Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

Comparing z score maps between 2 modalities in a group?
by Elijah Mak 18 Nov '16

18 Nov '16

Hi Freesurfer Team, We would like to compare Z-scored surface maps between different modalities (MRI and PET) within a single group. 1 subject = 2 measures. These are my steps so far, using mri_concat and fscalc for the generation of the Z score maps. Differences between Z-score maps are tested using the paired t-test approach as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis I am not sure if my following steps are correct, so confirmation will be much appreciated, many thanks for your time and help! // Generate mean/sd of healthy controls X mri_concat --f stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh --mean mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh --std Y mri_concat --f stacks__Y_HC_fsaverage --o group_mean_Y_HC_lh.mgh --mean mri_concat --f stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh --std QN: Should smoothing be applied here or before? // Derive individual Z-score map for X and Y X for i in `cat list`; do fscalc $i/surf/lh.X.fsaverage.mgh sub group_mean_X_hc_lh.mgh div group_std_X_hc_lh.mgh --o $i/surf/lh.Z.thickness.fsaverage.mgh; done for i in `cat list; do fscalc $i/surf/rh.X.fsaverage.mgh sub group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o $i/surf/rh.Z.thickness.fsaverage.mgh; done Y for i in `cat list`; do fscalc $i/surf/lh.Y.fsaverage.mgh sub group_mean_X_hc_lh.mgh div group_std_cth_hc_lh.mgh --o $i/surf/lh.Z.fsaverage.mgh; done for i in `cat list; do fscalc $i/surf/rh.Y.fsaverage.mgh sub group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o $i/surf/rh.Z.fsaverage.mgh; done // Derive paired-difference of Z scores between X and Y mri_concat --f stacks_XminusY_lh --paired-diff --o concat_XminusY_lh.mgh mri_concat --f stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh // Smooth concatenated maps of paired differences mri_surf2surf --s fsaverage --hemi lh --fwhm 4 --sval concat_XminusY_lh.mgh --tval concat_XminusY_lh_sm4.mgh // Test significance of paired differences within the group mri_glmfit --y concat_XminusY_lh_sm4.mgh --fsgd fsgd_pairediff dods --osgm --surf fsaverage lh --cortex --glmdir I used the --osgm flag as there are no covariates here.

2 1

Recon-all: stochastic mri_nu_correct error when run on HPC cluster
by Anders Perrone 18 Nov '16

18 Nov '16

Hi FreeSurfer Developers, I'm running freesurfer from the HCP pipeline developed by the Washington University in St. Louis. It ran just fine on our university's cluster, but when I migrated the pipeline to Exacloud, Intel's HPC cluster, the recon-all command began randomly failing. Occasionally it will work on the first try, but more often than not the same command has to be re-run upwards of 30 times before it will succeed. I've provided the recon-all command and the relevant section of the log file including the error here (attached is the full recon-all.log file): recon-all -i ./T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid ${SUBJECT_ID} -sd . /T1w -motioncor -tal airach -nuintensitycor -normalization ... [perronea(a)exanode-3-9.local${PWD}/T1w/washu_INV0WC5U4JA/mri/] [2016-11-17 13:08:38] running: /home/exacloud/lustre1/users/mirandad/usr/local/freesurfer53/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.223851/nu1.mnc ./tmp.mri_nu_correct.mni.223851/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:.........................................................................................................................................................mincresample: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_evaluate: crashed while running mincresample (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Linux exanode-3-9.local 2.6.32-504.30.3.el6.x86_64 #1 SMP Wed Jul 15 10:13:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s washu_INV0WC5U4JA exited with ERRORS at Thu Nov 17 13:08:40 PST 2016 It doesn't appear than any similar errors have been reported on freesurfer. Our current work-around is to simply re-run the job on different nodes until it works, but this is not a sustainable long-term solution. Any guidance on troubleshooting this error would be greatly appreciated. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Platform: CentOS release 6.5 (FINAL) uname -a: Linux exalab3.ohsu.edu 2.6.32-504.12.2.el6.x86_64 #1 SMP Wed Mar 11 22:03:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Thanks, Anders Anders Perrone, Research Assistant I Fair Neuroimaging Lab perronea(a)ohsu.edu<mailto:perronea@ohsu.edu> 503-418-1897 Oregon Health & Science University Mail code:L470 3181 SW Sam Jackson Park Road Portland, Oregon 97239-3098 [cid:image001.png@01D240D7.C6F2C170] "If there is no solution to the problem then don't waste time worrying about it. If there is a solution to the problem then don't waste time worrying about it." - Dalai Lama XIV

