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30132 discussions

mris_anatomical_stats input image?
by Winkelbeiner, Stephanie A 18 Jan '19

18 Jan '19

External Email - Use Caution Hi Freesurfers, I'm using the below command to extract GM values: mris_anatomical_stats -mgz \ -cortex label/lh.cortex.label \ -f stats/lh.250.aparc.pial.stats \ -b -a 250.aparc \ -c label/colortable.ctab \ $subject lh pial Specifying "pial" which image does the command actually use? The mri/orig.mgz? Thanks for your help! Stephanie The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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error while running trac-preproc
by Barletta, Valeria 18 Jan '19

18 Jan '19

Dear Freesurfers, I am trying to run the command trac-all -prep -c but I'm getting this error: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory Can you help me? Thank you, Vale

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wm and vcsf nuisance regressors
by Nasiriavanaki, Zahra 18 Jan '19

18 Jan '19

Dear Freesurfers Hi I am using white matter and CSF external nuisance regressors in my mkanalysis-sess. However, when I make these regressors, I use -mean in fcseed-config command, and so the .dat files only have one column (the mean values, I assume). I looked up in the freesurfer archive and I saw that It is recommended to use -nuisreg wm.dat 5 and -nuisreg vcsf.dat 5. My question is that what difference it makes to use mean of these regressors vs using only 5 of the columns. I appreciate if you could please reply whenever you had time. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Talairach Transform failure
by Daniel Ferreira 18 Jan '19

18 Jan '19

External Email - Use Caution Dear Bruce, Martin, and experts, I posted an issue a few days ago. I have been looking through the archives but can not figure out the solution myself. I was wondering if you would have any suggestion on how to fix the issue described further down? Thank you very much in advance Dani ---- Daniel Ferreira <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Wed, 09 Jan 2019 10:22:05 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri* * talairach_afd -T 0.005 -xfm transforms/talairach.xfm * *ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)* *Manual Talairach alignment may be necessary, or* *include the -notal-check flag to skip this test,* *making sure the -notal-check flag follows -all* *or -autorecon1 in the command string.* *See:* *http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>* *ERROR: Talairach failed!* *Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at tis 11 dec 2018 11:32:31 CET* Next, I tried to fix the issue by using tkregister: tkregister2 --mgz --s tal_before --fstal However, the Talairach volume does not load as a MOVEABLE volume. When I check the available recon-all output I only have: orig/001 --> looks good rawavg --> looks good orig --> its awful (it looks like millions of white tiny voxels on a black background) nu --> it is empty transforms/talairach.xfm --> is available I was wondering if you would know about any way to fix this? Thank you in advance, Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padi...(a)ki.se <daniel.ferreira.padi...(a)ki.se>*

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Re: [Freesurfer] Longitudinal subfields segmentation single time point
by Iglesias Gonzalez, Eugenio 18 Jan '19

18 Jan '19

External Email - Use Caution Thanks a lot for your email, Saskia. Does this happen for more than one subject? Can you reproduce the error? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology Lecturer on Radiology Harvard Medical School http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Koch, S.B.J. (Saskia)" <S.Koch(a)donders.ru.nl> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 18 January 2019 at 09:46 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Longitudinal subfields segmentation single time point External Email - Use Caution Dear FreeSurfer Developers, I am attempting to run the longitudinal hippocampal subfields segmentation, using the development version of FreeSurfer. This works perfect for subjects with multiple data time points, but I get the following error for subjects for which I have a single data time point (see attachment for the error log): ******************* Global iteration 2 ******************* ***** Estimating subject-specific atlas ***** Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/Matlab/kvlMatlabObjectArray.cxx:82: itk::ERROR: MatlabObjectArray(0x7f8686741c40): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155) Is it possible to run this longitudinal module on subjects with a single time point? Any thoughts on how to troubleshoot this? FreeSurfer version: freesurfer-Linux-centos7_x86_64-dev-20180118-d073f7e Platform: CentOS Linux 7 (Core) Uname -a: Linux mentat003.dccn.nl 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help! Saskia

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Longitudinal subfields segmentation single time point
by Koch, S.B.J. (Saskia) 18 Jan '19

