Re: [Freesurfer] recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh

du < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Dan Levitas > *Sent:* Thursday, March 21, 2024 11:56 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] recon-all mris_preproc error: Cannot find > surf/lh.w-g.pct.mgh > > > > *

[Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution Hello, I've been following the FreeSurfer longitudinal LME analysis tutorial ( https://secure-web.cisco.com/1UXjrD54pEj2u6JH6Y-Z-dHoSgY6qcbXqPg43uVU2GGyBvmGYSpOkab0ovGwllJVYA7PInB9Oa-cCSrq2yGN2zfn8EBAUtT_yeaabIRnE4HnyhF8G3FJoSd6nbCQUf195Ng-xfgCokq08rSx

[Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution After spending additional time working through this, here are the current steps I’ve taken for running a mass-univariate LME longitudinal analysis on both hemispheres: 1). mris_preproc --qdec-long long.qdec.table.dat --target fsaverage -

[Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution Hello, I wanted to bump this post once more to see if I can get any guidance here. I believe I am close to solving this problem, but I have two lingering questions that are preventing me from moving forward. Thanks again. Dan___

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution Hi Martin, Thanks for the response! After my original post I went through things more carefully based on my two original two questions and made a follow-up post here (https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-mDFOvCAyWs2k

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution Hi Kersten, Thanks for this helpful summary. It seems then that it’s best to apply the threshold to the *sig.mgh file and visualize its results since it contains the sign that specifies the direction of the interaction effect. Assuming this is the

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

External Email - Use Caution Hi Kersten & Martin, I just wanted to ping this thread again, as I'm still unsure about my pcor value (4.4) that I'm getting. I've seen other posts where the threshold (thmin) value specified in functions such as mri_surfcluster are around 2 (corres

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

NxQfU2HiLkjcTh7ymFt6BEzz3Zg8A/https%3A%2F%2Faka.ms%2FAAb9ysg> > > -- > *Von:* Dan Levitas > *Gesendet:* Dienstag, Mai 7, 2024 7:11:58 PM > *An:* djlevitas...@gmail.com > *Cc:* kersten.di...@dzne.de ; > mreu...@mgh.harvard.edu ; > freesurfer@nmr.mgh.harvard.edu > *Bet

[Freesurfer] Incoporating synthstrip and synthseg into recon-all

External Email - Use Caution Hello, I am using freesurfer version 7.4.1, and would like to incorporate the recently introduced synthstrip and synthseg functions into my recon-all command, if that's possible. From this archive message ( https://www.mail-archive.com/freesurfer@nmr.m

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

gt; > Malte > > [1] > https://github.com/freesurfer/freesurfer/blob/dev/distribution/etc/recon-config.yaml > [2] https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < &g

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

. Thanks again. On Fri, Jun 7, 2024 at 9:10 AM Dan Levitas wrote: > Hi Malte, > > Thanks for this helpful information. Based on your response, I have a few > follow-up questions. > > 1). Can the expert file (expert.opts) contain a line for the SynthStrip > workflow and another

[Freesurfer] Cannot find mri/transforms/talairach.m3z file

External Email - Use Caution Hello, I am following the longitudinal freesurfer pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) and getting this error on the final (LONG) portion: *ERROR: cannot find or read transforms/talairach.m3z* I can c

Re: [Freesurfer] Cannot find mri/transforms/talairach.m3z file

priate for longitudinal processing? On Mon, Jun 17, 2024 at 10:21 AM Douglas N. Greve wrote: > Yes, that is the problem, not a lot of great options. One thing you could > try is to run synthmorph to create the m3z. > > On 6/10/2024 2:36 PM, Dan Levitas wrote: > > External Email

Re: [Freesurfer] Cannot find mri/transforms/talairach.m3z file

perimental and I was not intending for anyone to use them yet. That's why > I put in the FS_ALLOW_DEEP hook to act as a barrier. You obviously have the > expertise to get past that barrier, but it put you into a no-man's-land > that we do not support./ > >

[Freesurfer] Differences between lme_mass_fit_vw and lme_mass_fit_Rgw

External Email - Use Caution Hello, I've been analyzing a dataset consisting of two groups (control, clinical), each with two timepoints (tp1, tp2), following FreeSurfer's LME longitudinal analysis pipeline, to assess cortical thickness differences. Given the relative simplicity

Re: [Freesurfer] Differences between lme_mass_fit_vw and lme_mass_fit_Rgw

. > > Best, Martin > > > On 25. Jun 2024, at 17:47, Dan Levitas wrote: > > Hello, > > I've been analyzing a dataset consisting of two groups (control, > clinical), each with two timepoints (tp1, tp2), following FreeSurfer's LME > longitudinal analysis pipe

[Freesurfer] LME longitudinal subcortical ROI analysis

External Email - Use Caution Hello, I recently performed an LME longitudinal mass-univariate (surface) analysis and am now trying to do something similar, but with subcortical (aseg) ROIs instead. I first created an aseg table with the following command: * asegstats2table \

Re: [Freesurfer] LME longitudinal subcortical ROI analysis

51 AM Reuter, Martin,Ph.D. < mreu...@mgh.harvard.edu> wrote: > Hi Dan, > > You could do either one. I would recommend the mass univariate for > multiple independent test with the same design. > > Best, Martin > > On 26. Jun 2024, at 17:20, Dan Levitas wrote: > > &

Re: [Freesurfer] LME longitudinal subcortical ROI analysis

External Email - Use Caution Hi Martin, I wanted to ping this thread again, to confirm that my proposed mass-univariate workflow using the subcortical segmented ROIs is appropriate for the LME longitudinal analysis. Thanks again. Dan On Thu, Jun 27, 2024 at 5:44 AM Dan Levitas

Re: [Freesurfer] LME longitudinal subcortical ROI analysis

ding columns in your matrix directly, similar to using co-variates > such as eTIV. > > Best, Martin > > > On 1. Jul 2024, at 14:03, Dan Levitas wrote: > > Hi Martin, > > I wanted to ping this thread again, to confirm that my proposed > mass-univariate workflow using the

[Freesurfer] Interpreting LME results with multi-row contrasts

External Email - Use Caution I am performing a longitudinal LME analysis in which participants were scanned anywhere from 2-6 times over the course of several years. There are 4 groups denoting participants: Controls (C, coded as 0), group 1 (G1, coded as 1), group 2, (G2, coded as

[Freesurfer] Extract surface vertex IDs from significance map

External Email - Use Caution I have been using the Matlab LME tutorial to assess several time*group interaction effects in my dataset. I successfully created *sig.mgh files and used *mri_surfcluster* to generate cluster summary (*thickness.clustersummary.txt), which include each cl

[Freesurfer] Extract surface vertex IDs from significance map

External Email - Use Caution I may have spoken too soon. It appears that the —olab flag option in mri_surfcluster provides .label files with vertex IDs for each cluster. Dan___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

[Freesurfer] Inconsistency between mean cluster cortical thickness value and lme_lowessPlot

External Email - Use Caution I've been performing a LME longitudinal analysis on a dataset with two groups (controls, clinicals), where each participant completed two MRI scans (pre, post). I was examining a particular surface cluster that arose from a time*group interaction effec