Freesurfer

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30132 discussions

Editing Parcellations
by Jennifer Bramen 09 Feb '10

09 Feb '10

Dear Freesurfer List I am trying to edit the parcellations using tkmedit, but I am unable to effect the Segmentation Brush label using the Configure Segmentation Brush window. Regardless of my selection, my drawing is labeled "out of bounds". I don;t see an apply button or anything like that, so I assumed simply highlighting the tissue class in the Configuration window would change the brush to my selected label. Is there some step I may be moissing when trying to make a selection? I am using the most up to date version of Freesurfer, and have also tried reverting to older versions, all with no success. Thanks for you your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)525-0865 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919

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Skull Stripping extra dura & vasculature
by Sherri Novis 09 Feb '10

09 Feb '10

Hello, I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.) I have rerun skull stripping changing the watershed value, however it's not making the distinction between dura and gray matter. (recon-all -skullstrip -wsthresh [tried 0..35] -clean-bm -no-wsgcaatlas -subjid [subject_id] - FS version: freesurfer-Linux-centos4-stable-pub-v4.3.0) I also attempted to edit 50% of the slices by erasing voxels to make a clear boundary between the dura and cortex and then re-ran autorecon2 to see if it would at least adjust the pial surfaces - however that did not work (pial surfaces still crossed the one pixel boundary I made into the dura). Can you recommend any other flags or things to try before I edit/erase the excess by hand? Thanks for your time - Sherri

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smooth pial surface in occipital pole region
by yzhangd＠artsci.wustl.edu 09 Feb '10

09 Feb '10

Hi experts, I found that the pial surface in the occipital pole region tends to be smooth, after running recon-all. Shallow sulci and fused sulci render a smooth surface (attached surface images). i tried to delete some voxels (arrows on the "flatpialsurf_volume.tiff") to force freesurfer to recognize these sulci. Are deleting voxels from the brainmask.mgz image an appropriate approach to correct the surface in this region ?? Thanks a lot Yuning

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ITI/ISI in optseq2
by Asaf Kaftory 09 Feb '10

09 Feb '10

hello list, 1. Is there a way to make sure Optseq2 inserts a "null" after each event (and thus creating an ISI/ITI between every conditions)? If not - how is it possible to make sure there's a minimal ITI/ISI between each stimuli? 2. If defining an ITI is possible in optseq2, Is there a way to determine its average and SD? thanks, asaf.

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dt-recon output file format
by Ed Gronenschild 09 Feb '10

09 Feb '10

Hi, Question for the developers. Is it possible to adjust the dt-recon tool such that the output files are in zipped NIFTI format (.nii.gz) in view of the enormous amount of data that is generated. It can accept .nii.gz files as input. Thank you in advance, Ed

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FS Deformable Xform
by Suresh Joshi 09 Feb '10

09 Feb '10

Hello all, short time reader, first time poster... I have a question regarding the current FreeSurfer volumetric pipeline. This page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview states that FreeSurfer has 5 stages and they are described in Fischl 2002,2004 (which I have read). As well, there is a "a high dimensional nonlinear volumetric alignment" (which I take to be deformable registration). So, now my question is: Can anyone give me any specifics about this non-linear transform? In the Fischl paper, the second transform gets reduced to a 12 parameter affine transform. As well, here is the new pipeline: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllBlockDiagram And it doesn't clearly answer my question. As well, there are talks of intensity normalization (ie. elimination of bias fields), but it there ever an intensity normalization step performed between the atlas and the target??? Thanks for the help, -SJ

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Invitation to connect on LinkedIn
by John Drozd 09 Feb '10

09 Feb '10

LinkedIn ------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - John Confirm that you know John Drozd https://www.linkedin.com/e/isd/1058664165/nSlXVFJx/ ------ (c) 2010, LinkedIn Corporation

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talairach2ras
by Ben Hamida Cammoun Leila Faiza 08 Feb '10

08 Feb '10

Hi Can you please help me to recover RAS voxel coordinates (I need to use them in the label file) from the talairach ones. I think that the transformation I should use is the one in Talairach.xfm (T), but If I copy one vertex coordinates P (MNI Tal) from tksurfer, apply the transformation: I don't have the coordinate of the same RAS vertex. Ps:I tried to add 0 0 0 1 to the transform to make it 4x4, and 1 to the point to make it 4x1 Please correct me if the transformation and the displayed values in Tksurfer are not related to the Subject transformation in Talaraich space. Thanks a lot Leila

