Re: [Freesurfer] Fw: glm error

External Email - Use Caution Mean correlation values to the seed from activations of a pcc.mgh map from each individual subject. On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > mean over what? a parcellation? an activation cluster? > > On

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Hi Andrew, I am very sorry for the delay of my answer.  Everything works with the patch.  Thank you so much! Cheers, Maxime On Oct 10, 2019, at 11:39 AM, Hoopes, Andrew wrote: Hi Maxine,

Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels

External Email - Use Caution Hi Kersten, Thanks you so much for your reply and sorry I missed your earlier message. I'll implement the suggestions you've suggested. Thanks again. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Mar

Re: [Freesurfer] Fw: glm error

mean over what? a parcellation? an activation cluster? On 10/31/2019 3:15 PM, Amrita Bedi wrote: External Email - Use Caution Thank you Dr Greve, that issue is resolved. I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subje

Re: [Freesurfer] Fw: glm error

External Email - Use Caution Thank you Dr Greve, that issue is resolved. I do have another question. I’m now trying to extract mean correlation values to the seed from each individual subject and not sure how to go about this. On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D

Re: [Freesurfer] nuisance factors

You have to specify that this is a DOSS analysis with --fsgd CMTX_b.fsgd doss On 10/31/19 12:38 PM, Georgina Angelopoulou wrote: > > External Email - Use Caution > > Dear Douglas, > > Thank you once again for your reply and your help. > > Attached please find the fsgd file (CMTX_b.fsgd)

Re: [Freesurfer] Cortical thickness values on a vertex base level

You can run mri_surfcluster with your fdr threshold as the --thmin value. This will output cluster number (ocn) map. This will assign the cluster number to a vertex. You can then use mri_segstats with --seg ocn.mgz --excludeid 0 and input being the mean thickness or area maps. When you use area

Re: [Freesurfer] PETsurfer issue

The MGX method is only valid in voxels that have some gray matter in them (defined as 1% in the command line below), so any WM is set to 0 (probably accounts for the big hole that you see). The mgx output is divided into cortical GM and subcortical GM, so you are probably looking at the cortica

Re: [Freesurfer] FSGD file formatting for Xhemi

There are not any restrictions, just do the same as you would for a non-paired analysis. In any event, you are creating a linear model y = a +b1*x1 + b2*x2 ... where y is the input (paired diff) and x1, x2, etc, are your factors. You are the one who knows your data and what models would be approp

Re: [Freesurfer] Cortical thickness values on a vertex base level

External Email - Use Caution Dear Greve, Thank you for your quick respons. Yes, I believe that is what I mean. Let me illustrate with some (fictive) data; We were able to prove these data for the entire hemisphere as can be seen below. Group 1 Group 2 Difference Sig. Th

[Freesurfer] PETsurfer issue

External Email - Use Caution Hello, Wondering if anyone has had issues with PETsurfer partial volume correction. When I have used it, there are large 'holes' in the white matter. I am mostly interested in the hippocampal area, which seems unaffected by these holes, but I'm not

Re: [Freesurfer] FSGD file formatting for Xhemi

External Email - Use Caution My doubt is, if it is possible to use a FSGD file to add variables to a --paired-diff analysis. If it is, what would be the right way to format the FSGD file. Thanks in advance. On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harv

Re: [Freesurfer] nuisance factors

External Email - Use CautionDear Douglas,  age_sim.mtx Description: Binary data CMTX_b.fsgd Description: Binary data Thank you once again for your reply and your help.Attached please find the fsgd file (CMTX_b.fsgd) including age row scores and the contrast file. The command line

Re: [Freesurfer] Fwd: Fw: glm error

You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz  file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz Where you have "bilat*", that should only be one folder On 10/31/19 12:04 PM, Amrita Bedi wrote: > > External Email - Use Caution >

[Freesurfer] Fwd: Fw: glm error

External Email - Use Caution -- Forwarded message -- From: *abedi...@citymail.cuny.edu * < abedi...@citymail.cuny.edu> Date: Thursday, October 31, 2019 Subject: Fw: glm error To: Amrita Bedi Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College

Re: [Freesurfer] Cortical thickness values on a vertex base level

I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area? On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote: > > External Email - Use Caution > > Dear developers, > > For a case-control study we are comparing the cortical thickness and > cortical surface