Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Error mric-convert
by Saurabh Thakur 19 Feb '14

19 Feb '14

Hello Everyone, I am facing small problem to create my own file //================================// saurabh@saurabh-Precision-WorkStation-T3500:~/Desktop/saurabh_freesurfer/bert/sam$ mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o $SUBJECTS_DIR/bert/mri/orig/005.mgz mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o /home/saurabh/Desktop/saurabh_freesurfer/bert/mri/orig/005.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001... Starting DICOMRead2() dcmfile = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 dcmdir = /home/saurabh/Desktop/saurabh_freesurfer/bert/sam Ref Series No = 501 *Found 156 files, checking for dicoms WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154* Found 151 dicom files in series. WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/PS_0151 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0152 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0153 WARNING: tag SeriesNumber not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 WARNING: tag image orientation not found in /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/XX_0154 First Sorting Computing Slice Direction Vs: -121.791 -125.08 -36.7045 Vs: -0.682698 -0.701136 -0.205747 Second Sorting Counting frames nframes = 1 nslices = 151 *ndcmfiles = 151 MRIalloc(0, 0, 151): bad parmNo such file or directoryERROR: mri alloc failed* //===============================================================// Please reply asap....i m waiting for the solution. Thanks in advanced. cheers Saurabh Thakur,

3 4

Dilated PV spaces
by Victor Kovac 19 Feb '14

19 Feb '14

Hello FreeSurfer experts, I have four scans from a subject who has ubiquitous, dilated perivascular spaces (image attached) that seem to be preventing recon-all from finishing. I have attached the recon-all.log from one of the scans. Any advice on what I could try to get these scans analyzed would be greatly appreciated. Thank you! Victor

2 1

fReadQdec question
by sabin khadka 19 Feb '14

19 Feb '14

Hi all, I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file. However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell (discounting for all tabs and spaces). I tried debugging the code but it seems to me like it is just a simple read file in matlab. Does the qdec.table.dat file need to be in certain format? -Sabin

3 5

Analysis of structural data acquired from multiple sites by using a mixed effect model approach
by Michael Notter 19 Feb '14

19 Feb '14

Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class GroupB; Class Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept GroupA GroupB Controll Age IQ Site1 Site2 Site3 Site4 1 1 0 0 11.1 99 0 0 1 0 1 0 1 0 11.1 101 0 0 1 0 1 1 0 0 11.4 95 1 0 0 0 1 0 0 1 12.4 100 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... connected to 8 workers. Starting model fitting at each location ... Location 24994: Index exceeds matrix dimensions. Location 24994: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. Location 62484: Index exceeds matrix dimensions. Location 62484: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. ... I've checked the matrix dimensions of X, Y, ni and lhcortex and compared them to the LME mass_univariate example stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. Has anybody encountered similar problems? Is my approach of specifying 'ni' as a vector of'1's even legitimate? Thanks, Michael

1 0

problems with control points
by pietro de rossi 19 Feb '14

19 Feb '14

Dear FreeSurfers, I have uploaded a subject I am trying to edit by using control points. Control points worked in most of the regions that needed to be edited....with the exception of right superior temporal gyrus. I tried to put control points there and re-running -autorecon2-cp -autorecon-3 several times but it didn't work... Could you please have a look? Any suggestion would be greatly appreciated :-) Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant'Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com

3 2

BVECS and BVALS file
by Alan Francis 18 Feb '14

18 Feb '14

Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header on MRICRON but how does one convert these values into table form. thanks so much, Alan Martinos Center.