18 Jan '19

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to run the longitudinal hippocampal subfields segmentation, using the development version of FreeSurfer. This works perfect for subjects with multiple data time points, but I get the following error for subjects for which I have a single data time point (see attachment for the error log): ******************* Global iteration 2 ******************* ***** Estimating subject-specific atlas ***** Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/Matlab/kvlMatlabObjectArray.cxx:82: itk::ERROR: MatlabObjectArray(0x7f8686741c40): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155) Is it possible to run this longitudinal module on subjects with a single time point? Any thoughts on how to troubleshoot this? FreeSurfer version: freesurfer-Linux-centos7_x86_64-dev-20180118-d073f7e Platform: CentOS Linux 7 (Core) Uname -a: Linux mentat003.dccn.nl 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thanks for your help! Saskia

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Help with finding which functional areas house certain electrodes
by Sparsh Jain 17 Jan '19

17 Jan '19

External Email - Use Caution Good afternoon, We want to find the functional areas where each electrode is located in patients. At present, we are finding the electrode RAS coordinates manually using CT-MRI co-registration. We are then manually searching for these locations in Freeview using the aparc.a2009s+aseg ATLAS (generated during MRI reconstruction) on top of MRI volume. This is giving us the exact anatomical/functional area where the electrode belongs. However, this is a very tedious and time-consuming process and we need to do this for many patients. We were wondering if there is 1. A way to automate this process by possibly entering all coordinates and using the LUT and atlas files to get the areas easily for all points. 2. More importantly, could you tell us how to establish a method where we can dump the anatomical region coordinates to a file, and then find the nearest functional area to a particular electrode automatically? For example, if a point lies in a white matter area, can we implement a process to find which functional area (gray matter region, or say hippocampus for example) lies CLOSEST to this electrode point in the white matter region. Can we implement this automated process in an efficient manner for all the points at once? We usually have anywhere between 140 -170 sets of coordinates for each patient, and doing this by hand on freeview is not practical. Instead of finding where exactly all the points lie, we would like to create a 'table' of all anatomical areas and then find out which area of relevance lies closest to a particular point. Thank you Sparsh Jain

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Issues parcellating with a custom atlas
by Michael Sughrue 17 Jan '19

17 Jan '19

External Email - Use Caution Hello My interest is to create an aparc+aseg file with a combination of a cortical parcellation with a custom cortical atlas and the subcortical grey matter components from the standard aseg....basically i want to mask and extract signal from multiple areas in a series of pipelines in python. The commands below are called from python, but edited to make it easy to read. About 50% of the time the code below works fine, but the other 50% it drops two cortical parcellations. Interestingly it is always the same two parcellations, both at the end of the left hemisphere list, that get dropped when making aparc+aseg. My only guess is that something about the aparc and aseg combination is causing them to be dropped. I have read the annot files it makes and the parcellations are made in the mris_ca_label step and making the aparc+aseg. I have viewed them in freeview and they are not there when viewed in the LUT for this atlas and I have tried omittng and excluding all forms of mri_binarize -replace commands (added to try to eliminate segmentations of the ventricle and white atter which i am trying to mask out of a resting state image), and this doesnt make a difference in the cases where it is failing. I have tried using the cases where it worked to train a new gcs file without success. I have also rune mri_aparc2aseg with and without the ribbon option, with all varieties of aseg files...etc etc. If there is something obviously wrong please let me know. Alternately, what is the best way to get aparc+aseg.mgz to print a list of what areas made it in there..in that case i can likely create a way to make sure the lables it is using for an adjacency matrix atleast match the rows and columns accurately..i tried using segstats but this wasnt always an accurate list as it sometimes created a mask with areas not on any LUT's i have and thus i have been unable to view them in freeview or the segstats list and figure out what is going wrong the commands i invoke from python are below...thanks in advance recon-all -subjid sub1 -autorecon1 -openmp 6 recon-all -subjid sub1 -autorecon2 -openmp 6 'recon-all -subjid sub1 -sphere -surfreg -jacobian_white -avgcurv -open mp6 mris_ca_label -l $SUBJECTS_DIR/sub1/label/lh.cortex.label -aseg $SUBJECTS_DIR/sub1/mri/aseg.presurf.mgz sub1 lh lh.sphere.reg $SUBJECTS_DIR/sub1/parc/lh.hcp-mmp_6p0.gcs lh.aparc.annot mris_ca_label -l $SUBJECTS_DIR/sub1/label/rh.cortex.label -aseg $SUBJECTS_DIR/sub1/mri/aseg.presurf.mgz sub1 rh rh.sphere.reg $SUBJECTS_DIR/sub1/parc/rh.hcp-mmp_6p0.gcs rh.aparc.annot recon-all -subjid sub1 -pial -cortribbon -hyporelabel -openmp 6 mri_binarize --i mri/aseg.presurf.hypos.mgz --o mri/aseg.mgz --replace 2 0 --replace 4 0 --replace 5 0 --replace 7 0 --replace 14 0 --replace 15 0 --replace 24 0 --replace 30 0 --replace 31 0 --replace 41 0 --replace 43 0 --replace 44 0 --replace 46 0 --replace 62 0 --replace 63 0 --replace 77 0 --replace 85 0 --replace 251 0 --replace 252 0 --replace 253 0 --replace 254 0 --replace 255 0') mri_aparc2aseg --s sub1 mri_binarize --i mri/aparc+aseg.mgz --o mri/aparc+aseg.mgz --replace 41 0

