Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

ROI extraction using functional masks
by Yann Quidé 06 Jun '18

06 Jun '18

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, the “end product” does not really look good, some of the extracted ROI for some subjects are empty. Does anyone have a clue of why? Here is what I have done: 1) transform .nii file to .mgz file $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/L_ROI.mgz $FREESURFER_HOME/bin/mri_convert $MASKS_DIR/ROI.nii $MASKS_DIR/R_ROI.mgz 2) to make sure our masks from SPM will match fsaverage templates, I did tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/L_ROI.mgz -fthresh 0.5 tkmedit -f $MASKS_DIR/avg152T1.mgz -overlay $MASKS_DIR/R_ROI.mgz -fthresh 0.5 It was fine. 3) I created a .dat file containing the registration matrix from avg152T1 onto fsaverage cd $SUBJECTS_DIR/fsaverage/surf spmregister --s fsaverage --mov $MASKS_DIR/avg152T1.nii --reg $REG_DIR/avg152T1_to_fsaverage.dat 4) Visualisation of the registration tkregister2 --mov $MASKS_DIR/avg152T1.nii --targ $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $REG_DIR/avg152T1_to_fsaverage.dat --surf orig The registration was bad, so… I manually relocate the TAL template onto the fsaverage template and saved a new avg152T1_to_fsaverage.dat file called avg152T1_to_fsaverage_edited.dat. This file is used for the next steps. 5) Visualisation of the registration of our mask onto fsaverage T1 cd $SUBJECTS_DIR/fsaverage/surf tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/L_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white tkmedit fsaverage T1.mgz \ -overlay $MASKS_DIR/R_ROI.mgz \ -overlay-reg $REG_DIR/avg152T1_to_fsaverage_edited.dat \ -fthresh 0.5 \ -surface lh.white -aux-surface rh.white Up to this sep, everything looks good. 6) Transformation of the ROI mask to surface and thickness mri_vol2surf --src $MASKS_DIR/L_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi lh --o $MASKS_DIR/L_ROI.mgh mri_vol2surf --src $MASKS_DIR/R_ROI.mgz --reg $REG_DIR/avg152T1_to_fsaverage_edited.dat --hemi rh --o $MASKS_DIR/R_ROI.mgh mri_cor2label --i $MASKS_DIR/L_ROI.mgh --surf fsaverage lh --id 1 --l $MASKS_DIR/L_ROI.label mri_cor2label --i $MASKS_DIR/R_ROI.mgh --surf fsaverage rh --id 1 --l $MASKS_DIR/R_ROI.label 7) Extraction of the ROI surface and thickness for analyses mris_anatomical_stats -l $MASKS_DIR/L_ROI.label -f $OUT_DIR/results_L_ROI_SubjID SubjID lh mris_anatomical_stats -l $MASKS_DIR/R_ROI.label -f $OUT_DIR/results_R_ROI_SubjID SubjID rh Thanks to anyone who will be able to help me with that! Yann

2 2

slice timing correction with mulit-band
by Xu, Yaoda 06 Jun '18

06 Jun '18

Dear all, I am trying to do slicing timing correcting with Siemens’s 3T Prisma data at acceleration 3. I am told that I can use “-ngroups” when running "preproc-sess”. How do I use the “-ngroups” flag? Should I do “-ngroups 3”? Would fs-fast automatically compute the slice timing file and apply it accordingly? I have the actual slice timing file. I tried to use "-sdf slicedelayfile”, but it does not seem to be a recognized flag. It appears that fs-fast does slice timing correction after motion correction. If the volume is going to be resliced after motion correction, thus each slice will no longer have its original timing, shouldn’t slice timing correction be done before motion correction? Is there a way in fs-fast to run slice timing correction before motion correction? I guess instead of running “preproc-sess”, I could first run “sts-sess” and then “mc-sess”? Any suggestions would be greatly appreciated. Thank you! - Yaoda Xu

5 9

selxavg3-sess /tmp dir out of space
by Jiahe Zhang 06 Jun '18

06 Jun '18

External Email - Use Caution Dear Freesurfer experts, While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248 It sounds like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space? Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649

3 5

Recon-all exited with errors
by Hanna Vasilevskaya 05 Jun '18

05 Jun '18

External Email - Use Caution Good afternoon all, I am new to Freesurfer (using version 6.0) and trying to run recon-all on multiple subjects. Every subject exited with errors. Specifically, a number of surfaces are missing from the "surf" subject's folder (only 30 files instead of 80). Would you happen to know how to fix it? Taken from the recon-all status log: #@# Smooth2 lh Mon Jun 4 16:26:27 DST 2018 #@# Smooth2 rh Mon Jun 4 16:26:31 DST 2018 #@# Inflation2 lh Mon Jun 4 16:26:35 DST 2018 #@# Inflation2 rh Mon Jun 4 16:27:02 DST 2018 #@# Curv .H and .K lh Mon Jun 4 16:27:29 DST 2018 Linux Laptop 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1062_2 exited with ERRORS at Mon Jun 4 16:27:32 DST 2018 I have also attached a recon-all.log for your convenience. Thank you, Anna

