Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Inconsistency in SI axis coordinate between FreeSurfer recon-all seg image and BrainVoyager
by Jerry Jeyachandra 18 Apr '17

18 Apr '17

Hi Freesurfer support team, I'm attempting to register coordinates between BrainVoyager anatomical images and freesurfer segmented images with both in native space, however I'm running into inconsistencies specifically along the inferior/superior dimension that I hope you can help me with BrainVoyager reports coordinates as voxel indices which I'm trying to match with FreeView's T1fs_nu_conform coordinates which I assume are in voxel indices as well. Both the AP and RL dimensions match in both programs across all our participants, however the SI axis does not, with offsets varying across participants. Does the recon-all function crop the image such that the Z dimension is no longer matched with native space? I've noticed that the images are cropped specifically from the bottom segment below the neck and was wondering if that was affecting the coordinate report in the SI axis. If this is the case, is this stored in freesurfer such that I can get coordinates relative to the uncropped image or just the offset value for the Z coordinate to compensate for it? Thanks, Jerry Jeyachandra

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Any advices for hires surface reconstruction?
by Damien MARIE 18 Apr '17

18 Apr '17

Hi, I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, skull strip was done despite a slight piece of dura is still present. For the data processed at native resolution, with the hires flag, I mainly used this: recon-all -subject -i -parallel -expert -hires The expert file indicating only mris_inflate -n 50 As a result, skull strip had to be fixed for 5 subjects (missing brain pieces). Bilateral temporal pole is missing in the reconstructed surfaces in 19 subjects. For the downsampled data, without the hires flag : recon-all -subject -i -parallel Bilateral temporal pole is missing in the reconstructed surfaces in only 1 subject. Surfaces are way smoother. I guess such differences between the classic pipeline and the pipeline tuned for hires data are expected. I was just wondering if I was missing something somewhere, some additional options that I would need to tweak, to get better surfaces with the hires data especially in the temporal pole. For now the only things I see that I could do are adding checkpoints or play with this command line: mris_make_surfaces -max_gray_at_csf_border X -max_csf Y Thank you and best, Damien

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Fixing a left/right flip
by Dan Grupe 17 Apr '17

17 Apr '17

Hi all, After running a bunch of subjects through FreeSurfer and making extensive manual edits to the white matter masks, we discovered that the data were left/right flipped during the dicom-to-nifti conversion process. I hope to maintain these manual edits while processing data in the proper orientation and running them through the rest of the pipeline. Is this possible to do? An old thread from 10 years ago directed me to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal that offered some tips on how to go about this. However, after confirming that the volume was reversed running recon-all -autorecon1 in a new directory, I encountered an error message: > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) This problem does not arise when running the same command on a copy of this subject’s non-flipped data. Are there different steps that I should be following to rectify the problem? Or can you help me troubleshoot this error? Best, Dan ------ Dan Grupe, Ph.D. Assistant Scientist Waisman Laboratory for Brain Imaging and Behavior and Center for Healthy Minds University of Wisconsin-Madison ------ grupe(a)wisc.edu<mailto:grupe@wisc.edu> 608-263-7572 http://brainimaging.waisman.wisc.edu/~dgrupe

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Matlab packages
by Iman Aganj 17 Apr '17

17 Apr '17

Dear FreeSurfer users, I have recently developed two Matlab packages and made them publicly available, which I'd like to share with you. They include source codes and compiled binaries, and are GPU-compatible. The first one is for deformable registration of same-contrast images, using the mid-space-independent <https://authors.elsevier.com/a/1UgxH3lc~q-QUS> approach. www.nitrc.org/projects/msi-register <http://www.nitrc.org/projects/msi-register> The second one is for diffusion-weighted MRI processing. It includes a pipeline for computation of the q-ball Orientation Distribution Function in Constant Solid Angle (CSA-ODF <http://www.ncbi.nlm.nih.gov/pubmed/20535807> ), in addition to Hough-transform <http://www.ncbi.nlm.nih.gov/pubmed/21376655> based tractography. www.nitrc.org/projects/csaodf-hough <http://www.nitrc.org/projects/csaodf-hough> These are first releases. I highly appreciate any feedback. Best regards, Iman Aganj Assistant Professor of Radiology Harvard Medical School Assistant in Neuroscience Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital

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Re: [Freesurfer] Control point in WM regions
by Antonin Skoch 17 Apr '17

17 Apr '17

Dear Shane, could you please post screenshots of ?h.orig.nofix and ?h.orig in the problematic regions? Antonin Skoch Hello Freesurfer Team, I am trying to recover thin WM strands in the temporal lobe by using control points but to no avail (screenshot) Any suggestions please? These regions also appear to be classified as WM (wm.mgz) but why are the surfaces inaccurate? Thanks for your help. Best Wishes,Shane

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ERROR
by Damien MARIE 17 Apr '17

