Freesurfer

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30083 discussions

Re: [Freesurfer] Viewing eroded structure after -seg-erode 1
by Elijah Mak 22 Apr '16

22 Apr '16

Hi Doug, I have pasted the previous emails below. I have computed mri_segstats to extract the FA and MD from resampled aparc+aseg.mgz in diffusion space. -seg-erode 1 was performed during mri_segstats. Now, I will like to visually inspect the results of that erosion for the left and right hippocampal structures. Is there anyway I can do that and compare that against the uneroded hippocampus? I don't think mri_segstats -seg-erode 1 produce any volumetric outputs so I am not sure. Thanks. Best Wishes, Elijah Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 11 Apr 2016 08:11:06 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> You can load it as an overlay in freeview make sure to specify the registration file as that compted for the DTI. Also make sure to set the threshold to something like 0.5 On 04/11/2016 09:41 AM, Elijah Mak wrote: > Hi Freesurfer Community, > > I have performed -seg-erode 1 during mri_segstats on resampled > subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 > anatomical space to visually inspect whether PVE has been adequately > accounted for? > > Thank you. > > Best Wishes, > Elijah

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Comparison of the slope of the pvr analysis between groups
by Sophie Maingault 22 Apr '16

22 Apr '16

Dear FS experts, There is already a post about that but the concerned person never answered so there is no solution. I’m currently running per-vertex analyses with the --pvr flag of mri_glmfit command. I did correlations between 2 vertex-wise variables correcting for age. I also would like to compare the slope of the pvr between 2 groups: in my fsgd file I have the subject ID and the group. I run the following command: mri_glmfit --y lh.1.448tvs.mgh --fsgd 448_cate30.fsgd --C contrast1.mtx --surf fsaverage lh --cortex --glmdir glm.lh.12_448tvs --pvr lh.2.448tvs.mgh with contrast1.mtx = 0 0 -1 1. I get the following error: ERROR: dimension mismatch between X and contrast contrast1.mtx X has 3 cols, C has 4 cols Do you know where is my mistake and if it possible to do comparison of the slope of a pvr analysis between groups with mir_glmfit ? Thank you for your help, Best regards, Sophie

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Qdec stats question
by Ajay Kurani 22 Apr '16

22 Apr '16

Hi Freesurfer Experts, I have used freesurfer smoothed images (lh.thickness.fsaverage.fwhm15.gii) to perform a cortical thickness analysis. I used qdec with a surface-based morphometric analysis to compare two groups. As my discrete fixed factor I used group membership. As Nuisance factors I used age (years), sex (0/1), site(1-10) and years of education(years). I used Threshold min=2, max=5 which I assume refers to a T-stat threshold. I see an FDR correction which and the Monte Carlo Null-Z simulation. 1) Do I run both monte carlo and fdr or just one after my figure apprears? Is the monte-carlo with threshold = 1.3(0.5) similar to a clusterwise threshold with a fixed p value? Are results valid when just setting the threshold min=2, max=5 but they are just uncorrected results? 2) When running Qdec with no nusiance factors and just a discrete fixed factor of group membership, my results look almost identical to AFNI's 3dttest++ output when the tmin=2. However, when I add the nuisance factors the results between the two softare packages are different. When nuisances covariates are added does Qdec still use a ttest or switch to some other method? How is centering assumed between groups for covariances? Is the mean from each covariate calculated and removed from each group separately based on group membership or calculated together with all subjects and removed? Does the analysis assume to have pooled or unpooled variance across the two groups? 3) For the viewer it displaces a logarithmic scale from what I have read in other papers. Is there a way to switch this to displace tvalue? 4) There was a previous post I saw yesterday saying qdec only uses 2 nuisance covariates and so I wanted to see if this is the case or not so I can try to understand why my afni and freesurfer results match with no covariates added but are very different once covariates are added. Thanks, Ajay

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Label registeration
by Mohamed Abdelhack 22 Apr '16

22 Apr '16

Dear all, I have been trying so far to export Freesurfer labels into a volume created by SPM I tried to coregister the anatomical data from Freesurfer and SPM and use the registeration file to turn my label file into volume but the resulting output just goes outside the brain. Has anyone tried to do that before that can advise me? Thank you, Best, Mohamed

