Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

Start a nNew thread

MS lesion - white / pial surface issue
by Fire Tech 05 Oct '16

05 Oct '16

2 1

Functional Connectivity Follow-up question
by ERIK JAHNER 05 Oct '16

05 Oct '16

Dear Free Surfer Experts, I have a follow-up question to a previous message sent by Lingqiang which you responded to on Dec 21st 2011. (I have included a copy of this message below, but here is a link https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021728.… ). In a functional connectivity analysis using a subject specific SURFACE label defined priori, you suggest using mir_label2vol to convert the surface label to a volume. However, I would assume that there is some benefit to using the smoothed values found in a surface vertices after preprocessing as opposed to voxels. If we use a .mgz segmentation file this seems to sacrifice the benefits of the free surfer pipeline. Or.... is this only used for reference and using the time course stored in the vertices on the surface and not actually just the 3d volume. To clarify my question... Is the functional connectivity processing stream using the time courses associated with the surface vertices after smoothing or is it just getting the time course of the voxels nearest the targeted label vertices? Thanks Erik --------------------------------------------------- Hi Lingqiang, convert your .label file to a volume using mri_label2vol for each subject, something like cd $SUBJECTS_DIR/$subject/mri mri_label2vol --label lh.yourlabel.label --temp orig.mgz --regheader orig.mgz --subject $subject --hemi lh --proj frac 0 1 .1 --o yourlabel.mgz When you run fcseed-config specify -segmentation yourlabel.mgz -segid 1 doug konglq at nmr.mgh.harvard.edu wrote: > Hi Freesurfers, > > We are trying to do a resting-state functional connectivity analysis using > freesurfer. Instead of using the aparc+aseg segmentations as seeds, we > would like to use a subject-specific surface labels that we have defined > apriori. > > In the fcseed-config step, we then don't have a "segid" as in the > anatomical seeds case. What should we specify as the -segid and -seg > (segmentation)? > > We also looked into the ROI-based options using "-roi" but this takes > seeds from output of "funcroi-config" and requires that we specify a > contrast and an analysis. How should we just specify a surface label > without generating a new analysis and contrast? > > Any help or suggestions are appreciated. > > > Lingqiang > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve at nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html --------------------------------------------------------

2 1

Input file in subcortical analysis using mri_glmfit
by Greenberg, Jonathan 05 Oct '16

05 Oct '16

Dear FS users I am trying to compare subcortical volumes of 3 groups (and no co-variates) pre and post an intervention using mri_glmfit in Paired-Analysis. My question pertains to which file I should specify as the input (--y) in the mri_glmfit command. The examples in the Wikis use either a preprocessed and smoothed surface file (e.g. “--y lh.paried-diff.thickness.sm05.MGH”) or “y.mgh”. The surface examples seem irrelevant since I am interested in subcortical volumes. When I try to follow the y.mgh example mri_glmfit \ --glmdir rh.paired-diff \ --y y.mgh \ --fsgd paired-diff.fsgd \ --C n-vs-w.mtx \ --C n+h-vs-w.mtx \ --C n-vs-h.mtx \ it seems it cannot locate the y.mgh file, and the following message is displayed …loading y from /autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh mghRead (/autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh -1): could not open file ERROR: loading y /autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh Should something be done to create y.mgh prior to running this command (given that qdec is not used)? Should a different input file be used instead? Thank you Jonathan

2 3

FSL-compatible surfaces
by saraizad＠alumni.ubc.ca 04 Oct '16

04 Oct '16

Hi Freesurfer team, I am trying to use Freesurfer surfaces to do tractography in FSL. I extracted two ROIs, one of which is the output of the following command: label2surf –s lh.white.gii –o lh.prefrontal.gii –l lh.prefrontal.txt and the other is the output of: mri_tessellate aseg.mgz 46 rh.cerebellum.wm My question is how to convert these files to fsl-compatible surfaces usable for tractography If I have to use surf2surf, I am not clear on how to do it. Should I change both the type and the convention of the images. Thanks a lot, Sara

2 1

QCACHE always produces zeros for some vertices in the left hemisphere
by Sam Mathias 04 Oct '16

