Re: [Freesurfer] Reviewer questions...

Hi Bruce, The hippocampal subfield segmentation. Regards, Jerome On 10 January 2017 at 15:25, Bruce Fischl wrote: > Hi Jerome > Do you mean the hippocampal subfield segmentation or the aseg whole > hippocampus one? > CheerS > Bruce > > > On Jan 9, 2017, at 6:37 PM, Jerome Maller > wrote: > > >

Re: [Freesurfer] Reviewer questions...

Hi Jerome Do you mean the hippocampal subfield segmentation or the aseg whole hippocampus one? CheerS Bruce > On Jan 9, 2017, at 6:37 PM, Jerome Maller wrote: > > Jerome ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

[Freesurfer] Reviewer questions...

Dear FreeSurfer development team, I have received Reviewer comments from a manuscript I recently submitted based on results from FreeSurfer (beta version) output. The focus of the study is the hippocampal tail. Whilst one Reviewer likes it, the other has asked a number of questions regarding the s

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

another question. How do I incoporate -cover_seg into it? do i need  surfaceRAS coordinates? On Mon, Jan 9, 2017 at 5:04 PM, miracle ozzoude wrote:Thanks for your response bruce. Do you think I can use it for 3T scans and do i need to specify a specific starting value? Best, 

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

yes, and you shouldn't need a starting value (not sure what that even means) On Mon, 9 Jan 2017, miracle ozzoude wrote: Thanks for your response bruce. Do you think I can use it for 3T scans and do i need to specify a specific starting value?  Best,  Paul On Mon, Jan 9, 2017 at 5:00 PM, Bruce

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

another question. How do I incoporate -cover_seg into it? do i need surfaceRAS coordinates for the seg? Thanks, Best Paul On Mon, Jan 9, 2017 at 5:04 PM, miracle ozzoude wrote: > Thanks for your response bruce. Do you think I can use it for 3T scans and > do i need to specify a specific starting

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Thanks for your response bruce. Do you think I can use it for 3T scans and do i need to specify a specific starting value? Best, Paul On Mon, Jan 9, 2017 at 5:00 PM, Bruce Fischl wrote: > Hi Paul > > it's to help with cortex where the deep layers are heavily myelinated and > the gray/white boun

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Hi Paul it's to help with cortex where the deep layers are heavily myelinated and the gray/white boundary isn't as big a jump in contrast as infragranular/supragranular. It usually is only needed for hires data cheers Bruce On Mon, 9 Jan 2017, miracle ozzoude wrote: hello Bruce, I have ano

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

hello Bruce, I have another question, what's the function of -first_wm_peak in mris_make_surfaces? I know it helps "settle WM surface at first peak in intensity profile insted of highest". what does this mean and do I need to specify a value for it. Thanks. Best, Paul On Mon, Jan 9, 2017 at 4:19 P

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Thanks a lot Antonin.I will try it out. I am trying to figure out how to use mris_make_surfaces to extend my pial surface with T2 argument included and also, play around with -first_wm_peak and -nsigmas On Mon, Jan 9, 2017 at 4:06 PM, Antonin Skoch wrote: > Dear Paul, > > you can also try to pl

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Hi Antonin the reason we didn't answer your post about the reposition tool is that it is really under development and for internal use only. You are welcome to try it out, but we don't have the bandwidth to support it at the moment. cheers Bruce On Mon, 9 Jan 2017, Antonin Skoch wrote:

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Dear Paul, you can also try to play with "reposition surface" tool in freeview, where you (apart from other options) can directly edit coordinates of the surface vertices. However, this tool is not well documented and I myself would like to know the significance of some of the parameters - see

Re: [Freesurfer] PETSURFER Tutorial Problems

That appears to be a problem finding a library. Unfortunately, the guy who would address this issue is gone until Jan 17. Can you wait until then? If so, please repost at that time. On 01/09/2017 03:27 PM, Anderson Napolitano wrote: > > Good Afternoon Support Team, > > > Per step one of your PE

[Freesurfer] PETSURFER Tutorial Problems

Good Afternoon Support Team, Per step one of your PETSURFER tutorial, the command: gtmseg --s ?, where the is the name of the subject that we had ran recon-all, outputs the error as described in out.txt attached in this email. If you have the time, it would be much appreciated if you can hel

