Freesurfer January 2014

freesurfer@nmr.mgh.harvard.edu

130 participants
211 discussions

Outputting all tracula statistics to table
by Salil Soman 05 Feb '14

05 Feb '14

Hi, What is the proper way to generate a single table containing all tracula generated statistics for all subjects in a study? I tought tractstats2table was the way to do this, I am confused as to how trac-all -stat factors into this process in the latest (12-09-13 version)? Thank you. -Sal

2 1

Tracula: from anatomical to diffusion space and FSL probtracx
by Garikoitz Lerma-Usabiaga 05 Feb '14

05 Feb '14

Hi Anastasia, I want to use a hippocampal subfield as a seed in FSL. I am having problems understanding how to change spaces around... 1.- Is this command ok? mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ mri/hippo_subfield_in_anatomical_space.mgz --inv --interp nearest --o mri/hippo_subfield_in_diffusion_space.nii --reg dmri/xfms/anatorig2diff.bbr.dat --no-save-reg 2.- I would like to visualize it in freeview in anatomical space to check if it is ok, if I load nu.mgz and hippo_subfield_in_anatomical_space.mgz and then load hippo_subfield_in_diffusion_space.nii with the registration file dmri/xfms/anatorig2diff.bbr.dat, should I visualize it ok? If I don't register it, they show to be displaced (more than expected). 3.- Afterwards I want to run probtracx with the following command (my doubt is mainly about the files to use, since FSL files are RAS, freesurfer anatomical are LIA and freesurfer diffusion are LIA, are all the files in the same format and FSL is ok with it?): /usr/local/fsl/bin/probtrackx --mode=seedmask -x mri/hippo_subfield_in_diffusion_space.nii -s dmri.bedpostX/merged -m dmri.bedpostX/nodif_brain_mask -o fdt_paths_hippo_subfields --dir=FSL_ConnResults_Hipp -c 0.2 -S 2000 --steplength=0.5 -P 5000 --opd many thanks! Gari

3 9

mris_divide_parcellation replication
by Christian Brodbeck 05 Feb '14

05 Feb '14

Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085) I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L4…) but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian

3 5

Re: [Freesurfer] High resolution GM/WM segmentation
by Megha K. 04 Feb '14

04 Feb '14

Dear Nick and the Freesurfer team, We are following the pipeline “HiResRecon” to process our 0.7mm isotropic data. The pipeline completed without error but we cannot visualize the Grey/White matter segmentation using "-surfs”. The error messages is shown below: TM:~ Timwang$ tkmedit hires_3 brainmask.mgz -surfs Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. tkmedit.bin(7641,0xa0a8d1a8) malloc: *** mach_vm_map(size=8388608) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug We would greatly appreciate your help on how we can visualize the GM/WM segmentation result of the HiResRecon pipeline. Many thanks, Megha Kaushik Save Sight Institute Sydney, Australia >

2 4

mri_vol2surf failed, segmentation error
by Qingyang Li 04 Feb '14

04 Feb '14

Hi all, I am new to the freesurfer world. I was running a pipeline where I met an error. Here is the command I run and the error message: Command: mri_vol2surf --hemi lh --noreshape --o /working_dir/SurfaceRegistration/_subject_id_sub/func_sampler_lh/mapflow/_func_sampler_lh4/lh.rest_mc.mgz --reg /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat --projfrac 0.500 --mov /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz Standard output: srcvol = /working_dir/SurfaceRegistration/_subject_id_sub/func_volreg/mapflow/_func_volreg4/rest_mc.nii.gz srcreg = /working_dir/SurfaceRegistration/_subject_id_sub/func_bbreg/mapflow/_func_bbreg4/rest_mc_bbreg_sub.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /NKI_recon_subjects/sub/surf/lh.white Done reading source surface Reading thickness /NKI_recon_subjects/sub/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Standard error: Segmentation fault Return code: 139 Interface SampleToSurface failed to run. Thank you all in advance! Yang ------ Qingyang Li Balance and focus. On Sun, Mar 18, 2012 at 8:28 AM, <freesurfer-request(a)nmr.mgh.harvard.edu>wrote: > Mailing list subscription confirmation notice for mailing list > Freesurfer > > We have received a request from 67.244.70.75 for subscription of your > email address, "congel(a)gmail.com", to the > freesurfer(a)nmr.mgh.harvard.edu mailing list. To confirm that you want > to be added to this mailing list, simply reply to this message, > keeping the Subject: header intact. Or visit this web page: > > > https://mail.nmr.mgh.harvard.edu/mailman/confirm/freesurfer/8f8fcc67483bbce… > > > Or include the following line -- and only the following line -- in a > message to freesurfer-request(a)nmr.mgh.harvard.edu: > > confirm 8f8fcc67483bbcee3ff0f76888c79e7704b4a03a > > Note that simply sending a `reply' to this message should work from > most mail readers, since that usually leaves the Subject: line in the > right form (additional "Re:" text in the Subject: is okay). > > If you do not wish to be subscribed to this list, please simply > disregard this message. If you think you are being maliciously > subscribed to the list, or have any other questions, send them to > freesurfer-owner(a)nmr.mgh.harvard.edu. > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

