Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

Average of surfaces
by john Anderson 22 Jan '19

22 Jan '19

External Email - Use Caution Dear FS experts, I resampled PET images for multiple subjects I used mri_vol2surfe to move these images onto fsaverage, not I have for every subject lh.PET and rh.PET How can I create the average of multiple surfaces. For example: on the left hemisphere of every subject I have lh.PET.subject1.nii,gz, lh.PET.subject2.nii,gz, lh.PET.subject3.nii,gz, .... lh.PET.subjectN.nii,gz How can I create the average of these surfaces? Thanks for any help John

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Surface maps of cortical thickness
by Schranzer René 22 Jan '19

22 Jan '19

External Email - Use Caution Hello everyone, I have some problems with the computation of the SD of thickness maps (mgh file) of 10 subjects. First I computed the average thickness map (to fsaverage) with the command: mris_preproc --fsgd qdec/subject_list.fsgd --target fsaverage --hemi lh --meas thickness --out avg-lh-thickness.mgh mri_surf2surf --hemi lh --s fsaverage --sval avg-lh-thickness.mgh --fwhm 15 --cortex --tval avg-lh-thickness.15.mgh Now I wanted to calculate also the thickness std mgh file. I tried this... mris_surface_stats -surf_name fsaverage/surf/lh.white -out_name lh_std.mgh -absmean lh_absmean.mgh -mean lh_mean.mgh -absstd lh_absstd.mgh avg-lh-thickness.15.mgh but this calculation of the SD mgh files does not work, because I get no output. Is there another way to calculate the surface maps of the SD of cortical thickness? Best, René

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Hippocampus subfield division error
by Yixin Ma 22 Jan '19

22 Jan '19

External Email - Use Caution Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an error message as attached, could you please help me with which part might have gone wrong? This subject's other recon-all worked but not for hippocampus subfields division. Thank you for your help. Best regards, Yixin [ > In segmentSubjectT1_autoEstimateAlveusML at 325] Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt -------------- Making Lateral-nucleus map to reduced label 1 Making Paralaminar-nucleus map to reduced label 1 Making Basal-nucleus map to reduced label 1 Making Accessory-Basal-nucleus map to reduced label 1 Making Corticoamygdaloid-transitio map to reduced label 1 Making Central-nucleus map to reduced label 1 Making Cortical-nucleus map to reduced label 1 Making Medial-nucleus map to reduced label 1 Making Anterior-amygdaloid-area-AAA map to reduced label 1 -------------- Making alveus map to reduced label 2 Making Hippocampal_tail map to reduced label 2 Making HATA map to reduced label 2 Making fimbria map to reduced label 2 Making parasubiculum map to reduced label 2 Making hippocampal-fissure map to reduced label 2 -------------- Making Left-Cerebral-Cortex map to reduced label 3 -------------- Making Left-Cerebral-White-Matter map to reduced label 4 -------------- Making Left-Lateral-Ventricle map to reduced label 5 -------------- Making Left-choroid-plexus map to reduced label 6 -------------- Making Unknown map to reduced label 7 -------------- Making Left-VentralDC map to reduced label 8 -------------- Making Left-Putamen map to reduced label 9 -------------- Making Left-Pallidum map to reduced label 10 -------------- Making Left-Thalamus-Proper map to reduced label 11 -------------- Making Left-Accumbens-area map to reduced label 12 -------------- Making Left-Caudate map to reduced label 13 Error using segmentSubjectT1_autoEstimateAlveusML (line 348) The vector of prior probabilities in the mesh nodes must always sum to one over all classes

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bug repport freeview crash with symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference
by Knut J Bjuland 22 Jan '19

22 Jan '19

External Email - Use Caution I have update to the latest freeview, when I start I got this error message. Copyright (C) 2018 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... Reading symbols from /usr/local/freesurfer/bin/freeview.bin...(no debugging symbols found)...done. (gdb) run Starting program: /usr/local/freesurfer/bin/freeview.bin warning: Loadable section ".note.gnu.property" outside of ELF segments /usr/local/freesurfer/bin/freeview.bin: relocation error: /usr/local/freesurfer/bin/freeview: symbol _ZN17QAbstractItemView11eventFilterEP7QObjectP6QEvent version Qt_5 not defined in file libQt5Widgets.so.5 with link time reference [Inferior 1 (process 298395) exited with code 0177] (gdb) Knut Jørgen BJuland

2 1

DKT40 classifier atlas
by Yixin Ma 22 Jan '19

22 Jan '19

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask how can I reconstruct the DKT40 classifier atlas. Is it included in recon -all? Thank you for your help. Best regards, Yixin Ma

2 1

how to register feature maps to fsaverage6?
by 310913949 22 Jan '19

22 Jan '19

External Email - Use Caution Dear freesurfer experts： I want to know how to register feature maps to an average space (fsaverage6) so that I can get an identical number of vertices(40962) for each hemisphere. Can you tell me what is the command line? I am looking forward to your reply!Thanks. ------------------ 邓刊 Kan Deng E-mail：310913949(a)qq.com TEL：13728774014

