Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

lgi for longitudinal scans
by Anna Jonsson 23 Jul '14

23 Jul '14

Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data? thank you, kind wishes Anna

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recon-all error
by Cheng Peng 23 Jul '14

23 Jul '14

Hi, Freesurfer experts: I encountered an error message while i was attempting to run a longitudinal study (following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 under workflow summary) egister_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=0.0 skull bounding box = (0, 0, 0) --> (255, 255, 255) using (85, 85, 128) as brain centroid... mean wm in atlas = 107, using box (53,53,96) --> (116, 116,159) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=1, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf It appears that the skull strip step has failed as brainmask.mgz is completely blank. I tried to look up the error message online but found little help there. I would really appreciate it if someone can explain the problem or where to look for an explaination. I attached the recon-all error log with this email, i would also include nu.mgz but the last email attached with that was blocked due to the size of the image. Thanks! Best Regards, Cheng Peng Maryland Neuroimaging Center

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running freesurfer subcortical segmentation on a T2 weighted image only ?
by Vincent Noblet 23 Jul '14

23 Jul '14

Dear all, I was wondering if there is a way to use the segmentation of freesurfer on a T2 weighted image only (without a T1 weighted image). Sincerely Vincent Noblet

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bad freesurfer segmentation
by Doety Prins 23 Jul '14

23 Jul '14

> Dear freesurfer experts, > > I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. > > Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? > > Thanks in advance, > > Doety

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Pathstat.byvoxel.txt question
by Sarina Sacco 23 Jul '14

23 Jul '14

Hi all freesurfer experts , I have a question about the command trac-all-stat-c ,what is the interpolation that uses?

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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

2 3

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

2 5

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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Freesurfer July 2014