Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

hippo subfield segmentation new beta version (version 6)
by Barbara Kreilkamp 23 Apr '16

23 Apr '16

Dear all, I've been reading the manuscript on version 6 freesurfer hippocampal subfield segmentation "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: application to adaptive segmentation of in vivo MRI" Can you please tell me if the type of sequence (e.g. coronal T2FLAIR vs T2STIR) and voxel sizes of .4x.4x2mm^3 vs .4x.4x4mm^3 really make a difference for this multi-modal algorithm? I previously ran recon-all on 1mm isotropic T1-w scans all with similar contrast. It seems that the mesh fitting in version 6 is driven by the relation of the subfields to each other rather than by contrast or signal intensities; and also I notice the algorithm brings everything to isotropic space anyway. Is this correct? Do you see a major methodological issue when using T2FLAIR (.4x.4x4mm^3) and T2STIR (.4x.4x2mm^3) subfield volumes together? Thank you very much, Best wishes, Barbara P.s. as a side-note, I've not noticed any major differences in subfield segmentations visually, when comparing segmentations via these two different T2 scans.

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Re: [Freesurfer] preproc-sess error opening tmp brain_mask
by Douglas N Greve 22 Apr '16

22 Apr '16

Is your $FSLDIR environment variable set? On 04/22/2016 02:09 PM, Mcnorgan, Christopher wrote: > That doesn't seem to be the problem. Attached are the file listings for the /usr/bin directory for fsl* for the working and not working computers. The symlinks for fsl binaries on both computers point to the same place, and I can run something like fslview on both computers. > ________________________________________ > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Sent: Friday, April 22, 2016 1:54 PM > To: Mcnorgan, Christopher > Subject: Re: [Freesurfer] preproc-sess error opening tmp brain_mask > > Do you have FSL installed on the machines that work and not on the > machine that does not work? > > On 04/22/2016 01:49 PM, Mcnorgan, Christopher wrote: >> Hi Doug, >> >> >> Thanks for your generous time donation resolving this problem. There >> was a delay in getting this diagnostic information to you (which is >> itself diagnostic) because prior to your response, I retraced my steps >> preparing the data for running FS-FAST using my wiki checklist, but on >> a different computer. After rerunning mkanalysis-sess, >> mkcontrast-sess, double-checking my par-files and any other related >> files that needed to exist, I reran preproc-sess on FS_T1_501 without >> incident ... on a different machine. >> >> >> This suggested that either I made a mistake that I fixed on my >> do-over, or else that the error is machine-specific. I'm repeating the >> procedure on data for the same participant doing the same task >> collected on the same scanner at time point 2, so the subject in >> question is FS_T2_501. Again I come to the same failure on the machine >> that seems to be giving me problems. >> >> >> I've attached the dng.log file you requested. I hope it has some >> useful clues. If you need to know anything about the particular >> computer configuration, let me know, though two other machines that >> work are similarly configured (one has identical hardware and all are >> accessing the fMRI data stored on a remote server on a cifs share >> mounted at ~/ubfs/). >> >> >> Can you run >> >> /mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/ |& tee dng.log >> >> and send me dng.log ? >> >> doug >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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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