Re: [Freesurfer] DICOM file organization

External Email - Use Caution This is typically done *before* running FreeSurfer, and to the best of my knowledge, there is no FreeSurfer tool that does it. Also I think there is no one way to do it in generak. The names produced depend on your DICOM to NIFTI conversion software

Re: [Freesurfer] using T2 for recon-all

You will definitely get systematic differences between using T2 and not, so you could have a false positive (or negative) if you are comparing those two groups. On the other hand, you probably changed the T1 protocol a lot between now and 10 years ago, so you are likely to have bias either way.

Re: [Freesurfer] How to measure correlation using FreeSurfer

You can run a group analysis https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis One of the outputs will be the correlation (along with the sig of the correlation) On 2/13/2022 6:35 PM, Koustav Chatterjee wrote: External Email - Use Caution Dear FreeSurfer experts, I

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

can you send your fsgd file and the Xg.dat file? On 2/14/2022 1:21 AM, 정현우 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare cortical surface area among three groups while controlling for estimated total intracranial volume (eTIV), as describ

Re: [Freesurfer] FW: Problems with recon for manually fixed Talairach

Yes, I still don't understand. That snippet of code that you point out is embedded in an if statement:  if($DoCleanTal || ! -e $xfm) then    Copy  endif ! -e $xfm means that the file must not already exist. So, as long as that file exists, it will not copy over it ($DoCleanTal is a special f

Re: [Freesurfer] hippocampal segmentation differences pediatric sample

I would not expect the different subjects to be the same (they are different subjects). I don't know how you'd get them back to native space. The opposite of how you normalized them I guess. On 2/12/2022 8:15 AM, Aleksandra Lecei wrote: External Email - Use Caution Hi, I'm new to th

Re: [Freesurfer] How to measure correlation using FreeSurfer

External Email - Use Caution Thanks. I am afraid since I am working on a single group ( only patient group), can I run the same? On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve, wrote: > You can run a group analysis > https://secure-web.cisco.com/1Ff-dG17xkRm3OY5bDYlwFveyhE5l-WyD

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

OK, I see. How would you recommend correcting for multiple comparisons if the perm option does not work with PVR? Also, are you saying that I should only use the glm.osgm.lh/eres.mgh file as a pvr argument? Does this look correct: mri_glmfit \ --y lh.cbf.fwhm10.mgh \ --fsgd cbf.fsgd \ --pvr glm

Re: [Freesurfer] How to measure correlation using FreeSurfer

Yes, single group just means a single class in the FSGD file. Then just include your clinical measure as a variable in the FSGD On 2/14/2022 11:39 AM, Koustav Chatterjee wrote: External Email - Use Caution Thanks. I am afraid since I am working on a single group ( only patient group)

Re: [Freesurfer] How to measure correlation using FreeSurfer

External Email - Use Caution Thanks a lot. On Mon, Feb 14, 2022 at 10:48 PM Douglas N. Greve wrote: > Yes, single group just means a single class in the FSGD file. Then just > include your clinical measure as a variable in the FSGD > > On 2/14/2022 11:39 AM, Koustav Chatterje

[Freesurfer] autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)

External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing t

[Freesurfer] How to find mean LGI?

External Email - Use Caution Hi, I was hoping to extract mean LGI, similar to how there is a mean thickness. But the default LGI output includes the eTIV rather. What would the command be to collect the stats into a csv for this mean LGI? Get Outlook for iOS

Re: [Freesurfer] [External] Re: [External] Re: white matter measurements for labels/annotations

External Email - Use Caution Is there an argument to put in a custom LUT? I don’t see it in the options for mri_surf2volseg. I’m assuming I have to put in average/colortable_vpnl.txt and average/colortable_BA.txt Get Outlook for iOS

[Freesurfer] PetSurfer: subcortical volume-based analysis

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I have completed all of the steps from the PetSurfer wiki. I now have the preprocessed, averaged, resampled, smoothed PET data in MNI305 space which is constrained to the

[Freesurfer] PetSurfer: CORTICAL volume-based analysis

External Email - Use Caution Dear Freesurfer Developers I am doing an ROI--based amyloid PET scan analysis. I am following the steps from the PetSurfer wiki. I see instructions for how to do a cortical surface-based group analysis. I also see how to do a subcortical ROI-based a

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you for your reply. I attached the fsgd file, mtx file and the Xg.dat file below. Hyunwoo Jeong 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이 작성: > can you send your fsgd file and the Xg.dat file? > > On 2/14/2022 1:21 AM, 정현우 wr

Re: [Freesurfer] Virtualbox: developer's password

External Email - Use Caution Sending the info to your email shortly. -  R. On Feb 13, 2022, at 04:56, Francois Leroy wrote:External Email - Use CautionHi,I am trying to set-up Freesurfer (fs_ubuntu_18_04_06) from Oracle VM Virtualbox.

Re: [Freesurfer] using T2 for recon-all

External Email - Use Caution Thank you. This is very helpful. And just a follow-up question about this: Can we use data that old? (And make a comparison to images collected this year). I mean is it possible to compare structural scans which were acquired such a long time ago and wi