Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

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

xhemi correct for multiple comparisons
by krista kelly 17 Jan '14

17 Jan '14

Hello, I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though. 1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is larger"? 2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions? 3) I've noticed from the archives that some people are performing laterality indices. How would I calculate laterality indices? Thanks! Krista

2 11

CUDA problem with FreeSurfer 5.3.0 on CentOS6
by Tran, Kevin (NIH/NIMH) [C] 16 Jan '14

16 Jan '14

Hi, We have encountered a serious problem running recon-all FREESURFER_HOME: /opt/freesurfer-530 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.5 (Final) Kernel info: Linux 2.6.32-431.el6.x86_64 x86_64 The entire command-line executed: /opt/freesurfer-530/bin/recon-all -use-gpu -all -s surface_1 The problem happened when it came to this point mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer-530/average/RB_all_2008-03-26.gca transforms/talairach.m3z nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 6.0 Runtime : 5.50 Acquiring CUDA device Using default device CUDA device: Tesla K20m not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer-530/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.22 (predicted orig area = 6.5) freeing gibbs priors...done. average std[0] = 5.0 AllocateHost: Warning - not thread safe! RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst GCAMcopyNodePositions: On GPU RecvAll: Did not reset gca in dst The same error message kept on repeating and, then, it said ============================================= GPU MRI Label timers -------------------- MarkLabelBorderVoxels Total : -nan ms (avg) 0 ms (tot) VoxInLabelWithPartialVolume Compute : -nan ms (avg) 0 ms (tot) Total : -nan ms (avg) 0 ms (tot) ============================================= CUDA Error in file 'mriconvolve_cuda.cu' on line 945 : unload of CUDA runtime failed. Abort (core dumped) ERROR: mri_ca_register with non-zero status 134 but continuing despite the error We have tried the same data with two different GPUs (Tesla K20m and Quadro K4000). They both had the same problem. Any suggestions? Thanks, -- Kevin Tran, Contractor UNIX System Administrator The National Institutes of Health NIMH, Laboratory of Brain and Cognition 10 Center Drive, Room 4C215 Bethesda MD 20892-1366

2 1

LME model
by Seán Froudist Walsh 09 Jan '14

09 Jan '14

Dear Jorge and FreeSurfers, Would you mind having a look at my set-up and advising on whether it is correct or needs changing? I have participants with one or two scans, who are divided into two groups. I'm interested in the longitudinal effects of aging, and the difference in the effect of age on the two groups. Not all people were scanned at exactly the same age, and the interscan interval in not exactly the same for each person. Rather, the age at scan looks like a bimodal distribution around the mean 1st and 2nd timepoint. I believe I read on the list that you should have more timepoints than random effects. I guess I should then only name one random effect (intercept). At the moment I have my model set up as follows: X = Intercept Group Age(at scan) Group*Age Gender [stats, st] = lme_mass_fit_vw(X,1,Y,ni,Mask,[],12); CM.C = [0 0 0 1 0] I guess I should then run * lme_mass_F(stats,CM);* and *lme_mass_FDR2.* Here I am trying to look find the areas that develop differently between the two groups over the timespan we are studying. If you would be able to advise me as to whether I have set up the model wrong it would be greatly appreciated. Age in this case refers to the the age at scan time, regardless of whether it is the first or second scan, so many participants will have two distinct values in the age column. Also, is it possible within this set-up to test the effect of age within a group, or would that require re-doing the design matrix? Finally, is it possible to include the by-subject random slopes for the effect of age? In R (lmer) it would be something like (1+age|subject). Best wishes y gracias, Seán

4 9

xhemi installation
by Sofie Valk 08 Jan '14

08 Jan '14

Dear FreeSurfers, I have a question regarding the installation of xhemi (I am using FreeSurfer 5.1) I tried to follow the guide on: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi to install the necessary files, however the following files do not seem to be present on the ftpserver: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.{… ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol.{… What could be wrong? Thank you very much!! Kind regards, Sofie Valk, ... PhD Candidate, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany

3 4

freeview error
by Rujing Zha 31 Dec '13

31 Dec '13

Hi Bruce and others, Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the nvidia drivers completely. Then I tried to run this command: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot . It did present the underlay(lh.inflated),overlay and annot, but it suspended when I click the button "configure overlay". Then freeview were suspended. The CPU ran "100%",and memory ran "23%". There was nothing to do but terminated it manually in the command console by "ctrl + c". I want to know why I cannot configure overlay. Is it a poor graphic card or CPU or memory? My graphic card is "NVIDIA GeForce 8600 GT", and CPU is "Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz 2.40GHz", and RAM is 2.00G. Thanks Bruce and others. All the best. 2013-12-30 Rujing Zha

3 4

Obtaining the center of mass coordinates of a label file
by Omar Singleton 31 Dec '13

31 Dec '13

Dear Freesurfer Community, Does anyone know of a way to get the coordinates of the center of mass of a FreeSurfer label? Is there any way of doing this? Thanks! Best, Omar

1 0

citation for smoothing method
by YUMI MAEDA 30 Dec '13

30 Dec '13

Hi, I have a question about citation for smoothing methods. In the following link, http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer there are statement " ....This data was smoothed in the volume at 5mm, but when preparing for a group surface-based analysis, we recommend that you smooth on the surface prior to group analysis and not smooth in the volume at all (or less than the voxel size) ...." Is there any reference paper that I can cite when I write a manuscript? thank you very much. YUMI

2 1

mri_mask output problem
by Caspar M. Schwiedrzik 30 Dec '13

30 Dec '13

Hi Freesurfer Experts, I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else. The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths. Any advice would be very much appreciated. Thanks, Caspar

2 6

freeview error
by Rujing Zha 30 Dec '13

30 Dec '13

1 0

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Freesurfer December 2013