Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Great! Thank you for all the help. On Wed, Jan 6, 2016 at 12:38 PM, Douglas N Greve wrote: > Yes. In theory you can compute the number of vertices by dividing by the > average vertex area > > On 01/06/2016 01:34 PM, Tara Miskovich wrote: > > Thank you for the clarification. So

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Thank you for the clarification. So even though it is a vertex-wise threshold, there is no minimum amount of vertices, it goes by area? Tara On Wed, Jan 6, 2016 at 12:21 PM, Douglas N Greve wrote: > Area in mm^2 > > On 01/06/2016 01:16 PM, Tara Miskovich wrote: > > Thank you s

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

ustersize must be at least 473.758 to have a > cluster p-value of .045775 > > clear? > > doug > > > > On 01/05/2016 08:35 PM, Tara Miskovich wrote: > > Hello Freesurfer experts, > > > > I need help me finding how to get the minimum number of vertices >

[Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Hello Freesurfer experts, I need help me finding how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations used in qdec for a surface based analysis? This is per a reviewer request, but I cannot find anything on the wiki or in the mail

[Freesurfer] Files needed for qdec

Hello Freesurfer experts, I need to upload some data to a public domain and I am trying to best limit the amount of files needed. I am wondering what subjects files are absolutely necessary to run an analysis in qdec. This is for an lgi analysis. I tried only using the surf directory, but qdec wo

[Freesurfer] minimum number of vertices for cluster-correction

Hello Freesurfer experts, I need help me finding how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations? Is there a way to figure this out? -- Thank you, Tara ___ Freesurfer mailing lis

[Freesurfer] minimum number of vertices for cluster-correction

Hi all, Can someone help me find how to get the minimum number of vertices required to pass the cluster-corrected threshold with monte carlo simulations? -- Thank you, Tara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

Re: [Freesurfer] pial_lgi option in qdec

it. And then open a new terminal and start qdec. > > Keep me posted! > > Marie > > On Sep 17, 2015, at 4:26 PM, Tara Miskovich > wrote: > > Thank you for the response Marie. By home directory do you mean the > freesurfer home directory? Currently, I have it in the qde

Re: [Freesurfer] pial_lgi option in qdec

copying the .Qdecrc, did you check that the .Qdecrc file is in your > home directory and that MEASURE1 = pial_lgi is listed there? When this is > fine, start with a new terminal and pial_lgi should be in the option among > other measures. > > Let me know, > > Marie > &

[Freesurfer] pial_lgi option in qdec

Hi all, I just transferred data from a drive to do some LGI analyses, and all the data has already been processed and cached, so I have all the results sample to the fsaverage at various levels of smoothing for each subject. Additionally, I added the .Qdecrc file so pial_lgi would pop up as an op

[Freesurfer] LGI Topological Defect

Hi all, I am getting an error that seems common for people running LGI where it crashes due to a topological defect. I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good. Any advice on any other steps I can take? I have al

Re: [Freesurfer] Need help with mris_convert

It worked! Thank you so much Bruce! Tara On Thu, Aug 7, 2014 at 1:59 PM, Bruce Fischl wrote: > you are missing one argument (the name of the label). It should be: > > mris_convert --label lh.cluster1.label NAME lh.white lh.cluster1.label.gii > > > > On Thu, 7 Aug 2014,

Re: [Freesurfer] Need help with mris_convert

surface (like connectivity) > > On Thu, 7 Aug 2014, Tara Miskovich wrote: > > Hi Doug thank you for the response. I just wasn't sure what was required >> here. Specifically why we need to call on the white matter surface. And >> what >> the second V1 would be for. >&

Re: [Freesurfer] Need help with mris_convert

Hi Doug thank you for the response. I just wasn't sure what was required here. Specifically why we need to call on the white matter surface. And what the second V1 would be for. Thank you, Tara On Thu, Aug 7, 2014 at 11:05 AM, Tara Miskovich wrote: > Hi all, > > I could really

[Freesurfer] Need help with mris_convert

Hi all, I could really use some help with this I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required h

[Freesurfer] Please need help with mris_convert.

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label aft

[Freesurfer] Help with mris_convert

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label aft