Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

About error message for the segmentation of hippocampal subfields in FreeSurfer
by Chi evelyn 24 May '18

24 May '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the segmentation of hippocampal subfields, as described on the segmentation of hippocampal subfields tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) however, I get the following error when I ran the segmentation of hippocampal subfields command: LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: > Invalid MEX-file '/tmp/MCR_183405186/.mcrCache8.0/segmen0/autofs/cluster/koen/eugenio/GEMS-Release-linux/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_183405186/.mcrCache8.0/segmen0/autofs/cluster/koen/eugenio/GEMS-Release-linux/bin/kvlGEMSMatlab.mexa64: undefined symbol: _ZZN3gmm13warning_level5levelEiE6level_ Error in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 100) MATLAB:invalidMEXFile I've searched the list and I found that a similar problem has been reported, however, without any conclusion. Dose anyone have any thoughts on how to trouble-shoot this error message? (1) FreeSurfer version : freesurfer-Linux-centos6_x86_64-v.6.0 (2) Matlab(R2012b) Thank you! Best Regard, EvelynChi

1 0

Statistical analyses
by Rosalia Dacosta Aguayo 24 May '18

24 May '18

External Email - Use Caution Dear Experts, I would like to run statistical analyses with the output of cortical thickness. The problem is that I would like to do it with FSL as I have more experience. Any one of you could tell me which are the two outputs (right and left hemisphere) I should consider to run the statistics? Best regard, Rosalia

2 2

Multivariate analysis of covariate with multiple dependent covariates
by Juergen Haenggi 24 May '18

24 May '18

External Email - Use Caution Dear Statistics Experts we performed a multivariate analysis of covariance (MANCOVA) between two groups using fractional anisotropy (FA), axial diffusivity (AD), radial diffusivity (RD), and mean diffusivity (MD) of the inferior fronto-occipital fasciculus as dependent variables. Because the two groups differ also in global (across the whole white matter) FA, AD, RD and MD values, we used all these four measures simultaneously as covariates of no interest. However, some authors challenge the usage of all four global measures simultaneously as covariates of no interest and denoted this procedure an inappropriate “overcorrection”. Is this procedure statistically problematic? Is it more appropriate to first regress out the global effect of each single measure and then run the multivariate analysis just on the residuals performing an MANOVA instead of a MANCOVA model? Any suggestions is highly appreciated. Thanks in advance Best regards Jürgen Hänggi ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. -----------------------------------------------------------------------------------------------------

1 0

Pial surface crosses medial line in GM
by Pam Garcia 23 May '18

23 May '18

External Email - Use Caution Hello, Freesurfer team. I have a problem with the pial surfaces when using T2 monkey image to remove the dura, in some areas the surface crosses the medial line in the cortex, but this happens only with the surface using T2 images since the surface with T1 image looks fine but the dura is the problem. I attach two images as example of the error. I have read about this error in the mail list but I haven´t found a good solution. In contrast with previous mails,my problem is not the aseg.mgz since this segmentation is good. I have read also that exist a new parameter for mris_make_surface, T2_threshold. Do you know if by modifying this parameter the problem could be resolved? Is histogram used to calculate the thresholds done outside of freesurfer? And if I am wrong ,do you have any suggestion to solve this error? Thanks a lot , best Pam

1 0

Re: [Freesurfer] Regressing out conditions of non-interest with selxavg3-sess
by Mcnorgan, Christopher 23 May '18

23 May '18

Hi Doug, Thanks for the prompt reply to what was essentially a 2-part question. Data were processed in both fsaverage and native space for different reasons, which is why I suggested the possibility of surface space incongruency on at the end, which your reply seemed to make more likely. It turns out that this was indeed the case, and so this thread will likely pop up in some google search by a future student who will no doubt have a similar problem. However you have also answered my second embedded question by confirming that what I was proposing seemed sensible at face value. Thanks again for your time. What you have described should work. The residuals will be in whatever space the analysis was made in (mkanalysis-sess). What ROI are you trying to get an average over? What are your mkanalysis-sess and mri_segstats commands? /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ <http://ccnlab.buffalo.edu/> * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ External Email - Use Caution

1 0

Regressing out conditions of non-interest with selxavg3-sess
by Mcnorgan, Christopher 23 May '18

