Freesurfer

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30076 discussions

Brodmann areas annotation files
by Alon Baram 15 Nov '18

15 Nov '18

External Email - Use Caution Hi, I'm quite new to Freesurfer so sorry if this is a basic question. I'm trying to overlay my results (which are in fsaverage space) over some anatomical annotation files. To do that I loaded the ?h.PALS_B12_Brodmann.annot file from the $SuBJECTS_DIR/fsaverage/label folder . It seems to me there are many inaccuracies in this file, and I'm wondering if I'm using it wrongly. I'm attaching a screenshot to show some examples. This issue is in contrast to (for example) the ?h.PALS_B12_Brodmann.OrbitoFrontal.annot file which seems to be very accurate. Examples: - BA 22 includes both the middle and the superior temporal gyrus (instead of just the latter - the brighter, most dorsal green bit in the temoral lobe. Unless I'm mistaken, the middle temporal gyrus should by BA 21? - The angular gyrus seems to be divided between BAs 40,7 and 39 instead of just the later. [image: image.png] [image: image.png]

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myelin group difference and pvr of thickness
by Damien MARIE 15 Nov '18

15 Nov '18

External Email - Use Caution Hi, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group difference with age and left average myelin as nuisance factors. Q1/ should I use smoothed thickness maps or unsmoothed? I used the mri_glmfit command line generated during that qdec analysis and added the pvr flag but I got that error message: ERROR: dimension mismatch between X and contrast /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat X has 7 cols, C has 6 cols I understood I had to change the contrast.mat and added a 0 at the end for the pvr: +1.00000 -1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 Q2/ Can you please tell me if it is correct??? Many thanks, Damien fsgd: GroupDescriptorFile 1 Title 10nov MeasurementName R1projfrac0.5 Class group1 Class group2 Variables LH_mR1 Age Input suj1 group1 0.080687 1.644444 … glm: mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh —fsgd /home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh —label /home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat --pvr lh.thicknessall.fsaverage.mgh

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Re: [Freesurfer] Surface failure in centos7 dev freesurfer
by fsbuild 14 Nov '18

14 Nov '18

External Email - Use Caution Hello Baxter, The daily/nightly builds happen at around midnight, so any changes made today won't get built until midnight.  There should be a new build tomorrow unless something fails the build. Baxter P. Rogers November 13, 2018 at 19:42         External Email - Use Caution         Ah - looking deeper, I think not. I'm not building it locally -  I downloaded today's available compiled version (commit 8abd50c judging by the build stamp) and it looks like the relevant fix was later, in commit 2720b25. Is there a way to tell what commit is available at the dev download URL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ ? Anyway, I will try again in a day or two assuming the dev binaries update, and let you know how it goes. Thanks much, Baxter Greve, Douglas N.,Ph.D. wrote: _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Greve, Douglas N.,Ph.D. November 13, 2018 at 19:28 did it include the update to mri_tessellate? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Baxter P. Rogers November 13, 2018 at 18:33 External Email - Use Caution I am still getting the same error with today's build of freesurfer-linux-centos7_x86_64-dev.tar.gz SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c Thanks, Baxter _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Greve, Douglas N.,Ph.D. November 13, 2018 at 10:49 I just fixed it _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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What is "...S_central" in Destrieux atlas?
by Colin Birkenbihl 14 Nov '18

14 Nov '18

External Email - Use Caution Dear all, I am currently working with MRI features calculated with the Destrieux atlas. As an output I have features named like: Vol_Right_S_Central Vol_Left_G_precentral or Vol_Left_S_orbital-H_Shaped I wanted to ask you, what these features stand for and if there is some mapping of those feature names to brain region names which are clearly interpretable. If not, it would be great if you could tell me what the above mentioned features refer to. It would be great if you could help me. Best wishes, Colin

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Freeview volume measurements on newly created VOIs
by Kim, Jisoo,M.D. 14 Nov '18