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

I think this problem is fixed in 6.0 (if and when we get it out) On Mon, 9 Jan 2017, miracle ozzoude wrote: Thanks bruce for your response. I accidentally listed number 3 twice instead of 4. Here's my 4th question: Which of the mris_make_surfaces can I use to correct the pial surface when it d

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Thanks bruce for your response. I accidentally listed number 3 twice instead of 4. Here's my 4th question: Which of the mris_make_surfaces can I use to correct the pial surface when it does cross the white matter and also, which is helpful with white matter surface extension? Please see attached sc

[Freesurfer] automatic segmentation of hippocampal subregions in young children

Dr. Inglesias I am a developmental psychologist studying memory and brain development in early childhood at the University of Maryland. My lab has acquired whole-brain standard resolution T1-weighted scans and ultra-high resolution T2-weighted scans from 125 child participants aged 4-8 years. We

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

hmmm, you had 3 numbered questions below, which is what my response referred to On Mon, 9 Jan 2017, miracle ozzoude wrote: Thanks bruce for your response. Please, which of my questions did you answer since I listed 4. Best, Miracle  On Mon, Jan 9, 2017 at 2:46 PM, Bruce Fischl wrote:

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Thanks bruce for your response. Please, which of my questions did you answer since I listed 4. Best, Miracle On Mon, Jan 9, 2017 at 2:46 PM, Bruce Fischl wrote: > Hi Paul > > for 1 and 2, these are run internally to recon-all and don't need to be > run again afterwards. 3. looks right to me > >

Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Hi Paul for 1 and 2, these are run internally to recon-all and don't need to be run again afterwards. 3. looks right to me cheers Bruce On Mon, 9 Jan 2017, miracle ozzoude wrote: -- Forwarded message -- From: miracle ozzoude Date: Mon, Jan 9, 2017 at 11:06 AM Subject: mri

[Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

-- Forwarded message -- From: miracle ozzoude Date: Mon, Jan 9, 2017 at 11:06 AM Subject: mris_make_surfaces scripts and how and when to use To: Douglas N Greve Hello Freesurfer, I was going to the ReconAllDevTable (https://surfer.nmr.mgh. harvard.edu/fswiki/ReconAllDevTable) an

Re: [Freesurfer] dice coefficient computing

yes, you can use mri_convert as follows: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz assuming the rawavg.mgz has the 208x176x176 dimensions (which it should) cheers Bruce On Mon, 9 Jan 2017, N Saf wrote: Dear Bruce, thank you for your fast reply ,I think I could not ex

Re: [Freesurfer] dice coefficient computing

Dear Bruce, thank you for your fast reply ,I think I could not explain the problem correctly . I want the number of slices in aseg file convert from 256x256x256 to 208x176x176(the subject size) so I can enable to compute the dice coefficient with my Matlab code ? any suggestions how can I make it

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Dr. Reuter, Thank you for the clarification. The differences I am seeing are also in the T1.mgz file in the longitudinal run folder. I assume it is okay to use the T1.mgz from the longitudinal outputs as the original image as I can easily compare the same slice across different time points? A

[Freesurfer] mris_make_surfaces scripts and how and when to use

Hello Freesurfer, I was going to the ReconAllDevTable ( https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) and i came across 3 different mris_make_surfaces scripts. 1) When do I use any of the 3 mris_make_surfaces scripts after running recon-all -all? 2) Is there a default/standard nsigma

[Freesurfer] ROI with precise coordinates

Dear all, I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10,-15,-5. Does a comman

Re: [Freesurfer] dice coefficient computing

Hi Nazanin all our segmentations are in subject space, so it should be pretty straightforward cheers Bruce On Mon, 9 Jan 2017, N Saf wrote: Dear freesurfers, I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have manual segmentation for hippocampus in my subject space(208x17

[Freesurfer] dice coefficient computing

Dear freesurfers, I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256) and I have manual segmentation for hippocampus in my subject space(208x176x176)as well. I want to compute the dice coefficient with one simple Matlab code. how can I do it correctly ?if I want to bring the aseg to subje