Freesurfer

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30132 discussions

fsaverage, brainstem and cerebellum
by john Anderson 22 Jan '19

22 Jan '19

External Email - Use Caution Dear FS experts, For visualization purposes, is there any way to show the cerebellum and brain stem regions (similar to the attached figure), this figure was published used CONN toolbox but I am not sure how they were able to map functional data in brain surface and show the cerebellum and brain stem with fsaverage. I appreciate any suggestion Jon

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Problems with GM segmentation
by Rosalia Dacosta Aguayo 22 Jan '19

22 Jan '19

External Email - Use Caution Dear Free Surfer team, I few days ago I sent you personally the dicom files as well as the mask of the lesion you asked me for as I am having problems with GM segmentation. I would greatly appreciate if you could help me with this issue and tell me how I could manage the problem so I can solve it as I have many participants with the same issue. Yours sincerely, Rosalia

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problems with bbregister's output image
by Sam W. 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, I have registered example_func.nii.gz to the anatomical image using bbregister and then I looked at the registered file with tkregister2. $ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o f-in-anat.nii.gz $ tkregister2 --s sub001 --mov f-in-anat.nii.gz --reg reg.lta --surf However if I click "coronal" tkregister2 shows the coronal surface as expected, whereas it shows the horizontal volume. If I click "horizontal" it shows the horizontal surface, whereas it shows the coronal volume. When I click "sagittal" the sagittal surface and volume are loaded, but the orientations are different. When I use the example_func as the mov image in tkregister2 I don't get this issue. I don't understand why the registered image "f-in-anat.nii.gz" is not aligned with the anatomical image with the tkregister2 command, because "f-in-anat.nii.gz" is exactly the output image of the bbregister transformation from functional to anatomical space, isn't it? Could someone please help me understand this? Thanks Sam

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Error using mri_convert and recon-all
by Isil Bilgin 22 Jan '19

22 Jan '19

External Email - Use Caution Dear All, I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I guess I will have to wait for IT to help me soon. Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause for that, though. So I might really appreciate your helps please. I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash. I found a similar discussion from the archive ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/02569…) but there was no agreed solution I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems are solved? Thank you very much for the help in advance Kind regards Isil

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Clinical Scan Thickness
by Sahnoune,Iman 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, I’m writing to ask whether clinical scans with thickness of 5mm are currently able to be analyzed using Freesurfer? This question has been asked in the archives, but it has been about 5 years so just writing to see whether that has changed or if a work around has been developed. Alternatively, the option exists to computationally make the slices thinner. Would running the software either as 5mm or thinner slices yield accurate and useful information cortically and subcortically? Thank you in advance for your help. The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Calculating global thickness
by Arsenije Subotic 22 Jan '19

22 Jan '19

External Email - Use Caution Dear experts, When calculating global thickness, is it fine to simply use an average of lh.thickness and rh.thickness, or is it necessary to weight it according to the area of each hemisphere, so that the calculation is (lh.thickness x lh.area + rh.thickness x rh.area)/(lh.area +rh.area)? Thanks! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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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

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