Freesurfer

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30096 discussions

Covariates for cortical Thickness and LGI
by Ajay Kurani 08 Sep '16

08 Sep '16

Hi Freesurfer Experts, I am comparing a control group and 2 patient groups (HC vs Group1, HC vs Group2, Group1 vs Group2). I am interested in seeing what is the most appropriate covariate to use for both a cortical thickness analysis and LGI analysis. I do not expect major changes in brain shape etc, and at most maybe some more cortical atrophy in one of the groups) I have seen several papers using ICV for cortical thickness analyses, however I am not sure if this makes the most sense. Does ICV really scale with thickness as a global measure to account for brain differences? To me something like left mean thickness and right mean thickness may make more sense, however, I am new to CT analyses and would like to get your feedback. Along with CT, I was interested in what covariate makes most sense in an LGI analysis. Since LGI may change depending on the location within the brain, does a global measure such as total surface area (or other measure) make sense? Is there a suggested covariate to use for this type of analysis? Are there any publications from your group regarind this issue? Thanks, Ajay

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recon-all/ mri_convert (preprocessing dicom file error)
by miracle ozzoude 08 Sep '16

08 Sep '16

Hello, I am trying to preprocess couple of dicom images (146 dicom image) and I constantly get this error. "dan% *recon-all -all -i IM-0065-0001.dcm -s fsdir (recon-all script)* Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3 Actual FREESURFER_HOME /Applications/freesurfer Darwin opennet-33-172.uhnres.utoronto.ca 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir \n mri_convert /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir/mri/orig/001.mgz \n mri_convert /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm... Starting DICOMRead2() dcmfile = /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/IM-0065-0001.dcm dcmdir = /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3 Ref Series No = 3 Found 150 files, checking for dicoms Found 146 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 1 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 146 ndcmfiles = 146 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.90-- Loading pixel data Segmentation fault Darwin opennet-33-172.uhnres.utoronto.ca 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 recon-all -s fsdir exited with ERRORS at Thu Sep 8 20:25:11 EDT 2016 For more details, see the log file /Users/dan/Desktop/paul/01-005-C/AX_FSPGR_3D_3/fsdir/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [opennet-33-172:paul/01-005-C/AX_FSPGR_3D_3] dan" Also, I tried "mri_convert" command and i received same error. Here's my script " setenv SUBJECTS_DIR ....... cd ........ *mri_convert -it dicom -i IM-0065-0001.dcm -ot nii -o 01005C.nii.gz"* *Please can anyone tell me where it went wrong. thank you. * *Paul*

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issues with GUI {Disarmed}
by C.Anastasopoulos＠lumc.nl 08 Sep '16

08 Sep '16

Dear freesurfers, I encounter problems with the GUI, for example I can't change the "Design name" from "Untitled" to a custom title. I get following error when I start qdec with .tcsh from the terminal, which might be related: pci id for fd 4: 80ee:beef, driver (null) libGL error: core dri or dri2 extension not found libGL error: failed to load driver: vboxvideo Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl I am using using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on a Ubuntu 14.04 Thanks, Constantin

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FreeSurfer registration tool in ASL image
by Frank Robert 08 Sep '16

08 Sep '16

Hello FreeSurfer expert I want to use registration tools of FreeSurfer to register arterial spin labeling (ASL) images to DWI images in stroke study. Is there any material to talk about this topic? I use mri_robust_register to register 8 slice ASL images to 28 slices DWI images, Attached is the images I got. After the registration, the orientation is different. <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register> Does anyone as suggestion? Frank Yu

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Spmregister issues
by Albrecht, Daniel S. 08 Sep '16

08 Sep '16

Hello, I've been using spmregister in order to coregister a static PET image to an MPRAGE, typically with good results. A representative run is as follows: spmregister --mov $file.nii --s $subj --reg SUV_lin_T1.dat --fsvol orig We then convert *.dat to *.mat with tkregister2, and apply the *.mat to the PET with FLIRT. However, the registration was unsatisfactory for a recent subject. While working through a couple different coregistration options, I tried running coregister (estimate and reslice) in SPM. The result from this was quite good. I was confused why this would give a different result from spmregister when I'm not changing any of the default parameters in SPM. Any ideas on why running a coregistration directly through SPM would give a different result? And as a secondary follow-up, are there any tools available to convert an SPM transformation matrix (e.g. x from x=spm_coreg) to a *.mat that can be used in FSL FLIRT? Thanks, Daniel S. Albrecht, PhD Research Fellow in Radiology Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-6748 Fax: (617) 726-7422 dsalbrecht(a)mgh.harvard.edu<https://owa.partners.org/cvpn/aHR0cHM6Ly9wcm94eS1vd2EucGFydG5lcnMub3Jn/owa/…>