2 4

Which is broken - GCC or Freesurfer build?
by Durai Arasan 18 Feb '14

18 Feb '14

Hi Freesurfer experts, so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. Thank you ********************************************************************************************************************************** Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /****************** Actual FREESURFER_HOME /************************************** Linux ***************************** SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl) tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar) mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize) mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed) mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut) mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment) mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label) mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register) mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize) mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_normalize) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_register) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_register) mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_register) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_label) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_label) mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_label) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_pretess) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_pretess) mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_pretess) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fill) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fill) mri_fill: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fill) mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_tessellate) mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_tessellate) mri_tessellate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_tessellate) mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_concatenate_lta) mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_concatenate_lta) mri_concatenate_lta: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_concatenate_lta) mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize_tp2) mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize_tp2) mri_normalize_tp2: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize_tp2) mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_smooth) mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_smooth) mris_smooth: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_smooth) mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_inflate) mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_inflate) mris_inflate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_inflate) mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature) mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature) mris_curvature: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature) mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_sphere) mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_sphere) mris_sphere: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_sphere) mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_fix_topology) mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_fix_topology) mris_fix_topology: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_fix_topology) mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_topo_fixer) mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_topo_fixer) mris_topo_fixer: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_topo_fixer) mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_ca_label) mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_ca_label) mris_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_ca_label) mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_euler_number) mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_euler_number) mris_euler_number: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_euler_number) mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_make_surfaces) mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_make_surfaces) mris_make_surfaces: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_make_surfaces) mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_register) mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_register) mris_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_register) mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_volmask) mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_volmask) mris_volmask: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_volmask) mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_anatomical_stats) mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_anatomical_stats) mris_anatomical_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_anatomical_stats) mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mrisp_paint) mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mrisp_paint) mrisp_paint: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mrisp_paint) mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature_stats) mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature_stats) mris_curvature_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature_stats) mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_calc) mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_calc) mris_calc: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_calc) mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_register) mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_register) mri_robust_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_register) mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_template) mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_template) mri_robust_template: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_template) mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_and) mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_and) mri_and: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_and) mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_or) mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_or) mri_or: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_or) mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fuse_segmentations) mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fuse_segmentations) mri_fuse_segmentations: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fuse_segmentations) mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segstats) mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segstats) mri_segstats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segstats) /****************/***444 mri_convert /********************/***_mp.nii /*******************/****444/mri/orig/001.mgz mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) Linux ************************************ ************************ SMP Fri Mar 22 ******** EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ***444 exited with ERRORS at Mon Feb 17 02:24:00 EST 2014 For more details, see the log file **********************/***444/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]
by Douglas Greve 18 Feb '14

18 Feb '14

oops, sorry! That command looks like it is correct. Can you say more about what is going wrong? How are you determining that something is going wrong? doug On 2/17/14 9:30 PM, Celine Louapre wrote: > Hi Doug > I don't know if you had the chance to read my email below to resample a > lesion mask on diffusion images. Anastasia gave me the registration file > to use (anatorig2diff.bbr.dat) in the command but the output mask file was > not registered anymore. So she asked me to rephrase my question more > generally on the mailing list to look for help with bbregister. > Thanks a lot > Celine > > > ---------------------------- Original Message ---------------------------- > Subject: [Freesurfer] Resample a mask on diffusion images using bbregister > registration matrix > From: "Celine Louapre" <celine(a)nmr.mgh.harvard.edu> > Date: Thu, February 13, 2014 9:58 pm > To: freesurfer(a)nmr.mgh.harvard.edu > -------------------------------------------------------------------------- > > Hello freesurfer team > I have binary lesions mask from T2star images (resolution 0.3*0.3*1) > already registered on freesurfer space that I would like to resample on > diffusion images to further exclude the lesion voxels on the DTI maps (and > to calculate DTI metrics within the lesions too). > Using mri_vol2vol command I think I am missing something because I tried > with the registration file produced by bbregister (through tracula) but > the result does not look correct. > I have the lesion mask in the freesurfer space that I can overlay on > brainmask or dtifit_FA.nii on freeview and it seems correctly registered > on both. > The command I am running is: > mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ > /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o > /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg > recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv > > And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size > is the same as the DTI images, but the lesions are not at the same place. > > On the mailing list I have also seen other options but I am not sure if > they would be appropriate? > I have seen mri_label2vol command where I could set the fill threshold > parameter but it does not solve the problem of the registration file? > also mri_convert > And eventually I also saw this command: > mri_mask but I guess that the mask volume needs to be in the same > dimension as the diffusion space? > > Thanks a lot > Best > Celine > > >

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postdoc in brain image analysis
by Thomas Yeo 18 Feb '14

18 Feb '14

Dear All, I am looking for a postdoc to work on brain image analysis, e.g., dynamic functional connectivity. See more information below. Regards, Thomas Job Title: Postdoctoral Fellow in Brain Image Analysis Project: Develop novel image analysis and machine learning tools for brain image analysis, (e.g. Dynamic Functional Connectivity). Research Webpage: http://yeolab.weebly.com/research.html Requirements: Ph.D. in computer science, electrical engineering, statistics or related fields. Candidates should have previously published research in image processing, computer vision, statistical or machine learning. Experience with functional MRI is preferred (but not required). Compensation: Competitive and commensurate with experience Institutes: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Successful candidates may be required to travel between Singapore and Harvard Medical School for certain projects. Contact: Email BT Thomas Yeo (thomas.yeo(a)nus.edu.sg) with your CV. Deadline: 1st May, 2014

1 0

trac-all -qa
by Gerit Pfuhl 17 Feb '14

17 Feb '14

Dear Freesurfer experts, we are curious whether we can run trac-all -qa in 5.3. and use it as regressors with our results from tracula 5.2. I.e. is it advisable or shall we run the complete analysis? Thanks, Gerit Pfuhl

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