2 2

pcc.mgh file missing
by jahanvi patel 05 Jun '18

05 Jun '18

External Email - Use Caution Hello together, We used the following command to perform correlation analysis. But we didn't obtain the "pcc.mgh" file which we want to extract the correlation coefficient from the significant cluster. Is there a command or way to generate the pcc.mgh file? Thank you in advance mri_glmfit \ --glmdir GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2 \ --y lh.testretest_only_TP2.thickness-pc1.stack.fwhm15.mgh \ --label lh.testretest.fsaverage.cortex.label \ --fsgd GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/TP1_TP2.fsgd \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/main.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_age.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_CesD_score.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_STATI_state.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_STATI_trait.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/ contrasts/Delta_total_medi_min.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f1.mtx \ --C GLM_dir_corr_behavior_lh_CT_tp1_tp2_plus_FFMQ_f1_f2/contrasts/Delta_FFMQ_f2.mtx \ --surf fsaverage lh Best, Jahanvi

2 1

PROBLEM DOWLOAD LINUX VERSION
by Davide Momi 05 Jun '18

05 Jun '18

External Email - Use Caution Dear Freesurfer expert, I'm not able to download the Linux version of Freesurfer by your website. For some reason it doesn't open the page. Could you please send me an another link or the version? Thanks in advance Davide

1 0

seek for help about recon-all
by 姜时泽 05 Jun '18

05 Jun '18

External Email - Use Caution | | Dear freesurfer experts, This is Shize Jiang from China. I am trying to run recon-all with Linux and Mac. All these files are finished without errors. However, Most of my cases will finish with around 270Mb. I was taught the size of each subject should be around 400Mb. I am not sure if there are some problems with my file. Would you please help me to tackle this problem? Thank you very much. Attached is the recon-all log file for one case. Best regards Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

2 1

matrix and contrast design for multi-centre study
by C.P.E. Rollins 05 Jun '18

05 Jun '18

External Email - Use Caution Dear Freesurfer developpers, I posted a while back asking how to control for scanner site in a multi-centre study. I think I now understand the formatting to do so for a DOSS model, but was wondering how this would look for a DODS model. There are 6 scanner sites and I also want to control for age and sex. However, there are no females in 3 of the sites. I tried to create the contrast for this but got the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y rh.5.lgi.centre.mgh --fsgd FSGD_centre.txt dods --glmdir rh.5.lgi.centre.glmdir --surf fsaverage rh --C H-NH_centre.dods.txt 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=1.000000 (col 4), Max=183.117447 (col 31) The scale is much different between columns 4 and 31, you may want to normalize by subtracting the mean and dividing by the standard deviation. My contrast was 1 -1 -1 -1 -1 -1 -1 -1 -1 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 and FSGD attached (does not include full list of subjects). Thanks very much, Colleen

2 2

How to create my own ASEG and APARC atlases
by arsene ella 04 Jun '18

04 Jun '18

External Email - Use Caution Dear All, I have a set of 7 NIIFTI images (0.5 mm isotropic) : - 2 average brain images (one T1W_MPRAGE and one T2W_SPACE template ) - 3 Tissue Probability Maps (Gray Matter, White Matter, CSF) - 2 Atlases (One for Gray matter structures and another for Internal brain structures (or subcortical structures) ) segmented from mean images, labelled and annotated. My question is: *How to used these images to build Freesurfer-Like Atlases (.gca and .gcs) ?* For the .GCA, I don't really know what to set as Flagged Arguments... mri_ca_train -node_spacing 4 \ # ? -prior_spacing 2 \ # ? -parc_dir esegatlast \ # Is that the directory of my segmented subcortical structures? -xform talairach_one.m3d \ # All the files are aligned, so which transform shold I set here? -input flash30_avg.mgz \ # Should I set the T1W-MPRAGE average here? -input flash5_avg.mgz \ # Should I set the T2W-SPACE average here? $SUBJECTS multi_one.gca What about the .GCS? Thanks in advance, Arsene

2 4

Re: [Freesurfer] Lookup table to surface overlay
by Funk, Quentin 04 Jun '18

04 Jun '18

External Email - Use Caution Freesurfer Experts, thanks for the response! There was no command for projabs, but looking through the help I think projdist was about what I needed? I was also curious though if there were a way to get it into an annotation--like the one available for the Yeo parcellations on the freesurfer webpage. Is there any way to convert a lookup nifti to an annotation, or one of these surface overlays into one? I can't seem to figure it out from the documentation, but it's almost surely user error... Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003<tel:713-363-9003> ________________________________ Message: 13 Date: Fri, 25 May 2018 11:06:15 -0400 From: Douglas Greve <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Lookup table to surface overlay To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5cb3e6da-99cb-8365-c4f5-4f1cb17f7150(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" You might be sampling outside of the brain. Try adding --projabs -2 To sample 2mm below the pial surface On 5/25/18 10:32 AM, Funk, Quentin wrote: > > > Freesurfer experts, > > > I have some lookup table volume files in MNI space that I'd like to > overlay on a surface (say, fsaverage's lh.pial). Currently I'm using > this command: > > > mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp > nearest --hemi lh --surf pial --o lh_lookup_overlay.mgh > > > Then I choose "color wheel" as the overlay option in freeview. This > works OK, but it's a bit imperfect. There are voxels that somehow > don't get a value (and show up in the configuration window as 0's > (even though the entire MNI brain is covered by the LUT), and it's a > bit 'edgy' and not smooth. > > > Are there any better ways to do this? > > > Thanks for any help! > > > > Quentin Funk, PhD > Houston Methodist Research Institute > 713-363-9003 <tel:713-363-9003> > > Houston Methodist. Leading Medicine. Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. 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