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Can't Load More Than Four Unique Overlays on TKSurfer From Command Line
by Taylor, Johnmark 08 Sep '16

08 Sep '16

Hello, I am trying to load five overlays on TKSurfer from the command line (actual command attached). The problem is this: if I try to load five different overlays, the fifth one will show up on Freesurfer as being identical to the first one (for instance, in this example, the "all-slope" overlay will appear visually identical to the "fs-slope" overlay, even though I've verified that the files are different). Furthermore, if you try to load six, then the fifth overlay will look the same as the first, the sixth will look the same as the second, and so forth. If I manually add the overlays from the menu in tksurfer this doesn't happen, but I'd prefer not to have to do this. Any idea what could be going on? Apologies that the command is a mess to read: in case it isn't clear, I am calling the overlay flag five separate times, once for each desired overlay. Thanks, JohnMark tksurfer green_ant lh inflated -gray -title green_ant_lh *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/fs-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/fo-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/ps-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/po-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5 *-overlay* /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/glm_sm5_ps/all-slope/sig.nii.gz -orf /ncf/vcn/jtaylor/mri-space/studies/supips_loccompare01/unpackdata/160805_xu_supips_loccompare01_sub01/bold/register.dof6.dat -fminmax 2 5

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Re Re: Extracting aseg.stats data
by Tamara Tavares 08 Sep '16

08 Sep '16

That seemed to work, thank you! Tamara

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Re: [Freesurfer] White matter surface don't change after editing
by Cong 08 Sep '16

08 Sep '16

Hi dear all I attach a new picture to illustrate this problem. I erased some voxels in wm.mgz and rerun. The lh.orig(blue line) looks well, but lh.white(yellow line) don’t along the white surface in some area. Could anyone give me some advice? Thanks very much. Best wishes Cong Chen >> Date: Sun, 4 Sep 2016 15:15:42 +0800 >> From: Cong <3110103623(a)zju.edu.cn> >> Subject: [Freesurfer] White matter surface don't change after editing >> >> Dear freesurfer team? >> I have some MRI images from a GE scanner, it seems that images? quality is poor because grey matter is bright in so much area and these grey matter is included in wm.mgz. So I deleted wrong voxels in wm.mgz by freeview and rerun through command ? recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But ?h.white (yellow line) don?t change after rerunning as you can see in the attached picture. Is this problem caused by deleting too many voxels and how to fix it? Thanks very much. >> >> Regards >> Cong Chen

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extract JUST pial surface for brain-printing purposes - what can I skip?
by djpeters＠u.washington.edu 08 Sep '16

08 Sep '16

Hi Freesurfer list, Say I was interested ONLY in extracting the pial surface for the purpose of getting a 3D print of a brain. Are there any time-intensive steps that can I safely exclude from the recon-all pipeline? For example, if I exclude the CARegister step ( -nocareg ), will I still get a good pial surface? Thanks so much, -Dan

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design matrix palm
by maaike rive 08 Sep '16

08 Sep '16

Hi all, I was adviced to use PALM for permutation of non-orthogonal surface data. However, I have some questions regarding the design matrix en contrast files to be used in PALM, but somehow I cannot subscribe to the FSL mailing list, and I was hoping one of the freesurfer users could help me out. I have a complex design and I would like to test for interactions as well for subgroups; in addition, I have several covariates. If I use the following collumns: A1 B1 A2 B2 cov1 cov2 cov3 I assumed I can at least test for the effects of A vs B (1 - 1 1 -1 0 0 0) and 1 vs 2 (1 1 -1 -1 0 0 0) and interactions (1 -1 -1 1 0 0 0). Q1: Is it true that I cannot compare subgroups, because columns denoted zero will be handeled as being a covariate? i.e. the contrast 1 -1 0 0 0 0 0 is inappropriate and I would have to build a new design matrix (A1 B1 cov1 cov2 cov3)? This is what I was told previously when using randomise for DTI data, but I'm not sure PALM works the same way. Q2: What I also understood from randomise is that you have to define both 1 -1 and -1 1; there is no option for a 2tailed t-test or F test. Is that correct and does it also apply to PALM? Thanks, Maaike

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