Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Lme and random effect
by Patrizia Dall'Acqua 29 Apr '16

29 Apr '16

Dear FS-Group I use the lme matlab tools for my longitudinal analysis and everything works fine. My dataset consists of 2 time-points and 2 groups (patients and controls) and my design matrix X contains 4 columns (1. intercept, 2. time, 3. group, 4. interaction group*time). As suggested from the mailing list archive, I used the intercept as the random effect since I have only 2 time points and I found some interesting results. However, I still don’t understand why I should choose the intercept for my model and not for example the time or the interaction as the random effect. THANK you for any help! All best wishes, Patrizia

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Re: [Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess
by Mcnorgan, Christopher 28 Apr '16

28 Apr '16

?That seems to have been the problem: Running the data through Slicer as suggested elsewhere fixed the slice time code, but then saved only a single frame of the 4D data. I had been poking around the file header looking for a corresponding field, not suspecting that it was a calculated value and that my data had been truncated, nor noticing that my image dimensionality field had changed value. I wrote a MATLAB script to modify the slice time value (in addition to the TR value, which was also incorrectly set in my data) and was going to publicize the script, only to discover the FSL program fsledithd already exists and is clearly preferable to the Slicer solution for fixing strange NifTI header information. The data now run through preproc-sess without error. So to summarize for search engines: slice_code errors and other strange header information can be repaired with fsledithd, and the DOF=0 error was the result of an unexpected deletion of all but one time point by Slicer. Incidentally, the data were converted from DICOM to NifTI using MRI Convert (Windows), so it is possible that this program populates some header fields with strange default values -- I mention this because 5 is not a valid slice code according to the NifTI header specification, and others have posted problems related to this header field. Thanks, Chris Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Thu, 28 Apr 2016 10:05:59 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Does that run only have 1 time point?

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ROIs2Label
by Sahil Bajaj 28 Apr '16

28 Apr '16

Dear FreeSurfer experts, I have a surface ROI defined in MNI co-ordinate system, ROI.mgh, I am interested in converting it into label. I tried following steps: (1). mri_cor2label --i ROI.mgz --id 1 --l X.label (2). mri_label2label --srclabel X.label --s fsaverage --trglabel Xnew.label --hemi lh --paint 30 This gives me final .label file as Xnew.label, then I tried to check if this is correct using: (3). tksurfer fsaverage lh inflated -overlay ROI.mgh -fthresh 0.5 and then on top of it File>load label>Xnew.label Now the new Xnew.label is not matching with ROI.mgz. Can someone please help me to figure out what I am doing wrong here? Also, how can I view the label in FreeView i.e. is there any way to load this new label just like LookUp Table? Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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ERROR: DOF=0 in call to mri_glmfit by preproc-sess
by Mcnorgan, Christopher 28 Apr '16

28 Apr '16

Hi, First, thanks to Doug Greve for helping me isolate my previous problem, which turns out to have resulted from a conflicting fsl installation. Now that that's resolved, I'm having a problem on a first-level analysis. In preparation for calling selxavg3-sess, I am running preproc-sess on an individual and am running into an error where the reported DOF is 0. The peculiar thing is that these steps work fine with another data set -- from the same participant at an earlier time point doing the same task with the same parameters (though the procedure to convert the DICOM to nii data was not necessarily the same at both time points; unfortunately the original DICOM files are unavailable to me). I am able to take the time1 data to the completion of FS-FAST, but the time2 data halts at this error. A potentially relevant difference between the two data sets is that, for the functional data that worked, I was able to carry out these steps on the original f.nii file, whereas problematic data was first converted to a .mgz file in Slicer to fix an "unsupported slice timing pattern 5" error (a search in the archives suggested that Slicer would solve this problem, which seems to be the case). I'm not clear where this dof value comes from and if anything about the .nii file header can be manipulated to fix the problem. The fact that the slice timing pattern was off in the problematic data might be symptomatic of a generally compromised .nii header (SPM doesn't seem to do anything with much of this header information, allowing some invalid header information to go undetected). Thanks Below is the tail end of the preproc-sess output where it reports the error: $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold cmdline mri_glmfit --table /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat --glmdir /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm --osgm --y-out /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/y.out.nii --pca sysname Linux hostname accumbens machine x86_64 user chris FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat logyflag 0 usedti 0 glmdir /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm Loading y from /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat Found 6 data colums Found 1 data rows Saving design matrix to /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 0 ERROR: DOF = 0

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Group analysis GLM
by WENJunhao 28 Apr '16

