On Jul 11, 2018, at 3:49 PM, srishti goel <23srishtigoel@gmail.com> wrote:

Hi Rupoeng,

Yes it says built in February 2018.

Could you please tell me once the Mac build of Freeview is updated so I can download the newest version.

Thank you so much, really appreciate it!

Best,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Wed, Jul 11, 2018 at 3:35 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:

Hi Srishti,

The mac build of freeview on our download page appears to be quite old. If you go to About menu, you should see the build time. We will update it shortly.

Best,
Ruopeng

On 07/11/2018 03:02 PM, srishti goel wrote:

Hi Rupoeng,

I dowloaded the nightly as you had suggested, followed the steps in the link you had sent but I am still not able to see the z-order function. I tried it a couple of time, deleting and re-doing everything again but I can't see the z-order option in Freeview.

Please let me know what else can I do to check that. 

Best,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Wed, Jul 11, 2018 at 2:59 PM, srishti goel <23srishtigoel@gmail.com> wrote:

Hi Rupoeng,

I dowloaded the nightly as you had suggested, followed the steps in the link you had sent but I am still not able to see the z-order function. I tried it a couple of time, deleting and re-doing everything again but I can't see the z-order option in Freeview. I have attached two screenshots of what the Freeview looks like to me.

Please let me know what else can I do to check that. 

Best,

Srishti

<Screen Shot 2018-07-11 at 2.43.41 PM.png>

<Screen Shot 2018-07-11 at 2.44.02 PM.png>

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Thu, Jul 5, 2018 at 1:43 PM, srishti goel <23srishtigoel@gmail.com> wrote:

Thanks so much Ruopeng

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Thu, Jul 5, 2018 at 1:40 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:

After you load the label or overlay you should see it on the left panel.

Best,

Ruopeng

On Jul 5, 2018, at 12:54 PM, srishti goel <23srishtigoel@gmail.com> wrote:

        External Email - Use Caution        

Hi Rupoeng, 

We downloaded the nightly build for that option but I don't see it coming on the GUI. I scrolled through every option on the task bar and also the left panel on the GUI but nothing corresponded to 'z-order'. Could you please direct me to where exactly should I be looking for this option?

Thanks,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:

Yes, I have put an option called z-order in the GUI to control order of rendering for overlays, labels and annoations. To use it you will need to download and install the nightly build from here:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best,

Ruopeng

On Jun 9, 2018, at 11:04 AM, srishti goel <23srishtigoel@gmail.com> wrote:

        External Email - Use Caution        

Hi Ruopeng,

I just wanted to check and see if there is any update about adding the option of changing surface labels to come below overlays in Freeview.

Thanks!

Best,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtigoel@gmail.com> wrote:

Thanks a lot Ruopeng, really appreciate it.

Best,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:

It will be added very soon. I'll let you know when it is ready.

Best,
Ruopeng

On 05/28/2018 05:35 PM, srishti goel wrote:

Hi Ruopeng,

Thank you so much! That option will be super helpful. Are you planning to add that option to Freeview soon?

Best,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:

Hi Srishti,

In freeview surface labels are always displayed on top of overlays. I will add an option to change that.

Best,

Ruopeng

On May 28, 2018, at 9:18 AM, srishti goel <23srishtigoel@gmail.com> wrote:

Hello,

I did use Freeview but I think using either TkSurfer or Freeview won't matter because what I am trying to figure out is what the fthresh value means for the map.

From reading the archive, I understand that, for instance, fthresh value of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on intensity/ only voxels which are overlaid by 50% of the subjects. In my case, the maps are visible at fthresh 0.1 and below but since these are already thresholded maps from a meta-analysis I am not very clear on how to interpret the fthresh here. Is it voxels overlaid by ~80% of studies?

The other thing I want to figure out is that right now when I view my overlay with two other labels, the labels (when in solid color and not outline) cover my overlay. But I would want it the other way round such that the overlay comes on top of the solid colored labels. Does anyone know how I can achieve that?

Thank you so much!

Best,

Srishti

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

On Fri, May 25, 2018 at 10:09 AM, Douglas Greve <dgreve@mgh.harvard.edu> wrote:

I don't know anything about neuroelf, but unless your have a binarized map, then the map is going to change when you change the threshold. BTW, if you wan to use freeview, you can run tksurferfv with the same args as tksurfer

On 5/22/18 3:49 PM, srishti goel wrote:

       

Hello,

I am trying to view network based maps produced from a meta-analysis using neuroelf on the surface in freesurfer. The meta-analytic maps are thresholded maps that represent the proportion of contrasts that activated at each voxel

I projected my maps on the surface using:

mri_vol2surf --src negative_allsocial_proportion.img --regheader mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5

Then to view it used:

tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii -fthresh 0.05

The issue I have is with the fthresh value. I read the wiki and some stuff on archive about the fthresh value but I am unsure what it exactly means and does. My issue is that the display of my maps changes when I change the fthresh value even though the maps have been k-thresholded using neuroelf before exporting them to freesurfer. More area is marked up when I decrease the threshold value from 0.1 to 0.05 and nothing is visible above 0.1

Does anyone have any thoughts about what might be going on there and how I can fix it?

Do I need to do something totally different from what I am doing?

Best,

Srishti

Social/Clinical Research Specialist

Child Imaging Research and Life Experiences Lab

University of North Carolina at Chapel Hill

email (W): srishtig@email.unc.edu

skype: srishti.goel12

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