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Re: [Freesurfer] Tracula: Transform streamlines to T1 RAS coordinates
by Yendiki, Anastasia 22 Jan '19

22 Jan '19

Hi Donald - Both your input and output reference volume are in diffusion space and there is no transformation specified, so the output is also in diffusion space. These are voxel, not RAS, coordinates. Best, a.y On Jan 22, 2019 7:14 AM, "Krieger, Donald N." <kriegerd(a)upmc.edu> wrote: External Email - Use Caution I extract the streamlines for each tract from path.pd.trk to an ascii file and then wish to transform the coordinates to RAS T1 coordinates in millimeters. My results are not correct. Here is the extraction command I’m using. Is this correct? Perhaps I should be using orig.mgz as the outref volume? I do not understand –inref and --outref dmri_trk2trk –in path.pd.trk –inref path.pd.nii.gz –outref path.pd.nii.gz –outasc test.streamlines Given the above command, I am assuming that the output I’m getting is in the diffusion frame in voxel coordinates. I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 3-vector before applying them of course. Here is the most compact approach I’ve tried 1st transform: mri_info –in path.pd.nii.gz –vox2ras-tkr 2nd transform: mri_info –in orig.mgz –tkr2scanner I’ve also tried this: 1st transform: mri_info –in path.pd.nii.gz –vox2ras 2nd transform: mri_info –in path.pd.nii.gz –scanner2tkr 3rd transform: mri_inf –in orig.mgz –tkr2scanner I’ve tried some other sequence since I’m not sure what frame is the target output for the–vox2ras* transforms stored in path.pd.nii.gz . Those are the only transforms which contain the multiplication factors needed to get to millimeters from voxels. Rather than continuing to fumble around, some direction from you who know would be very much appreciated. Best - Don

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Fwd: Hippocampal subfields
by Ainara Gomez 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, We have tried running hippocampal subfields module and we get an error with one of the subjects analyzed. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c The error we get is the following (the log file has been attached): ransforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points numberOfLabels: 25 Rasterizing mesh...here: 25 Killed Started at Tue Jan 22 11:06:54 CET 2019 Ended at Tue Jan 22 11:25:14 CET 2019 #@#%# recon-all-run-time-hours 0.306 recon-all -s LR008 finished without error at Tue Jan 22 11:25:14 CET 2019 done Any help will be appreciated, Thank you very much, Leire -- -- Leire Zubiaurre-Elorza Assistant Professor Department of Methods and Experimental Psychology Faculty of Psychology and Education Tel.: +34 944 139 000-(ext.2299) Unibertsitateen Etorbidea, 24 48007 Bilbo-Bizkaia www.deusto.es -- -- Leire Zubiaurre-Elorza Assistant Professor Department of Methods and Experimental Psychology Faculty of Psychology and Education Tel.: +34 944 139 000-(ext.2299) Unibertsitateen Etorbidea, 24 48007 Bilbo-Bizkaia www.deusto.es

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Using PetSurfer to derive R1 values from early-phase dynamic PET
by Elijah Mak 22 Jan '19

22 Jan '19

External Email - Use Caution Hello Doug and PetSurfers, I would like to extract relative regional cerebral blood flow (R1) data from early time-interval of dynamic PET data (i.e. 11C-PiB) using the MRTM2 technique in PetSurfer. The time interval that I am interested in is between 0 and 6 minutes. Do you have any advice on how to go go about doing this? Thanks. Best Wishes, Elijah

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Tracula: Transform streamlines to T1 RAS coordinates
by Krieger, Donald N. 22 Jan '19

22 Jan '19

External Email - Use Caution I extract the streamlines for each tract from path.pd.trk to an ascii file and then wish to transform the coordinates to RAS T1 coordinates in millimeters. My results are not correct. Here is the extraction command I'm using. Is this correct? Perhaps I should be using orig.mgz as the outref volume? I do not understand -inref and --outref dmri_trk2trk -in path.pd.trk -inref path.pd.nii.gz -outref path.pd.nii.gz -outasc test.streamlines Given the above command, I am assuming that the output I'm getting is in the diffusion frame in voxel coordinates. I extract 4x4 transforms and apply them in sequence; I append 1.0 to each 3-vector before applying them of course. Here is the most compact approach I've tried 1st transform: mri_info -in path.pd.nii.gz -vox2ras-tkr 2nd transform: mri_info -in orig.mgz -tkr2scanner I've also tried this: 1st transform: mri_info -in path.pd.nii.gz -vox2ras 2nd transform: mri_info -in path.pd.nii.gz -scanner2tkr 3rd transform: mri_inf -in orig.mgz -tkr2scanner I've tried some other sequence since I'm not sure what frame is the target output for the-vox2ras* transforms stored in path.pd.nii.gz . Those are the only transforms which contain the multiplication factors needed to get to millimeters from voxels. Rather than continuing to fumble around, some direction from you who know would be very much appreciated. Best - Don

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Freesurfer January 2019