3 2

Version 6 Beta on Virtual Box problem
by Jeffrey Crawford 18 Nov '16

18 Nov '16

Hello everyone! I am currently using Virtual Box to run Freesurfer and I was wondering if my plan to put the version 6 beta on to my current virtual box was a valid one. My plan was to delete the Freesurfer folder off of the 5.3 virtual box and replace it with the Freesurfer version 6 folder. However, the virtual box is not letting me delete the Freesurfer folder. So I have some questions: 1. Does anyone have an idea of how I would go about deleting the original Freesurfer folder, so I could continue with this plan? 2. Is this plan a good one? 3. Should I try and download another linux virtual box somewhere and put the version 6 beta on that?

3 3

Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
by Antonin Skoch 18 Nov '16

18 Nov '16

Dear Bruce, see the screenshot in the attachment. The coords (RAS) are: 2.2 -23.3 35.9. The subject I have uploaded has this issue on multiple spots. The issue is quite frequent, I have seen similar spots in several other subjects I have checked so far. Antonin ------------------------------------------- Hi Antonin I'm having trouble parsing your image. Could you:1. Send the voxel coords of the location that you see overlap. 2. Send an image with *only* the two overlapping surfaces on, shown in different colors? thanks Bruce On Fri, 18 Nov 2016, Antonin Skoch wrote: Dear FreeSurfer experts, I am using HCP pipelines with my custom modifications of FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to generate white and pial surfaces. I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems with surfaces I found previously with 5.3.0_HCP version. This update helped to fix my problems but I found that with v.6.0 there is a new issue with overlaping pial surfaces in hemispherical region. This issue is not present in 5.3.0 version of mris_make_surfaces. My command line is mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires -mgz -sdir my_subject_dir -orig white.deformed -nowhite -orig_white white.deformed -orig_pial pial -T2 my_subj/mri/T2w_hires.norm -T1 T1w_hires_norm my_subject_id lh The previous invocation of mris_make_surfaces in FreeSurferHiResWhite.sh (which does not use T2 refinement): mris_make_surfaces -variablesigma 4 -white NOWRITE -aseg aseg.hires -orig white.deformed -filled filled.hires -wm wm.hires -sdir my_subject_dir -mgz -T1 T1w_hires_norm my_subject_id lh produces surfaces which do not overlap. It seems to me that -aseg option of mris_make_surfaces (preventing surfaces to crossing the midline) is not active in case of -T2 refinement. I also tried to add -white NOWRITE or -cover_seg parameters, but it did not helped either. See attached screenshot aseg.hires overlaid with surfaces: blue are surfaces without T2 refinement (without interhemispheric overlap), yellow are surfaces after T2 refinement (with interhemispheric overlap). Attached is also the log file of my mris_make_surfaces -T2 command. I also uploaded the subject overlapping_surfs.tar.gz to your FTP file exchange server. Regards, Antonin Skoch

1 0

v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
by Antonin Skoch 18 Nov '16

18 Nov '16

Dear FreeSurfer experts, I am using HCP pipelines with my custom modifications of FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to generate white and pial surfaces. I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems with surfaces I found previously with 5.3.0_HCP version. This update helped to fix my problems but I found that with v.6.0 there is a new issue with overlaping pial surfaces in hemispherical region. This issue is not present in 5.3.0 version of mris_make_surfaces. My command line is mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires -mgz -sdir my_subject_dir -orig white.deformed -nowhite -orig_white white.deformed -orig_pial pial -T2 my_subj/mri/T2w_hires.norm -T1 T1w_hires_norm my_subject_id lh The previous invocation of mris_make_surfaces in FreeSurferHiResWhite.sh (which does not use T2 refinement): mris_make_surfaces -variablesigma 4 -white NOWRITE -aseg aseg.hires -orig white.deformed -filled filled.hires -wm wm.hires -sdir my_subject_dir -mgz -T1 T1w_hires_norm my_subject_id lh produces surfaces which do not overlap. It seems to me that -aseg option of mris_make_surfaces (preventing surfaces to crossing the midline) is not active in case of -T2 refinement. I also tried to add -white NOWRITE or -cover_seg parameters, but it did not helped either. See attached screenshot aseg.hires overlaid with surfaces: blue are surfaces without T2 refinement (without interhemispheric overlap), yellow are surfaces after T2 refinement (with interhemispheric overlap). Attached is also the log file of my mris_make_surfaces -T2 command. I also uploaded the subject overlapping_surfs.tar.gz to your FTP file exchange server. Regards, Antonin Skoch