23 May '18

Hi, I have some BOLD data from a fast event-related experiment with 3 experimental conditions, 1, 2 and 3. A reviewer wants me to isolate the signal for condition 1. Under the assumptions of the GLM, the signal is a linear combination of A1+B2+C3+Error, so it seems that I need to construct a design matrix that contains only the onsets for B and C, and then run selxavg3-sess with the —svres argument given. The residuals should thus be the best estimate available of condition 1 + error. So in a nutshell, I want the best approximation of the preprocessed BOLD time series, as though conditions 2 and 3 never happened, but without any other transformation of the BOLD data. I have a student working on this, but he’s running into a problem of the residuals no longer being in anatomical space, or at least the same anatomical space he started in (mri_segstats is reporting a dimension mismatch, which is why I emphasized above I don’t want any other transformations applied to the data). The data were originally processed in fsaverage space. Barring my student accidentally switching to the subject’s native surface space, is there any reason what I’ve described above shouldn’t work? /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ <http://ccnlab.buffalo.edu/> * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ External Email - Use Caution

2 1

voxels with mislabeled hemisphere
by Catarina Saiote 22 May '18

22 May '18

External Email - Use Caution Hi freesurfer team, I found in my datasets some scattered voxels with mislabeled hemisphere (see example figures in the attached pdf). I see the labeling error in aparc+aseg and aseg.mgz but aseg.auto and aseg.presurf appear to be labeled correctly. Also, I see nothing wrong with the surfaces where this is happening but several (if not all) of the mislabeled voxels are right at the white surface. I found this happening both with V6.0.0 and v6.0.1 for Linux (in both cases using the -hires flag). This seems to happen to very few scattered voxels and I suppose it probably doesn't quite affect volumes and thickness. But it might matter more if one is using the ROIs to e.g. average functional data. I'd like to know your view on whether it is important to fix this and the best to way to do it. Thank you in advance, Catarina -- Catarina Saiote, PhD Postdoctoral Associate Department of Neurosurgery | neurosurgery.umn.edu <http://www.neurosurgery.umn.edu> University of Minnesota | umn.edu csaiote(a)umn.edu

2 2

Tutorial data for 'Practice working with data'
by Nuckle, Genevieve 22 May '18

22 May '18

External Email - Use Caution Hello , I am trying to do the tutorial on ''Practice Working With Data'' , but I can't find the tutorial data for it, it doesn't seem to be in buckner_data-tutorial_subjs.tar.gz<ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz>. I've downloaded it and cannot find the 'practice_with_data' directory as described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice Thank you for your help, Genevieve

1 0

Displaying insular electrode contacts on an inflated brain surface
by Giulia Liberati 22 May '18

22 May '18

External Email - Use Caution Hello, I would like to prepare two figures in which I show the locations of depth electrode contacts located in the human insula (respectively left and right), on inflated surfaces. I have identified each electrode contact with a vertex in either the left or the right insula. Can these same vertices be used to locate the contacts on an inflated brain (e.g. with coordinated specific for the inflated surface)? What makes me a bit skeptical is that my contacts are located deep in the brain, so I am afraid that the alteration would be too large. Thanks in advance for your help. -- Giulia Liberati, PhD Institute of Neuroscience (IoNS) Université catholique de Louvain Avenue Mounier 53 bte B1.53.02 à 1200 Woluwe-Saint-Lambert Claude Bernard; Etage 02; Local 0826; Site Bruxelles Woluwe Brussels, Belgium

2 1

mris_preproc error
by Barletta, Valeria 22 May '18

22 May '18

Hi Freesurfers, I used the command mris_preproc to have all the surfaces of my cohort concatenated in fs average and I obtained this error message from several of my subjects: #@# 3/11 MS073_R01_05/Bay8_3T/fs/MS073_R01_05 Fri May 11 14:24:58 EDT 2018 -------------- ----------------------- mri_surf2surf --srcsubject MS073_R01_05/Bay8_3T/fs/MS073_R01_05 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval /autofs/space/alicudi_002/users/mscat/users/valeria/CMEt2star/11Subj/tmp.mris_preproc.10346/MS073_R01_05.Bay8_3T.fs.MS073_R01_05.3.mgh --sval /autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 124277 Number of value vertices = 124470 Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = MS073_R01_05/Bay8_3T/fs/MS073_R01_05 srcval = /autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic/MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/overlay/lh.MS073_R01_05-t2star_05iso_corr_disco_r0.8_depth0.5_fwhm3.mgh srctype = trgsubject = fsaverage trgval = /autofs/space/alicudi_002/users/mscat/users/valeria/CMEt2star/11Subj/tmp.mris_preproc.10346/MS073_R01_05.Bay8_3T.fs.MS073_R01_05.3.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /autofs/space/alicudi_002/users/mscat/users/gabriel/R01_Automatic//MS073_R01_05/Bay8_3T/fs/MS073_R01_05/surf/lh.sphere.reg Loading source data I saw that the problem could be related with the sphere file and I tried re-running -autorecon2 and -autorecon3 but it did not solve the problem. Could you please help me out with this? Thank you, Valeria

2 3

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