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mri_convert doubling file size
by Afzal, Afsana 22 Apr '16

22 Apr '16

Hi everyone, I'm using mri_convert to reinforce TR information into the Nifti header in the following manner: mri_convert $FILE $FILE -tr $TR Before the conversion, my file size is usually around 550MB but after the conversion is doubles in size to ~1.1GB. In the Nifto file header I've noticed that the data type usually changes from int16 to float32. Is there a quick way to decrease the file size or revert back to int16 without affecting the data? Thanks for you help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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mri_vol2vol question
by pfotiad＠nmr.mgh.harvard.edu 22 Apr '16

22 Apr '16

Dear FS community, I used mri_robust_register to register a volume to the fsaverage space, and then tried to use the resulting .lta file to register another vol on the same space as the original volume, to fsaverage, using mri_vol2vol. The structure of the command I used is: mri_vol2vol --mov <file_to_move> --targ <fsaverage orig.mgz path> --lta ./<register_file>.lta --o <output_vol> However, I keep getting the error: MatrixAsciiReadFrom: could not scanf parms Do you happen to know what is the cause of that error? Thanks in advance. Best, Panos

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MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label
by DeCross, Stephanie N. 22 Apr '16

22 Apr '16

Hi, I’m trying to take an ROI in MNI152 volume space and make it into a cortical surface label, for visualization purposes. With my input being the lh thresholded, binarized MNI152 nii.gz label (when I visualize it, it looks as it should in fslview), I ran: mri_vol2vol -- mov <labelinput.nii.gz> -- targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz -- o <outputname.nii.gz> -- regheader -- talres 2 -- interp nearest mri_cor2label -- c <outputname.nii.gz from above> -- id 1 -- l ./<newoutputname.label> My commands above seem to have run fine, but when I open the lh in tksurfer and try to load the new lh label file, the dialogue runs for a little but then errors out: 12304 unassigned vertices in label - building spatial LUT… assigning vertex numbers to label... MatrixMultiply: m2 is null! And then tksurfer closes. I’m not sure what’s going wrong - does anyone have any pointers or troubleshooting methods I can try? Thanks, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: (617) 724-3283 Fax: (617) 726-4078

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Image geometries differ across time
by Lars M. Rimol 22 Apr '16

22 Apr '16

Hi, I'm running longitudinal recon-all (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 14.04.4, with three timepoints per subject. I get this warning about geometry (please see below). All three images have been converted from dicom to .mgz using mri_convert. From a previous question on the list from last year, I get the impression this warning should not appear if all images have been transformed the same way. I've pasted mri_info on both images at the bottom of the e-mail. The transformation matrices differ from timepoint to timepoint and I suspect this might be the reason for the warning. Is this a cause for concern? Thank you! #@# Longitudinal Base Subject Creation fr. 22. april 09:07:47 +0200 2016 /media/lmr2/subjects/TBI/artifakt_qc/KT5065_base mri_diff --notallow-pix /media/lmr2/subjects/TBI/artifakt_qc/Kt5065_2/mri/rawavg.mgz /media/lmr2/subjects/TBI/artifakt_qc/KT5065_1/mri/rawavg.mgz Volumes differ in geometry row=1 col=4 diff=1.606422 (1.60642) mri_diff --notallow-pix /media/lmr2/subjects/TBI/artifakt_qc/kt5065_reskann_2/mri/rawavg.mgz /media/lmr2/subjects/TBI/artifakt_qc/KT5065_1/mri/rawavg.mgz Volumes differ in geometry row=1 col=4 diff=1.713524 (1.71352) ******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ******************************************************************************* --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Comparison using mri_info [09:27 lmr@dmed4870] > mri_info KT5065_1/mri/orig/001.mgz Volume information for KT5065_1/mri/orig/001.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -0.5000 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 87.5000 -1.0000 -0.0000 -0.0000 128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -1.0000 0.0000 0.0000 87.5000 0.0000 0.0000 0.0000 1.0000 [09:27 lmr@dmed4870] > mri_info Kt5065_2/mri/orig/001.mgz Volume information for Kt5065_2/mri/orig/001.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -2.1064 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = -3.2129 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -5.6225 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 85.8936 -1.0000 -0.0000 -0.0000 124.7871 0.0000 -1.0000 0.0000 122.3775 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 124.7871 -0.0000 -0.0000 -1.0000 122.3775 -1.0000 0.0000 0.0000 85.8936 0.0000 0.0000 0.0000 1.0000 [09:28 lmr@dmed4870] > mri_info kt5065_3/mri/orig/001.mgz Volume information for kt5065_3/mri/orig/001.mgz type: MGH dimensions: 256 x 256 x 176 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -88.0, zend: 88.0 TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = 1.2135 : x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a = 8.4827 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -11.9426 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: -0.0000 -0.0000 -1.0000 89.2135 -1.0000 -0.0000 -0.0000 136.4827 0.0000 -1.0000 0.0000 116.0574 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -0.0000 -1.0000 -0.0000 136.4827 -0.0000 -0.0000 -1.0000 116.0574 -1.0000 0.0000 0.0000 89.2135 0.0000 0.0000 0.0000 1.0000 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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AAL 3D rendering with subcorticals
by João V. Dornas 21 Apr '16

