Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Re: [Freesurfer] Longitudinal pipeline {Disarmed}
by vittal korann 30 Nov '20

30 Nov '20

External Email - Use Caution No problem, thanks! So I shall send an email only to freesurfer or would it fine if I put you in cc? With regards Vittal On Mon, Nov 30, 2020 at 4:25 PM Diers, Kersten /DZNE <Kersten.Diers(a)dzne.de> wrote: > Hi Vittal, > > Sorry, I can only help on the public freesurfer list, so I suggest moving > the discussion back to there. > > Best, > > Kersten > > Am 27.11.2020 um 18:21 schrieb vittal korann <vittalkorann(a)gmail.com>: > > Hi Kersten > > Thank you for kind response. > > I think we need to talk about the design matrix X first (sorry, I did not > look at your xlsx file; I think it's probably better to send simple csv > files if at all). > I attached longitudinal data in csv format. > > Besides the covariates that you mention, the matrix needs to contain an > intercept, a variable for ?time?, a variable for ?group? (assuming you have > a control group also), and a group-by-time interaction term in order to > asses differential change over time (again, if you have a control group). > I do not have a control group. Right now I have only schizophrenia > patients who underwent 2 scans: first is baseline and second one is after 3 > months of yoga therapy. Wish to know the how can I proceed with my availabe > data. > > Just to make sure: ?age? should be ?age at baseline? (i.e. constant across > time per subject), otherwise it will be confounded with time. > Yes, I used same across the study. > > Could you review (and possibly adapt) your design matrix X with respect to > which columns it contains, and write it in the reply? > I tried but couldn't get there. > > Looking forward to your response. > > Thanks, > Vittal > <longitudinal_data.csv> > > > -- > Kersten Diers > Image Analysis Group (AG Reuter) > German Center for Neurodegenerative Diseases (DZNE) > B.1.114 | Building 99 | Venusberg-Campus 1 | 53127 Bonn | Germany > https://secure-web.cisco.com/17CxNooomAxq34c9Xe027kzVg8TPcPTffQaYq5Q3lzWgiM… > Phone: +49 / 228 / 43302 - 381 > >

1 0

lme_mass_fit_Rgw will only fit 20 % and then it quits using Matlab 2020b
by Knut J Bjuland 30 Nov '20

30 Nov '20

External Email - Use Caution Dear freesurfer experts When I run lme_mass_fit_Rgw it stop fitting after i have runed 20 % as seen below. I have listed freesurfer matlab toolbox first in the Matlab 2020b path list. I am running on Fedora 33 and the mgh files work when I am running the same script on a macbook. Are there any step I can take to debug this issues? Region 4214: Convergence at iteration 9. Initial and final likelihoods: 3004.2484, 3047.3654. Region 4227: Convergence at iteration 15. Initial and final likelihoods: 2466.513, 2550.6373. Region 4234: Convergence at iteration 16. Initial and final likelihoods: 2091.6167, 2576.1704. Region 4247: Convergence at iteration 11. Initial and final likelihoods: 1638.1748, 1830.6099. Region 4254: Convergence at iteration 11. Initial and final likelihoods: 1963.5263, 2122.7052. Region 4267: Convergence at iteration 7. Initial and final likelihoods: 1917.7245, 1924.1933. Region 4274: Convergence at iteration 15. Initial and final likelihoods: 1787.8884, 1895.3745. Region 4287: Convergence at iteration 6. Initial and final likelihoods: 1935.1202, 1950.6581. Region 4294: Convergence at iteration 5. Initial and final likelihoods: 2173.2547, 2185.9629. Region 4307: Convergence at iteration 4. Initial and final likelihoods: 1025.3896, 1058.5496. Region 4314: Convergence at iteration 13. Initial and final likelihoods: 1209.8828, 1245.91. Region 4327: Convergence at iteration 26. Initial and final likelihoods: 1132.3554, 1321.7057. Region 4334: Convergence at iteration 9. Initial and final likelihoods: 1157.4764, 1196.4451. Region 4347: Convergence at iteration 7. Initial and final likelihoods: 1432.242, 1437.6161. Region 4354: Convergence at iteration 11. Initial and final likelihoods: 1187.0457, 1282.0549. Region 4367: Convergence at iteration 8. Initial and final likelihoods: 1340.9078, 1494.0789. Region 4374: Convergence at iteration 8. Initial and final likelihoods: 1071.3221, 1095.6163. Region 4387: Convergence at iteration 11. Initial and final likelihoods: 1202.6703, 1227.2202. Region 4394: Convergence at iteration 9. Initial and final likelihoods: 1067.2966, 1100.0462. Region 4407: Convergence at iteration 12. Initial and final likelihoods: 1190.4148, 1221.8727. Region 4414: Convergence at iteration 5. Initial and final likelihoods: 1190.0332, 1193.3426. Region 4427: Convergence at iteration 10. Initial and final likelihoods: 1295.3867, 1416.8343. Region 4434: Convergence at iteration 14. Initial and final likelihoods: 1479.4723, 1498.5227. Region 4447: Convergence at iteration 4. Initial and final likelihoods: 492.8232, 495.8952. Region 4454: Convergence at iteration 4. Initial and final likelihoods: 345.9289, 350.5215. Region 4467: Convergence at iteration 4. Initial and final likelihoods: 420.0601, 420.7848. Region 4474: Convergence at iteration 5. Initial and final likelihoods: 543.539, 554.8185. Region 4487: Convergence at iteration 4. Initial and final likelihoods: 425.3509, 428.4245. Region 4494: Convergence at iteration 3. Initial and final likelihoods: 458.8256, 459.5319. Region 4507: Convergence at iteration 3. Initial and final likelihoods: 372.6527, 373.0735. Region 4514: Convergence at iteration 5. Initial and final likelihoods: 389.5679, 392.0076. Aproximate percentage of fitted locations: 100% Parallel pool using the 'local' profile is shutting down. Summary: Algorithm did not converge at 0.022139 percent of the total number of regions. Elapsed time is 3.7353 minutes. Saving output ...