14 Nov '18

Hello Freesurfer developers, I am trying to get volume measurements (mm^3) on VOIs (volume of interest) that I created on Freeview. All I can do is to export the VOI as an .mgz file. Do you know of an easy way to get the stats in .txt or any other formats? 1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) OS: MacOS Sierra Thank you very much. Best, Jisoo

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Re: [Freesurfer] freeview crash when launch in ubuntu 18.04 {Disarmed}
by fsbuild 14 Nov '18

14 Nov '18

External Email - Use Caution Hello Knut, You might be better off using the gcc 4.8 compilers on Ubuntu 18 which you can install with$ sudo apt-get install gcc-4..8 g++-4.8 gfortran-4.8 Then on your cmake command line you could set those before the actual cmake command.  I've listed some other options you could try as well after the cmake command (apart from whatever other options you may be using). $ CC=/usr/bin/gcc-4.8  CXX=/usr/bin/g++-4.8  FC=/usr/bin/gfortran-4.8  cmake  -DFS_PACKAGES_DIR=/path_to_the_3rd_packages_after downloading_them  -DCMAKE_INSTALL_PREFIX=/path_to_install_location  -DCMAKE_EXE_LINKER_FLAGS=-Wl,--disable-new-dtags -L/usr/lib/x86_64-linux-gnu -L/usr/local/lib -lz  -DGFORTRAN_LIBRARIES=/usr/lib/gcc/x86_64-linux-gnu/4..8/libgfortran.so - R.On Nov 14, 2018, at 04:08, Knut J Bjuland <knutjorgen(a)outlook.com> wrote:        External Email - Use Caution        Dear Freesurfer… source $FREESURFER_HOME/bin/tcl_setupknutjb-HP-Z640-Workstation:~/abel/data/tracula> source $FREESURFER_HOME/bin/vtk_setupknutjb-HP-Z640-Workstation:~/abel/data/tracula> #source $FREESURFER_HOME/bin/qt_setup#source: Command not found.knutjb-HP-Z640-Workstation:~/abel/mci_data/tracula> gdb freeview.binGNU gdb (Ubuntu 8.1-0ubuntu3) 8.1.0.20180409-gitCopyright (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-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 freeview.bin...(no debugging symbols found)...done.(gdb) runStarting program: /usr/local/freesurfer/bin/freeview.bin [Thread debugging using libthread_db enabled]Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".[New Thread 0x7fffe6839700 (LWP 515411)][New Thread 0x7fffdc539700 (LWP 515412)][New Thread 0x7fffdbd38700 (LWP 515413)][New Thread 0x7fffda2a1700 (LWP 515414)][New Thread 0x7fffca424700 (LWP 515418)]Thread 1 "freeview.bin" received signal SIGABRT, Aborted.__GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:5151 .../sysdeps/unix/sysv/linux/raise.c: No such file or directory._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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aparc table multiple comparisons
by Ralf Veit 14 Nov '18

14 Nov '18

External Email - Use Caution Dear list members, I run mri_glmfit using the aparc stats tables as input and I got a sig.table.dat file with -log10(p-values) for each ROI and contrast. Are the p-values already corrected for multiple comparisons? If not, what do I have to do in order to get corrected p-values (using aparc stats file as input). Best Ralf Ralf Veit PhD Institute of Medical Psychology and Behavioral Neurobiology Otfried-Müller str. 47 72076 Tübingen phone: +49-7071-2987703 fax: +49-7071-295706

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co-registration between slab of DTI image
by Yixin Ma 14 Nov '18