04 Oct '16

Dear list, I'm trying to extract vertex-level measures of thickness, area, etc, for all of my subjects. I ran recon-all -all on all subjects as normal, then ran: recon-all -s {subject} -qcache where {subject} is the subject ID. This was followed by `mris_convert` to make the values human-readable: mris_convert -c {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.mgh {fsavg_dir}/surf/lh.sphere {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.asc I did this for each subject, hemisphere, and measure (thickness, area, sulc). Many of the vertices in the left hemisphere always produce values of 0, for every subject, and for every measure. The first offending vertex is #9. So if I head a randomly chosen file, I get: [sm2286@grace0 surf]$ head lh.area.fwhm25.fsaverage.asc 000 0.00000 0.00000 100.00000 0.43150 001 27.64000 -85.07000 44.72000 0.39083 002 89.44000 0.00000 44.72000 0.33804 003 27.64000 85.07000 44.72000 0.81910 004 -72.36000 52.57000 44.72000 0.41731 005 -72.36000 -52.57000 44.72000 0.37795 006 -27.64000 -85.07000 -44.72000 0.77490 007 72.36000 -52.57000 -44.72000 0.49643 008 72.36000 52.57000 -44.72000 0.00000 <--- this value This is a different subject: [sm2286@grace0 surf]$ head lh.sulc.fwhm25.fsaverage.asc 000 0.00000 0.00000 100.00000 0.00692 001 27.64000 -85.07000 44.72000 -0.45451 002 89.44000 0.00000 44.72000 0.38711 003 27.64000 85.07000 44.72000 0.17178 004 -72.36000 52.57000 44.72000 -0.54163 005 -72.36000 -52.57000 44.72000 -0.01465 006 -27.64000 -85.07000 -44.72000 -0.07269 007 72.36000 -52.57000 -44.72000 0.46408 008 72.36000 52.57000 -44.72000 0.00000 <--- this value Bizarrely this also happens when I switch the target of qcache to fsaverage5. The right hemisphere is never affected. Does anyone have any clue what's going one here? -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com

2 1

From structural ROIs to functional data
by Nick Corriveau Lecavalier 04 Oct '16

04 Oct '16

Hi Freesurfer team, I used Qdec to do my group analysis (MCI vs Control). I also analyzed fMRI data with SPM. My plan is to investigate functional activity where there are group differences in thickness. Is there a way to make a ROI using Qdec and to transfer it into SPM/MarsBar format (.mat) so I can get the functional beta values in this ROI? I tried to make functional ROIs with MarsBar by taking the coordinates of the thickness clusters, but the size and shape of those ROIs are kind of arbitrary. Do you have anything to suggest? Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

1 0

[Verification for fully automated analysis of FreeSurfer]
by 김정식 04 Oct '16

04 Oct '16

2 1

Re: [Freesurfer] QCACHE always produces zeros for some vertices in the left hemisphere
by Sam Mathias 04 Oct '16

04 Oct '16

Just a correction from my previous message; this issue actually affects both hemispheres, but different vertices in each one. -- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com

1 0

Error using LGI script despite making suggested chages to Matlab script.
by prasser 03 Oct '16

03 Oct '16

Hi, I'm looking to please get some help with -lgi. I'm using matlab R2015b and FS5.3 with recon-all -s subj_id -lgi on os x 10.11. Looking at the output, the first error occurs about here: preparing pial mesh structure ... ...searching for mesh edges...done (206.94 sec). ... creating path file for vertex 1 / 65274 area file for outer ROIs saved at 1 In an assignment A(:) = B, the number of elements in A and B must be the same. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); I have changed the script SearchProjectionOnPial.m as suggested on the ReleaseNotes page. Any help would be much appreciated. Thanks.

2 3

Output uncorrected p-values using mri_surfcluster
by Corinna Bauer 03 Oct '16

03 Oct '16

Hello all, I would like to get a table of the uncorrected p-values to compare with the corrected ones obtained using mri_glmfit-sim. I tried the following, which outputs a table of clusters and their vertices, but it does not include p-values. Is there a flag that I shoudl include to output the p-values? mri_surfcluster --in sig.mgh --sign abs --subject fsaverage --hemi lh --surf white --annot aparc --no-adjust --bonferroni 2 --no-fixmni --ocn cache.uncorr.abs.sig.ocn.mgh --oannot cache.uncorr.abs.sig.ocn.annot --cwsig cache.uncorr.abs.sig.cluster.mgh --thmin 2.3 --sum cache.uncorr.abs.sig.ocn.dat Thanks corinna

2 4

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