21 Apr '16

Dear friends, I am following this procedures to plot a 3D rendering of the AAL volume (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27707.html) My problem is the following. When I execute this command: mri_cor2label --i lh.Colin27_aal2std.mgh --id 75 --l lh_Pallidum_L specifically for the ROI Pallidum, a subcortical ROI, I receive the following error $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ Loading mri lh.Colin27_aal2std.mgh Loading /Applications/freesurfer/subjects/FS_spm_CanonicalBrain/surf/lh.white Scanning the volume Found 0 label voxels ERROR: found no voxels matching id 75 This happens both for Pallidum Left and Pallidum Right, but all other AAL ROI work fine. I have an almost complete 3D rendering for my AAL. Only these subcortical regions are missing. Someone knows what could be happening? Thanks for the help. best, -- João V. Dornas Phd student in Neuroscience Cognitive Biology Group, Institute of Biology Otto von Guericke University, Magdeburg Germany

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lme model for within-subjects repeated measures design
by martina.papmeyer＠puk.unibe.ch 21 Apr '16

21 Apr '16

Dear FreeSurfer experts I have one question regarding my data analysis and would be extremely thankful for any advice! My data-set is as follows: I have repeated measures (time point 0 (T0), time point 1 (T1)) of several subjects. All individuals underwent an intervention at one of the time points and a placebo condition at the other time point in a fully randomized fashion. Thus, half of the subjects received treatment at T0 and half of them at T1. I am interested in the putative effect of the intervention on cortical thickness in a ROI. A major challenge is that the time between T0 and T1 varies between individuals and that I expect the time to impact on my dependent variable and to likely interact with the condition (treatment versus placebo). I thought about conducting a simple repeated-measures ANOVA. However, as stated, I want to take the time between the two sessions into account. I also thought about an analysis of rates or percent changes. However, this approach does not model the correlation among the repeated measures and is thus associated with a reduction in power. Accordingly, I am trying to use lme models to analyse my data. Since I have no between-group variable but a within-subjects design, I am concerned if my thoughts are correct and would be grateful for feedback. I ran the longitudinal FS stream and followed the longitudinal lme model tutorial. I propose the following lme model with one random factor: thickness = intercept (random factor) + time since baseline + ICV + condition (placebo or treatment) + timeXcondition + Age (does not change across time interval) + gender The analysis finishes with 0% non-covergence. Can you tell me if my model is suitable given the fact that it is a within-subjects design? I also started wondering if it was possible to model time as a random factor but I think that I read that this is not suitable if you only have two groups (in my case: conditions). Thank you very much for help and advice! All best wishes, Martina Universitäre Psychiatrische Dienste Bern (UPD) Universitätsklinik für Psychiatrie und Psychotherapie Systemische Neurowissenschaften der Psychopathologie Zentrum für Translationale Forschung Dr. phil. Martina Papmeyer, Wissenschaftliche Mitarbeiterin Bolligenstrasse 111, CH-3000 Bern 60 Tel: ++41 0(31) 930 9599, Fax: ++41 0(31) 930 9961 Mail: Martina.Papmeyer(a)puk.unibe.ch www.puk.unibe.ch

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