14 Nov '18

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about coregistration between a thin oblique coronal slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size anatomical image (volume size is 256x256x256), with additional whole brain low-resolution DTI to assist registration. The codes I use are as attached: I have few concerns: 1) the input oblique coronal slab of DWI image does not have header information, should it be better if I input the DWI slab in RAS coordinates (axial volume)? 2) Should I zero-fill the DWI slab to match the volume of T1.mgz? I already did that because it won't start to calculate the cost function between the thin DWI slab and anatomical image if I don't zero-fill. However, I feel like the cost function cannot make sense of the fact that the zeros are already outside the region of interest. 3) Should I use --init-fsl /--init-spm in this case? Neither of these two worked. Is there a better optimization function recommended? I have been using fsl flirt function 2 step registration (from DWI slab to whole brain DWI; From whole brain DWI to whole brain anatomical image) to do the registration. But I don't think it's the best way. For freesurfer bbregister, I have been trying to change things here and there, but the co-registration does not work well. Do you suggest to look at any parameter particularly based on this scenario? Thank you for your help, Yixin Note that isoDWI111_256_axial.nii is the slab of DWI image EPI_iso111_256_axial.nii is the whole brain DWI image [The freesurfer reconstruction is performed before all these] bbregister --s 30426 --mov isoDWI111_256_axial.nii --*int* EPI_iso111_256_axial.nii --init-fsl --reg xform_freesurfer.dat --dti tkregister2 --reg xform_freesurfer.dat --mov isoDWI111_axial.nii mri_vol2vol --reg xform_freesurfer.dat --mov isoDWI111_axial.nii --fstarg --o isoDWI111-*in*-anat.mgh mri_convert isoDWI111-*in*-anat.mgh isoDWI111_reg.nii

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MRISalloc
by Chris Petty 14 Nov '18

14 Nov '18

External Email - Use Caution I’ve tried processing a healthy brain through v6.0.0 and _dev versions only to get hung at this step in each of the versions. The brain looks normal. I’ve tried adjusting the skull strip and using control points in a location that the brain was not found correctly, but it always stops at this exact step. I’ve tried processing with the RAW data as well has HCP preprocessed anatomicals. Any insight into this error? Is this some sort of convoluted memory error? ERROR: MRISalloc: nfaces=-1392508735 < 0 2714 using vox2ras matrix: 2715 -1.00000 0.00000 0.00000 128.00000; 2716 0.00000 0.00000 1.00000 -128.00000; 2717 0.00000 -1.00000 0.00000 128.00000; 2718 0.00000 0.00000 0.00000 1.00000; 2719 2720 rm -f ../mri/filled-pretess255.mgz 2721 2722 2723 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 2724 2725 ERROR: MRISalloc: nfaces=-1392508735 < 0 2726 2727 Linux blade21.dhe.duke.edu<http://blade21.dhe.duke.edu/> 3.10.0-862.2.3.el7.x86_64 #1 SMP Tue May 8 14:55:36 CDT 2018 x86_64 x86_64 x86_64 GNU/Linux 2728 2729 recon-all -s sub-00001 exited with ERRORS at Tue Nov 13 14:13:07 EST 2018 2730 2731 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Questions on ApplyMorph of electrodes coordinates to a common template
by Liu, Feng 14 Nov '18

14 Nov '18

Dear freesurfer users, I have a problem regarding to how to map the electrode coordinates to a common template. After running mri_cvs_register, I got a cvs subfolder, and then I run applyMorph --template /autofs/cluster/freesurfer/centos7_x86_64/dev/subjects/cvs_avg35_inMNI152/mri/orig.mgz --transform $SUBJECTS_DIR/$subid/cvs/combined_tocvs_avg35_inMNI152_elreg_aseg.tm3d point_list $SUBJECTS_DIR/$subid/cvs/coord_xyz.txt $SUBJECTS_DIR/$subid/cvs/transformed_coord.txt linear where coord_xyz.txt contains all the original coordinates information, but after that I did a visualization using freeview, and the transformed coordinates looks outside of the brain. Anyone knows how to fix this problem? Or what is the cause of this problem. The original RAS coordinates align well for the brain of each subject. I searched a lot of email archives, but didn't find a good answer. Thanks. Best regards, Feng [cid:1b19e3e7-51a7-4abb-afdb-c81cb9adc99e]

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