28 Apr '16

Hello, freesurfer experts:I am following the tutorial of freesurfer group analysis of command-line_GLM, and for practice, i just include four subjects, which are divided into two groups, AD and CN, so I want to test if the thickness of the two groups differs from zero!I just followed the tutorial: here is my command for the different steps: #first step: set the SUBJECTS_DIR!export SUBJECTS_DIR=/aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer #second step: assemble the datamris_preproc --fsgd disease_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage \ --hemi lh \ --out lh.disease_age.thickness.10.mgh### in this step, we will use the commands: mris_preproc, and mri_concat, which is to concatenates the input data sets #third step: GLM analysis(mri_glmfit)mri_glmfit \ --y lh.disease_age.thickness.10.mgh \ --fsgd disease_age.fsgd dods \ --C lh_thickness_age-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.disease_age.glmdir #4th step: visualize the datafreeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.disease_age.glmdir/lh_thickness_age-Cor.mtx/sig.mgh:overlay_threshold=4,5 -viewport 3d but after the third step, in the directory 'lh.disease_age.glmdir', i missed a lot of files, I just got four files, (mask.mgh, mri_glmfit.log, surface, Xg.dat), in the tutorial, there are a bunch of files and a subdirectory which should be 'lh_thickness_age-Cor', so I think i will miss the sig.mgh for the fourth step.... I checked all my step, before the third step, everthing is ok, and from the terminal , here is the result of the GLM analysis: gdfReadHeader: reading disease_age.fsgdINFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous Variable Means (all subjects)0 age 71.5 6.34429Class Means of each Continuous Variable1 CN 69.5000 2 AD 73.5000 INFO: gd2mtx_method is dodsReading source surface /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/fsaverage/surf/lh.whiteNumber of vertices 163842Number of faces 327680Total area 65416.648438AvgVtxArea 0.399267AvgVtxDist 0.721953StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $cwd /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glmcmdline mri_glmfit --y lh.disease_age.thickness.10.mgh --fsgd disease_age.fsgd dods --C lh_thickness_age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.disease_age.glmdir sysname Linuxhostname HP1973machine x86_64user wenFixVertexAreaFlag = 1UseMaskWithSmoothing 1OneSampleGroupMean 0y /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm/lh.disease_age.thickness.10.mghlogyflag 0usedti 0FSGD disease_age.fsgdlabelmask /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/fsaverage/label/lh.cortex.labelmaskinv 0glmdir lh.disease_age.glmdirIllCondOK 0ReScaleX 1DoFFx 0Creating output directory lh.disease_age.glmdirLoading y from /aramis/home/wen/HAO_lab/Nipype/Data_AD/Group_analysis_freesurfer/glm/lh.disease_age.thickness.10.mghINFO: gd2mtx_method is dodsSaving design matrix to lh.disease_age.glmdir/Xg.datNormalized matrix condition is 278.004Matrix condition is 10286.8Found 149955 points in label.Pruning voxels by thr: 0.000000Found 149955 voxels in maskSaving mask to lh.disease_age.glmdir/mask.mghReshaping mriglm->mask...search space = 74612.965197DOF = 0ERROR: DOF = 0 does anyone can give me a hint? cuz i have been stuck for a while...Thank you Junhao WEN Institut du Cerveau et de la Moelle épinière - ICM CNRS UMR 7225 - Inserm U 1127 - UPMC-P6 Équipe ARAMIS / Projet CLINICA Hôpital de la Pitié-Salpêtrière - 47, boulevard de l'Hôpital – 75013 Paris Tél:+ 33 (0)1 57 27 40 00

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ROIs and labels during functional connectivity
by Martin Juneja 28 Apr '16

28 Apr '16

Dear FreeSurfer experts, I am using FsFast functional connectivity walkthrough steps to analyze fMRI data from: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… I am able to run all these steps successfully and can view the voxel-wise distribution maps. I was wondering if it's possible to: (1). overlay externally defined ROIs (e.g. R1.nii) on these maps e.g. on pcc (partial correlation coefficient) to find the correlation coefficient between R1.nii and seed region, may be averaged over voxels or voxel-wise? (2). display labels (name of the areas) as well on the distribution maps? Any help would be really appreciated. Regards, MJ

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Hippocampal subfields, stuck?
by BAUTISTA-PERPINYA Maximilià 28 Apr '16

28 Apr '16

Dear all experts, I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1". Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log. More info: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 --------------------------------------------------------------------- -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpinya(a)etu.unistra.fr maxbauper(a)gmail.com

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Longitudinal stream - Single time-point subjects
by Joann Poh 27 Apr '16

27 Apr '16

Dear All, When I was inspecting the longitudinal data for single time-point subjects, it differed quite a bit from the cross section. Can someone please explain why this is/could be so? How is the template generated for a single time-point subject? I'm using FS 5.3. I did my edits at the cross sectional, generated the template and ran the longitudinal processing. The edits I made in the cross was not carried over to the template, and it also did not show in the long. Thank you very much. Regards, Joann

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FLIRT in Han et al., 2006
by Lars M. Rimol 27 Apr '16

27 Apr '16

Hi, I wish to test the reliability of series of three T1 scans that were collected over a period of a few months. The Han et al., 2006 paper recommends using FLIRT to do a linear registration between the scans and then the volumetric registration matrix is applied to the corresponding surfaces (please see quote at the bottom of this e-mail). I was wondering if this is the way to reproduce what was done in that paper: 1) recon-all -all on all three scans 2) register e.g., the 001.mgz from tp2 and tp3 to tp1 using FLIRT; which timepoint was chosen as the reference tp in Han et al.? Or was some type of average template created? Registering all other images to one timepoint seems contrary to the thinking behind the FreeSurfer longitudinal stream (which of course didn't exist at that time). Would you recommend using the FS longitudinal stream in stead? 3) apply the registration matrix to 'h.area and *h.thickness. Here the question is how do I apply the registration matrix to the area and thickness files? I saw mris_apply_reg was recommended in order to register to xhemi.rh.w-g.pct.mgh but I'm not sure if I can use mris_apply_reg here? from the 2006 paper: "[..] a simpler linear registration is adopted to perform the intrasubject surface alignment, and surface point correspondence is then built according to their Euclidean distance in the registered space [..]. The linear registration is computed using the FLIRT linear registration tool (Jenkinson et al., 2002). The volumetric registration matrix is then applied to the corresponding surfaces." Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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labels
by Trisanna Sprung-Much 27 Apr '16

27 Apr '16

Hi there I have two questions regarding using the labels with tksurfer: 1. What exactly has been done to change the .label (e.g. lh BA44.label) to .thresh.label (e.g. lh BA44.thresh.label? 2. The instructions on this page https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps to overlay the labels and set the Min and Max do not seem to work for me - I cannot seem to alter the Min from 2 and the Max from 5. Any thoughts as to why? thanks very much! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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