2 1

differences between OS recon all output, longitudinal data
by anonymous anonymous 18 Nov '16

18 Nov '16

Hi I am using recon-all in some longitudinal data on a ubuntu 16.04, and using the development version of freesurfer as I was told here, because the other current version doesnt work on ubuntu 16.04. The problem is that the first scans were probablly processed using virtualbox in a windows and an older version of freesurfer. i think I already know the answer, that I can't do this if I dont want to bias my results. Can I? But I'm using a better computer now and I use the one with windows for other analyses, so I wanted to know if I could install Virtual box on my ubuntu 16.04 computer, and install the same version of linux used to process the first measure. Should I also need to use the same version of freesurfer? f the computer's specs are dfferent, does it matter? And if I assign different cpu and ram on my virtual machine? Thank you!

3 2

mris_make_surfaces in longitudinal stream - explanation of parameters
by Antonin Skoch 18 Nov '16

18 Nov '16

Dear experts, I am trying to understand how the pial and white surfaces are generated in longitudinal stream using information from the reconstructed base template (freeSurfer development version). In longitudinal stream, apart from the -orig, -orig_pial and -orig_white there are also parameters -long and -max 3.5. May I ask what is the significance of these parameters? -max 3.5 means constraining cortical thickness to 3.5 mm? Why this constraint is applied specifically in longitudinal stream? In mris_make_surfaces.c I found that -long means that initial pial vertex positions are set between final white and orig pial, slightly inside orig_pial. What is the significance of this setting in longitudinal stream? Last question, not related specifically to longitudinal stream: What is the difference between -orig and -orig_white parameters of mris_make_surfaces? From the reading of source codes (quite tough to me) I got an impression that from -orig the gray and white matter histogram values are computed whereas -orig_white defines initial position of the vertices in the first iteration (which, for some reasons, does not necessary has to be identical to -orig). Am I correct? Regards, Antonin Skoch

2 1

Re: [Freesurfer] Questions about outputs in Longitudinal Stream
by Tamara Tavares 18 Nov '16

18 Nov '16

Thank you for the clarification Martin I have a follow-up question. When I load the base to make sure it doesn't look blurry, should I check the norm.mgz or brainmask.mgz? Online says norm.mgz but I just want to make sure. Also, would the "blurriness" be obvious? Similarly, when I open the base and the longitudinal runs to see whether they align, again should I load the brainmask.mgz for these as well? Thank you in advance for your help, Tamara

2 1

Re: [Freesurfer] Two Stage Longitudinal Model
by Timothy Hendrickson 18 Nov '16

18 Nov '16

Hi Martin, Thank you for your reply. I am glad to hear that I am doing that correctly. I am running into an error when I attempted to run my GLM. I have looked at my fsgd and qdec files for errors, however I cannot seem to find anything. The error is in the attached .txt file named illCondMatrix_twoStage_years_10_31_16.txt. Additionally I've included my fsgd file for stage two and my qdec file for stage one. Any assistance would be extremely helpful, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

2 1

Longitudinal analysis
by Jaiashre Sridhar 18 Nov '16

18 Nov '16

Hi FreeSurfer Team, We are doing a longitudinal analysis with three time points which are six months apart. The subjects at any time point were scanned on either one of the two scanners (both Siemens 3T TIM TRIO) and we used FreeSurfer v5.1 for our analysis. Most of the subjects show decrease in cortical volume over time except a few of them, who show a huge increase in volume at their 6th-month visit (or at their 12th-month in a couple of cases). When we tried to look at the reconstructed surfaces of the long brains in Freeview, the gray matter and white matter boundaries of the 6th-month were bigger overall than the boundaries of the baseline and 12th-month. Could you share with us your thoughts on what factors (with MPRAGE/Scanner/FreeSurfer) might have caused this problem? Thank you, Jaiashre.

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