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Cannot Configure Segmentation Brush WHen Editing Subcortical Parcellations
by Jennifer Bramen 08 Feb '10

08 Feb '10

Dear Freesurfer Support Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0 Kernel info: Darwin 9.8.0 i386 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name 6002 2) the entire command-line executed tkmedit 6002 brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white - segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt & 3) the error message generated n/a I am trying to edit the subcortical parcellations. I found the wiki instructions, and have followed (I think) to a t. I am unable to effect the Segmentation Brush label by using the Configure Segmentation Brush menu. But regardless of my selection, my drawing is labeled "out of bounds". I have updated to the most recent version of Freesurfer. I also attempted to use an older version, in case it was a recent bug, incompatible with recon-all done in an older version, etc. However, no version changes have helped. Can someone tell me what I am missing? FYI - When I select a label type, I have tried both having the "Segmenmtation Brush Info" window open, with my slection highlighted, and highlighting and closing the window. I am hoping I am simply missing a step though obvious to the wiki creator. Here is the link to the "Editing" instructions I have been following: http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithDat… 4) optionally include the subject's /script/recon-all.log (n/a) Thanks for your assistance. Best regards, Jennifer Bramen, Ph.D. Assistant Research Neuroscientist UCLA Center for Cognitive Neuroscience Developmental Cognitive Neuroimaging Suite 17-369 740 Westwood Plaza Los Angeles, CA 90095 Phone: (310)525-0865 Fax: (310)206-5518 Email: jbramen(a)mednet.ucla.edu

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Re: [Freesurfer] Error mris_thickness_diff
by Martin Reuter 08 Feb '10

