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
>
>
>
> *
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Hello,
I've been following the FreeSurfer longitudinal LME analysis tutorial (
https://secure-web.cisco.com/1UXjrD54pEj2u6JH6Y-Z-dHoSgY6qcbXqPg43uVU2GGyBvmGYSpOkab0ovGwllJVYA7PInB9Oa-cCSrq2yGN2zfn8EBAUtT_yeaabIRnE4HnyhF8G3FJoSd6nbCQUf195Ng-xfgCokq08rSx
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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 -
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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___
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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
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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
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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
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
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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
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
.
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
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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
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
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./
>
>
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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
.
>
> 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
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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 \
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:
>
>
&
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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
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
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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
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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
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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___
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Freesurfer@nmr.mgh.harvard.edu
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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
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