17 Apr '17

Hi, I ran recon-all on a server where Ubuntu is running. Recently I installed separately freesurfer on a macbook, it is working (e.g. tkmedit bert), I moved my processed subjects to freesurfer/subjects on the macbook but I can not work with them. I have the below error. I changed the permission to 777, it is still not working. Now what is really strange is that, using the finder I do not see the files in freesurfer/subjects but by doing ls -l in a terminal, I can see them… Please note that SUBJECT_DIR is defined. Any idea is welcome. Thank you and best, Damiens-MacBook-Pro-2:subjects dmarie2$ tkmedit hires_ct_pp1_N4_bet_MP2RAGEcorr/ brainmask.mgz -aux T1.mgz ERROR: cannot find subject hires_ct_pp1_N4_bet_MP2RAGEcorr/ in /Applications/freesurfer/subjects or it is not readable by you Damien

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Control point in WM regions
by Shane Schofield 17 Apr '17

17 Apr '17

Hello Freesurfer Team, I am trying to recover thin WM strands in the temporal lobe by using control points but to no avail (screenshot) Any suggestions please? These regions also appear to be classified as WM (wm.mgz) but why are the surfaces inaccurate? Thanks for your help. Best Wishes,Shane

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ERROR
by Damien MARIE 17 Apr '17

17 Apr '17

Hi, Just a follow-up about the message I posted. Problem is solved. I just moved freesurfer/ outside of the Applications folder (from /Users/me/Applications/freesurfer to /Users/me/freesurfer ). So now I can work with my macbook on subjects previously processed with another system. Probably an issue with mac os (10.11.6 ?) and copy pasting files in a subdirectory of the Applications folder… Thanks, Damien _______________________________________________ Damien MARIE <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Sat, 15 Apr 2017 06:22:31 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi, I ran recon-all on a server where Ubuntu is running. Recently I installed separately freesurfer on a macbook, it is working (e.g. tkmedit bert), I moved my processed subjects to freesurfer/subjects on the macbook but I can not work with them. I have the below error. I changed the permission to 777, it is still not working. Now what is really strange is that, using the finder I do not see the files in freesurfer/subjects but by doing ls -l in a terminal, I can see them… Please note that SUBJECT_DIR is defined. Any idea is welcome. Thank you and best, Damiens-MacBook-Pro-2:subjects dmarie2$ tkmedit hires_ct_pp1_N4_bet_MP2RAGEcorr/ brainmask.mgz -aux T1.mgz ERROR: cannot find subject hires_ct_pp1_N4_bet_MP2RAGEcorr/ in /Applications/freesurfer/subjects or it is not readable by you Damien _______________________________________________

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Corrupted annot file
by Das S. 16 Apr '17

16 Apr '17

Hi, I have created an .annot file from label files using mris_label2annot command. mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_ label/MyColorLUTnew.txt --a eqnew40aparc --ldir 100307/label/eq_parcellation_label/ Then I have created a .gcs file from the above .annot file. mris_ca_train -t 100307/label/eq_parcellation_label/MyColorLUT.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.left40aparc.annot 100307 100307/label/lh.reg40aparc.gcs Then from the .gcs file I have another .annot file. mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.eqnew40aparc.gcs 100307/label/lh.aparc.annot The 2nd annot file is corrupted and showing a big gray patch.While checking the annotation file in matlab, found that the those vertex on the .annot file were not assigned any colorcode from colortable. Here is the content of MyColorLUTnew.txt: 0 unknown 1 1 1 0 1 node1 70 130 180 0 2 node2 245 245 245 0 3 node3 205 62 78 0 4 node4 120 18 134 0 5 node5 196 58 250 0 6 node6 0 148 0 0 7 node7 220 248 164 0 8 node8 230 148 34 0 9 node9 0 118 14 0 10 node10 70 118 14 0 11 node11 122 186 220 0 12 node12 236 13 176 0 13 node13 12 48 255 0 14 node14 204 182 142 0 15 node15 42 204 164 0 16 node16 119 159 176 0 17 node17 220 216 20 0 18 node18 103 255 255 0 19 node19 80 196 98 0 20 node20 60 58 210 0 21 node21 160 58 210 0 22 node22 120 58 210 0 23 node23 40 58 210 0 24 node24 60 120 60 0 25 node25 255 100 0 0 26 node26 250 165 0 0 27 node27 0 255 127 0 28 node28 165 42 42 0 29 node29 135 206 235 0 30 node30 160 32 240 0 31 node31 0 200 200 0 32 node32 100 50 100 0 33 node33 135 50 74 0 34 node34 122 135 50 0 35 node35 51 50 135 0 36 node36 74 155 60 0 37 node37 120 62 43 0 38 node38 74 155 60 0 39 node39 122 135 50 0 40 node40 70 130 180 0 Any help will be much appreciated, why the file is getting corrupted in the 2nd step? Thanks Sarbani

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Missing S_interm_prim-Jensen??
by Kevin Japardi 16 Apr '17

16 Apr '17

Hello Freesurfer group, I'm going through my Destrieux Atlas data (?h.aparc.a2009s.annot), with a total group N of 91, and there is a single person without a row for S_interm_prim-Jensen for Left Hemisphere ONLY. Any thoughts on why this would be? I reran recon-all with autorecon3, seeing as the file is created during this stage block. The issue unfortunately didn't resolve itself. Any feedback would be greatly appreciated. Find it odd. Everyone was run using the same Freesurfer version and around the same month/ish. Thank you! Kevin Japardi

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Freesurfer April 2017