08 Feb '10

Hi Jürgen, the transforms found in the base are for each timepoint to the base and vice-versa. You'd need the registrations between the time points, so for example: tp2_to_tp1.long.base.lta from the tp1.long.base/mri/transform directory (registering tp2 to tp1). >From my test-retest analysis I see that the lta is more accurate than the -register (internal surface registration) of mris_thickness_diff. But I only tested this on a 15 subjects test population. Anyway, there is a third way of doing the thickness comparison for longitudinally processed data (and this is what I would recommend, also based on my test with the test-retest data set): As the surfaces in the longitudinal stream are in vertex correspondence across time, you do not need to spatially register at all. Just smooth, subtract, average etc the time points surface measures directly. So you can e.g. modify Han's method for step 2 similar to this: mris_thickness_diff -src_type curv \ -out $SUBJECTS_DIR/1001/surf/lh.thickness_diff.mgh \ -nsmooth 50 \ -abs -S 1001 \ -L $SUBJECTS_DIR/1001/surf/lh_thickness_diff.log \ $SUBJECTS_DIR/1001/surf/lh.white \ $SUBJECTS_DIR/1001/surf/lh.thickness \ $SUBJECTS_DIR/1001/surf/lh.white \ <------ ! $SUBJECTS_DIR/1001a/surf/lh.thickness Note that here I specify the same lh.white surface for both time points. Therefore the registration is skipped and only smoothing etc. applied. Alternatively you can do all this directly with other freesurfer commands (mris_calc ...). Han's steps 3 and 4 deal with Group analysis and should stay the same independently of cross sectional or longitudinal processing. Cheers, Martin On Mon, 2010-02-08 at 18:41 +0100, Jürgen Hänggi wrote: > Hi Martin > > Thanks a lot. In the past, I used the -xform /../mri/transforms/.. .lta, but > then I saw an email from Doug where he recommended to use -register for > longitudinal data. > However if I use lta, which transform do I have to use? > > Base_to_tp1.lta > Base_to_tp2.lta > tp1_to_base.lta > tp2_to_base-lta > > From Base/mri/transform > > Or any of the numerous transforms found in the tp1.long or tp2.long folder? > > In older versions, I think, there was a kind of combined transform that have > to be used. > > Do I'am right that when using longitudinal processed data, only step2 of > Han's four steps described under > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility > > have to be run? > > Thanks in advance > Cheers > Jürgen > > > > On [DATE], "Martin Reuter" <[ADDRESS]> wrote: > > > Hi Jürgen, > > > > I have seen this error before. Not sure exactly what is going on. There > > could be a bug in Han's code, but I could not find it quickly. > > I don't recommend the rigid alignment in mris_thickness_diff anyway. I > > have not seen any evaluation on the accuracy of the registration and do > > not trust it (it is a rigid surface based alignment using the nearest > > neighbor approach). > > > > Instead try to specify the lta (transform) for the two corresponding > > volumes. If you use the longitudinal stream, these transforms should be > > available (either in the <base>/mri/transform or in the > > <longitudinal-tp>/mri/transform dir). If you are processing your data > > cross sectionally: > > I would recommend to do it longitudinally. > > If that is not an option use mri_robust_register to register the > > norm.mgz and use that transform for the mris_thickness_diff. > > > > Cheers, Martin > > > > > > > > On Mon, 2010-02-08 at 08:30 +0100, Jürgen Hänggi wrote: > >> Dear FS experts > >> > >> when running mris_thickness_diff the following error occurred: > >> > >> mris_thickness_diff \ > >> ? -src_type curv \ > >> ? -out amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness_diff.mgh > >> \ > >> ? -register \ > >> ? -abs -S amblyo_pat01_tp3.long.amblyo_pat01_base1_3 \ > >> ? -L amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh_thickness_diff.log \ > >> ? amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.white \ > >> ? amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.thickness \ > >> ? amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.white \ > >> ? amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness > >> Output differences to file > >> amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness_diff.mgh > >> Do a rigid alignment of two surfaces before mapping to each other > >> logging results to > >> amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh_thickness_diff.log > >> Reading first surface file > >> amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.white > >> Surface1 has 137991 vertices > >> Reading in first data file > >> amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.thickness > >> Reading second surface file > >> amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.white > >> Surface2 has 137991 vertices > >> Reading in second data file > >> amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness > >> Register surface 2 to surface 1 (rigid mapping using ICP) > >> > >> ERROR: FindClosest: MHTfindClosestVertexNo returned annIndex=-1, which is > >> invalid! > >> > >> What does it mean? > >> > >> > >> Thanks in advance > >> Regards > >> Jürgen > >> > >> > >> ---------------------------------------------------------------------------- > >> Jürgen Hänggi, Ph.D. > >> Division Neuropsychology > >> Institute of Psychology > >> University of Zurich > >> Binzmuehlestrasse 14, PO Box 25 > >> 8050 Zurich, Switzerland > >> 0041 44 635 73 97 (phone office) > >> 0041 76 445 86 84 (phone mobile) > >> 0041 44 635 74 09 (fax office) > >> BIN 4.D.04 (office room number) > >> j.haenggi[at]psychologie.uzh.ch (email) > >> http://www.psychologie.uzh.ch/neuropsy/ (website) > >> http://www.juergenhaenggi.ch (private website) > >> > >> This e-mail (and any attachment/s) contains confidential and/or privileged > >> information. If you are not the intended recipient (or have received this > >> e-mail in error) please notify the sender immediately and destroy this > >> e-mail. Any unauthorised copying, disclosure or distribution of the > >> material in this e-mail is strictly forbidden. > >> ---------------------------------------------------------------------------- > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > > ---------------------------------------------------------------------------- > Jürgen Hänggi, Ph.D. > Division Neuropsychology > Institute of Psychology > University of Zurich > Binzmuehlestrasse 14, PO Box 25 > 8050 Zurich, Switzerland > 0041 44 635 73 97 (phone office) > 0041 76 445 86 84 (phone mobile) > 0041 44 635 74 09 (fax office) > BIN 4.D.04 (office room number) > j.haenggi[at]psychologie.uzh.ch (email) > http://www.psychologie.uzh.ch/neuropsy/ (website) > http://www.juergenhaenggi.ch (private website) > > This e-mail (and any attachment/s) contains confidential and/or privileged > information. If you are not the intended recipient (or have received this > e-mail in error) please notify the sender immediately and destroy this > e-mail. Any unauthorised copying, disclosure or distribution of the > material in this e-mail is strictly forbidden. > ---------------------------------------------------------------------------- > > > > >

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