 1/28/2020 7:56 PM, Monica Bondy wrote:  

Re: [Freesurfer] Question longitudinal study about treatment effect with change of scanner and head coil?

External Email - Use Caution Thank you, Anastasia, that was my thoughts also. So there is no way regressing this out, right? Best, Markus Le sam. 1 févr. 2020 à 00:10, Yendiki, Anastasia a écrit : > Hi Markus - If you were to find longitudinal changes in this study, you > would

Re: [Freesurfer] Extract specific LGI and Volume values

External Email - Use Caution Thank you for your response. I used longitudinal pipeline for my data set with two time points and calculated the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on sub

Re: [Freesurfer] Question longitudinal study about treatment effect with change of scanner and head coil?

No, because it is not balanced. None of your subjects were scanned on the Prisma at baseline and on the Trio at follow-up 🙁 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Markus Gschwind Sent: Friday, January 31, 2020 6:17 PM To: Freesurfer support l

[Freesurfer] orig2rawavg transformation matrix

External Email - Use Caution Hello! How can I get a transformation matrix that maps orig.mgz to rawavg.mgz? I only see examples bringing freesurfer results into original anatomical space with mri_vol2vol, but I really just want the transformation matrix. Thanks! Best regards, Sam _

Re: [Freesurfer] mri_glmfit with flag -pvr

It can be dods or doss. If you don't specify, then it will use doss. To specify, add doss after the fsgd file On 1/29/2020 10:53 AM, Vicky Shi wrote: External Email - Use Caution Hi Doug, Thank you so much for your respond. Greatly appreciate it!! I have one more question. If I run

Re: [Freesurfer] medial wall metric file

should be something like mri_label2label --srclabel input.label --trglabel ouput.label --outmask label.mask.nii.gz --regmethod surface --hemi lh --srcsubject subject --trgsubject subject On 1/30/2020 10:07 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Having diffic

Re: [Freesurfer] orig2rawavg transformation matrix

check out this http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 1/31/2020 6:36 PM, Sam W wrote: External Email - Use Caution Hello! How can I get a transformation matrix that maps orig.mgz to rawavg.mgz? I only see examples bringing freesurfer results into original an

Re: [Freesurfer] PetSurfer questions

On 1/30/2020 3:39 AM, Soo-Jong Kim wrote: External Email - Use Caution I ran gtmseg for my partial volume correction 1. but I have a question. What regions are for the detail?? in this option. mri_gtmpvc --default-seg-merge. I searched mri_gtmpvc --help but it is default schema for

Re: [Freesurfer] make_average_surface with unique surface

What are you trying to do? Just collect/average the ratio maps? If so, then use mris_preproc instead of make_average_surface. You don't actually have a surface there but a surface overaly. On 1/29/2020 7:19 PM, Gabrielle-Ann Torre wrote: External Email - Use Caution Hello developers,

Re: [Freesurfer] Extract specific LGI and Volume values

External Email - Use Caution Can you read my message? I used longitudinal pipeline for my data set with two time points and measured the LGI differences between them. Then I created the label based on significant clusters which showed in QDEC. I tried to load the label on the subje