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Exporting mean curvature indices
by Martin Juneja 17 Jan '19

17 Jan '19

External Email - Use Caution Hi Freesurfer experts, I am interested in estimating mean curvature index for each of the 7 networks (Yeo7 atlas) for my data of healthy controls. I am able to estimate this subjectwise, and the output stats file for each subject looks like following: # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd FreeSurfer_Defined_Medial_Wall 8952 5993 1906 0.916 1.370 0.082 0.026 85 7.4 7Networks_1 23231 15309 34881 2.139 0.685 0.125 0.028 261 25.2 7Networks_2 20682 12735 35481 2.511 0.746 0.101 0.022 167 17.7 7Networks_3 14062 9362 24591 2.423 0.569 0.107 0.021 124 11.4 7Networks_4 12798 8490 25886 2.776 0.656 0.109 0.023 115 11.4 7Networks_5 10915 7302 26939 3.047 0.899 0.122 0.030 133 12.6 7Networks_6 15373 10259 28312 2.539 0.698 0.123 0.027 164 15.9 7Networks_7 32448 21779 70662 2.773 0.695 0.124 0.028 375 36.0 I have 123 such files from a set of 123 subjects. I was just wondering how can I save mean curvature indices from all the subjects in one file (text or excel)? I defined my Subjects.txt file with subject IDs of each subject. I am not sure how to proceed from there to save curvature indices. I tried to run following command, but that does not work: aparcstats2table --subjectsfile Subjects.txt --hemi lh --meas white.H -t MCI.txt I would really appreciate any help.

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convert surface-based label to volumetric space...mri_label2vol?
by Stephanie Hare 17 Jan '19

17 Jan '19

External Email - Use Caution Good afternoon, I'm new to Freesurfer; my background is resting-state fMRI using SPM. Years back, left and right cortical thickness measures were calculated for our sample of schizophrenia patients using the Desikan-Killiany atlas and were input to an SPSS spreadsheet. In an exploratory analysis of the data, I found that behavioral performance on a skills assessment was correlated with thickness of lh_rostralmiddlefrontal and lh_parstriangularis regions. I'd like to perform a follow-up resting-state fMRI analysis, using these two surface-based parcellations ( lh_rostralmiddlefrontal and lh_parstriangularis) as seed regions and use those behavioral performance scores as a regressor. Is there a simple way to convert these two 2D-surface-based atlas measurements to masks in nifti format in 3D-volumetric space? I was doing a quick google search and came across the mri_label2vol command. Would this be helpful? Sorry for my naiveté. I appreciate your time. Best, Stephanie Hare Postdoctoral Fellow Neuroimaging Research Program Maryland Psychiatric Research Center

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