4 4

Re: [Freesurfer] Freesurfer, Matlab and Maverick
by Dusan Hirjak 03 Feb '14

03 Feb '14

Dear Freesurferexperts, I still have the Problem because I can not run the the mris-command to estimate the gyrification-index, because Freesurfer is not recognizing Matlab: "ERROR: Matlab is required to run mris_compute_lgi"Im not sure why this is happening? Does someone have an idea??? Im starting Freesurfer as follows: FREESURFER_HOME=/Users/dhirjak/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh (than I get the following output) Dusan-Hirjaks-MacBook-Pro:~ dhirjak$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Users/dhirjak/freesurferFSFAST_HOME /Users/dhirjak/freesurfer/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2MNI_DIR /Users/dhirjak/freesurfer/mniFSL_DIR /Users/dhirjak/fsl export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer In have the following lines in my matlab startup-file: fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; Thanks!!! Dusan Hirjak

4 6

Destrieux Atlas with Kid brains
by Mher Alaverdyan 03 Feb '14

03 Feb '14

Hi all, I just wanted to know if it is acceptable to use the Destrieux atlas in FS for parcellation of brain images of pre-adolescents. If not this atlas, then which would be a recommended atlas to use for this population. Thanks

2 5

A question regarding DODS or DOSS
by KimMJ 02 Feb '14

02 Feb '14

Dear Doug and experts My question is about the choice of DODS or DOSS.I want to compare cortical thickness between 2 groups (disease group and control group), while controlling for the effect of age (nuisance covariate).I've already read through the mailing list about the issue of DODS and DOSS designs. If I understand correctly, I have to first use DODS (QDEC) in order to find areas of significant group*age interaction by using the contrast (0 0 1 -1).Given there is no area of interaction that survived multiple comparisons correction, I can go with DOSS (1 -1 0) using mri_glmfit (command line) to test between-group differences in cortical thickness, controlling for the effect of age. Am I right? My another question is that 'MUST' I rerun DOSS model after confirming no group*age interaction in DODS ? Or can I directly use the results of DODS to look for between-group differences controlling for age (1 -1 0 0), since there is no group*age interaction ?Is there much difference in results between the above-mentioned two approaches?I've found a reply by Doug from the mailing list: If there is no interaction, then either DODS or DOSS is appropriate. DOSS will be more powerful and a little more interpretable (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33418.html) From this context, what does the 'powerful' mean? Does DOSS yield higher statistical values than DODS? Apology for the beginner's questions.Thank you in advance for your help. MJ

4 5

LGI ERROR: make_roi_paths did not complete successfully!
by Wanda Truong 31 Jan '14

31 Jan '14

Hello Marie, I am trying to conduct a local gyrification index analysis, however I am getting this error ERROR: make_roi_paths did not complete successfully! Which is the same as the one posted earlier by someone else: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html I added the "patch": function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step) % step is typically set between 5 and 10. Default is 7, increasing it will % limit redundancies in the resulting path file. verticeslist=[]; si=max(size(perim)); for t=1:step:si [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); verticeslist= [verticeslist nearestIndexMT]; end verticeslist=unique(verticeslist); to my $freesurfer_home/matlab directly as a .m file. However, I'm still getting the same error: Error in dsearchn (line 80) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! Darwin Vinas-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s SFS026 exited with ERRORS at Thu Jan 30 14:26:16 MST 2014 Thanks, Wanda -- Wanda Truong, MSc

2 3

ERROR: dimension mismatch between y and X.
by Wanda Truong 31 Jan '14

31 Jan '14

Hi everyone, I get this error when running surface area analysis in QDEC: Vinas-iMac:~/Documents/Wanda/Wanda_SFS] vinagoghari% mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat gdfReadHeader: reading /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 40.6327 13.0176 1 IntraCranialVol 1.50352e+06 187456 Class Means of each Continuous Variable 1 GroupControl 38.8261 1480505.5707 2 GroupRelative 42.2308 1523881.3029 INFO: gd2mtx_method is dods Reading source surface /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /Users/vinagoghari/Documents/Wanda/Wanda_SFS cmdline mri_glmfit --y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh --fsgd /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd dods --glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled --surf fsaverage lh --label /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Avg-Intercept-area.mat --C /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/contrasts/lh-Diff-Control-Relative-Intercept-area.mat sysname Darwin hostname Vinas-iMac.local machine x86_64 user vinagoghari FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh logyflag 0 usedti 0 FSGD /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/qdec.fsgd labelmask /Users/vinagoghari/Documents/Wanda/Wanda_SFS/fsaverage/label/lh.aparc.label maskinv 0 glmdir /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled Loading y from /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/y.mgh INFO: gd2mtx_method is dods Saving design matrix to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/Xg.dat Normalized matrix condition is 400.101 Matrix condition is 1e+08 Found 148151 points in label. Pruning voxels by thr: 0.000000 Found 148025 voxels in mask Saving mask to /Users/vinagoghari/Documents/Wanda/Wanda_SFS/qdec/Untitled/mask.mgh Reshaping mriglm->mask... search space = 73649.347769 ERROR: dimension mismatch between y and X. y has 3528 inputs, X has 49 rows. My QDEC table has 49 subjects,2 groups, and 4 variables. Many thanks, Wanda -- Wanda Truong, MSc

2 11

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 January 2014