2 1

how to convert .vtk file to .annot file?
by 1248742467 30 Nov '20

30 Nov '20

External Email - Use Caution Hello, Fs Do you know how to convert the .vtk to .annot file? I want to visualization with. Annot file by freeview. Looking forward to your reply!

1 0

Mean Curvature
by Letitia Schneider 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer team, When I analyse the mean curvature value of a particular ROI, do I have to control for overall brain curvature, to make sure the results are not driven by individual differences in overall brain curvature? Best wishes, Letitia Schneider

3 2

mri_segstats question
by RENXI LI 29 Nov '20

29 Nov '20

External Email - Use Caution Hi Freesurfer experts: I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal from are close to the cerebral white matter that some voxels at the boundary may not contain any signals. Is there any arguments in mri_segstats that I can use to only extract voxels that has non-zero time-series? Best, Renxi

2 3

Re: [Freesurfer] error: MatrixMultiply: m1 is null
by Hoopes, Andrew 29 Nov '20

29 Nov '20

Hi Noam, Do the volumes look okay? I’m seeing a lot of ‘non-orthogonal axes’ warnings in the log. If that’s not the issue, this could be a bug that’s randomly occurring with parallel recons in v7. Although, I’ve never seen it fail during mri_convert. Can you try to rerun? It might succeed the second time. If not, can you send us the input scan and try again without the -parallel flag. best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Peled, Noam" <NPELED(a)mgh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, November 24, 2020 at 10:10 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] error: MatrixMultiply: m1 is null Dear FreeSurfer community, I encountered a recon-all error where I couldn’t find on the web. The error message is: “error: MatrixMultiply: m1 is null!”. You can find the complete log attached. I used the stable7.1.1 version. Thanks, Noam

4 3

(no subject)
by Sara Lyn 29 Nov '20

29 Nov '20

External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if there was a flag to regress out eTIV in the model. Thank you

2 1

Mean Curvature for whole hemisphere
by Josue Luiz Dalboni Da Rocha 29 Nov '20

29 Nov '20

External Email - Use Caution Dear FreeSurfer, Why an average whole hemispherical value for mean curvature is not provided by Qdec? Is there geometrical reason? Best regards, Josue

3 2

PETSurfer voxelwise statistic
by Boris Rauchmann 29 Nov '20

29 Nov '20

External Email - Use Caution Dear all, How can I run a voxelwise statistic using grey and white matter uptake? mgx.ctxgm.nii.gz and the other files in output all only include gm as I understand. My goal is to run whole brain volume-based analysis. Like in this example for subcortical analysis: mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta --tal --talres 2 --o subctxgm.mni305.2mm.sm00.nii.gz Thanks, Boris

2 1

Splitting a label region?
by Hyon, Justin J. 29 Nov '20

29 Nov '20

External Email - Use Caution Hello, I am wondering whether there is a way to split a labeled region in a volume into 2 labels, perhaps by using the Freeview gui? I just need to roughly split one region generated via one of the default atlases into 2 custom labels. I tried using the tools in Freeview, but I can only seem to edit 1 layer of the volume at a time. Thank You!

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer