Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30086 discussions

Diffusion analysis qs
by Rotem Saar 23 Jul '14

23 Jul '14

Dear Anastasia & Michael, Thank u for your answers (I attached my last email and your answers at the end of this email. I still want to specify my question. If I only want to extract FA values using the following script (see script below), and I know that an angle was applied during the dMRI scans, should I use the rotated gradient matrix ? When I first analyzed 20 subjects with the gradient matrix that is published for a T3 Philips magnet (I also read the gradients from the dicom header - they were the same) I got reasonable results - but now I don't know what to think of them... __________________________________________________________________________________ source ~/Desktop/fs_script dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/brain.mgz /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg=register.dat:colormap=heat:heatscale=.2,.2,1 tkmedit Anatomy0207 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap=lut mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap=lut mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked __________________________________________________________________________________________________________________ It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: > > FS uses FSL tools under the hood, so you want to use the bvecs that are > rotated into the axes of the scan. > > cheers, > -MH > > --? > Michael Harms, Ph.D. > ----------------------------------------------------------- > Conte Center for the Neuroscience of Mental Disorders > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO ?63110 Email: mharms(a)wustl.edu > > From: Rotem Saar <saar.rotem(a)gmail.com> > Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Date: Monday, July 21, 2014 1:54 PM > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Diffusion analysis qs - gradient matrix > > Dear freesurfer experts, > > For diffusion analysis in freesurfer - I want to know which gradient matrix > freesurfer expects. > > The thing is - when I look at the gradient matrix created using a MATLAB > script that reads the directions from the dicom header - I get one table, > but the bvecs file created in MRIconvert (for converting dicoms to nifti) > looks different. > > This is the situation when an angle is applied during the acquisition of the > dMRI scans, which means that each subject has its own gradient matrix. > > So my question is which table should I use for diffusion analysis in > freesurfer? The one that was created from the dicom header or the one > created for NIFTI format using MRIconvert ?? > > Thanks Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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Custom ROI surface visualization
by Shannon Buckley 23 Jul '14

23 Jul '14

Hi experts, I'm trying to create a pretty picture via Freesurfer / freeview. Specifically, I have 6 regions that I want to combine into 2 rois (1 color for each 3-region-roi ) that would display over a gray-background. So in Freeivew, my goal is to see a gray pial surface with roiA displayed in red and roiB displayed as blue with all other labels present, but gray. I've already read through the FAQ and attempted what I've seen work for others, but I seem to be hitting some kind of trouble and I'm not sure which steps / flags to adjust. Here is what I've tried so far: 1) mri_annotation2label -surf pial -hemi rh -outdir ./roi a. This got me all my rh.label files . 2) Then I used: mri_mergelabels -i rh.insula.label -i rh.fusiform.label -i rh.isthmuscingulate.label -o rh.ins_fus_icing.label (and repeat this for the next roi, using different labels) a. This got me a 2 new .label files that overlay great in Freeview if I load them individually on the rh.pial surface. The problem is that I can only seem to load ONE label at a time for the overlay, which does not meet my goal. So, to load multiple labels I tried combining them via. 3) mris_label2annot --s $code --hemi rh --ctab /home/vhasfcbuckls/Freesurfery/$code/label/roi/roi_added_bgGray.aparc.annot. ctab \ --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/$code/label/roi/rh.ins_fus_icing.label \ --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ling_ tpole_parah.label I've attached 2 screenshots: one where I've successfully loaded just ONE of the ROIs on the rh.pial (roiA_label_loaded.png); the other shows what I see after loading the product from step3 (annot_loaded_roiAB_graybg.png), which shows all 6 regions, but they aren't grouped into 2 rois by color, and the background is black instead of gray. The annotation seems to think I only have the 2 regions indicated in the std out (below), which is unexpected. I feel like there is some flag I'm missing here. I've attached the modified ctab file used as an input to mris_label2annot, wherein I've appended my custom labels to the standard aparc.annot.ctab and assigned new RGB colors. All other regions were changed to 127 127 127 0 to make them gray. Question: Can you please tell me which steps / flags/ inputs that need adjustments in order to reach my goal? Or is there a better tool / method that I should use for this visualization instead? Please let me know if you need more information. Thanks very much for your time, ~Shannon +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Here is the std out for step3: mris_label2annot --s $code --h rh --ctab /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_adde d_GrayBG.aparc.annot.ctab --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ins_f us_icing.label --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ling_ tpole_parah.label Using Freesurfer version 5.1. Subjects Directory is /home/vhasfcbuckls/Freesurfery Sessions Directory is /home/vhasfcbuckls/sessions Reading ctab /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_adde d_GrayBG.aparc.annot.ctab Number of ctab entries 38 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi cmdline /opt/freesurfer5.1/bin/mris_label2annot --s PPMI_012_S_3181m00_i357579 --h rh --ctab /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_adde d_GrayBG.aparc.annot.ctab --a newrois.graybg.aparc --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ins_f us_icing.label --l /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/rh.ling_ tpole_parah.label sysname Linux hostname london.v21.med.va.gov machine x86_64 user vhasfcbuckls subject PPMI_012_S_3181m00_i357579 hemi rh SUBJECTS_DIR /home/vhasfcbuckls/Freesurfery ColorTable /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/roi/roi_adde d_GrayBG.aparc.annot.ctab AnnotName newrois.graybg.aparc nlables 2 LabelThresh 0 0.000000 Loading /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/surf/rh.orig 1 8355711 bankssts 2 8355711 caudalanteriorcingulate Mapping unhit to unknown Found 114343 unhit vertices Writing annot to /home/vhasfcbuckls/Freesurfery/PPMI_012_S_3181m00_i357579/label/rh.newrois.g raybg.aparc.annot +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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dwi_motion Tracula
by Cat Chong 23 Jul '14

23 Jul '14

Hello Anastasia, I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I would like to use the command "dwi_motion" on my data. I have installed the updates, but will I have to completely reprocess my data inducing steps trac-all -prep, trace-all -bedp, and trac-all path in order to use dwi_motion? cheers, Cat

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Watershed
by SOURAV RANJAN KOLE 22 Jul '14

22 Jul '14

Hello Freesurfer community, 1. I am using watershed to perform more aggressive skull stripping but it seems to be not working for me. Command I am using: recon-all -subjid 1203 -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -no-isrunning Please see attachments for before and after watershed images. After watershed, skull stripping seems almost worse and it is not respecting the manual edits that I have done either. You can see the manual edits in the Before_Watershed.png file if you zoom in. 2. Which version of FreeSurfer do I need to have to use gcut as it is giving me the following error- recon-all -skullstrip -clean-bm -gcut -subjid 10 ERROR: Flag -gcut unrecognized. This is the FreeSurfer version that I am using: freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0 Thank you very much for your help. Regards, Sourav

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question regarding control point edits
by Adam Mezher 22 Jul '14

22 Jul '14

Hi FreeSurfer group, I was wondering if there is a way to include control points in my command line when I run recon-all. We are working with a large dataset and many of the subjects have underestimations in the anterior temporal lobes so it would be beneficial to expand the WM surface slightly on numerous cases rather than doing control point edits on each case individually. Thank you, Adam Mezher

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Question with QDEC annotations and mri_convert and mri_annotation2label
by Tara Ann Miskovich 22 Jul '14

22 Jul '14

Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara

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ERROR: Could not open [..]/bvals for reading
by Elia S. 22 Jul '14

22 Jul '14

Dear Freesurfer Community, Running Tracula preprocessing produces this error: ERROR: Could not open /home/elia/scripts/Tracula/LCL/dcmTimePoints_tar/T13D/timePoint1/dmri/bvals for reading I think the error described is the same as here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34169.html And as suggested here (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/035935…) I swapped the dmri_motion from the centos4 updates with the dmri_motion from the centos6 updates, and it works. Now here's the situation, I need to run tracula on machines where is not possibile to install the centos6 updates, since the message i get is this: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Do you have any advice for me? Thanks in advance,Elia. ---------------------------------------------------------------------------------------------------------------------------Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP WedOct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux My Current Working Directory: /home/elia

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DTImap
by Shantanu Ghosh 22 Jul '14

22 Jul '14

Hi FS experts, Is the DtiMap software (www.kennedykrieger.org) compatible with Freesurfer/Tracula? Thanks Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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freeserver versions
by Gianluca Rambaldelli 22 Jul '14

22 Jul '14

Hi, two years ago I processed a lot of data using freesurfer v5.1. Now I'm using v5.3 on a different group of subjects, I'm wondering if I can use together all the subjects from the different versions. Or there is a way to re-run it using the last version? I suppose that I can copy the 'control.dat' file that I saved into the new version but how can I add wm edits if I didn't saved it in a single file (for example edit.dat). Instead of creating an edit file, I saved every variations onto brainmask.mgz changing the original mask created by the recon -all procedure. I need to compare those old subjects because after a machine upgrade it has been installed the new version and I started a new project with v5.3. Thank you Gianluca Rambaldelli

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Extract curvind，folding, gauscurv, meancurv, thickness std in the whole vertices
by Qiongmin 22 Jul '14

22 Jul '14

Dear Experts, I used ‘mri_surf2surf’ to get the area, thickness, volume of all the vertices in the brain. I am wondering what functions can I use to get other information, such as ‘curvind, foldind, gauscurv, meancurv, thicknessstd’ ? I know FreeSurfer provides these statistic data according to two kinds of parcellations of the brain, but I need these information in a vertex-wise way. Thanks very much! Best, Qiongmin

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