Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

mri_glmfit-sim cluster output issue
by jordan wagner 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, My name is Jordan and I am working on cluster correction between two groups. I ran the step before: "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh". I was able to find many significant values of p<0.05. However, when I ran the cluster correction there were no significant cluster in any of my group comparisons. I had to run mri_glmit-sim in the terminal each time for every directory because running the script that looped resulted in "cwp: command not found". I was wondering if there is something I could look for that is causing an issue or something else I can do to fix this. I wanted to reach out to make sure my results aren't completely null. Thank you, Jordan Wagner

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Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline
by fsbuild 20 Jul '23

20 Jul '23

External Email - Use Caution The  .mexa64 file is a matlab shared library and that error is from the linker saying it is not allowed to link in that library.  Note that it did not say there was a permission denied error or that the .mexa64 file could not be found.   This Mathworks posting indicates that error can happen on systems when SElinux security is enabled, https://secure-web.cisco.com/1mMj5et2sBrHqKCyLNcFSpIV6dYytw3Jjg5sIR39GiUNHH… This part of LD_LIBRARY_PATH looks like the standard setting after running fs_install_mcr script with the Matlab runtime environment installed in the freesurfer distribution.  I'm assuming accessing MALAB runtime environment this way is already known to work on your cluster and does not generate any run time linker errors. LD_LIBRARY_PATH is .:/usr/local/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//bin/glnxa64:/usr/local/freesurfer/7.1..1//MCRv84//sys/os/glnxa64:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/freesurfer/7.1.1//lib/vtk/lib - but the path to that .mexa64 file is not part of the standard LD_LIBRARY_PATH settings and looks like it is on some temporary mount point, /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64': /tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64 - so I'm guessing there is some system and/or security setting that does not allow loading 3rd party libraries from paths like that.   I would ask your IT folks about it.  I could be wrong, but if kvlGEMSMatlab.mexa64 needed to be re-compiled to run on your system, then I would expect to see a different error. -R. On 6/27/23 22:08, Mengjie Huang (mhua0773(a)uni.sydney.edu.au) wrote: Invalid MEX-file '/tmp/MCR_65032579/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64' : failed to map segment from shared object: Operation not permitted

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F.mgh file
by Lyna Mariam El Haffaf 20 Jul '23

20 Jul '23

External Email - Use Caution Dear FreeSurfer team, We are conducting a study with the ADNI database using FreeSurfer g3v1. I was wondering if the mri-segstats can be used to extract statistics from F.mgh file? Also, can the F-value be obtained via this F.mgh file? Thank you in advance! Lyna Mariam El Haffaf Ph.D. student in clinical neuropsychology University of Montreal

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Use synthetic in recon-all pipeline
by Ruifeng Dong 20 Jul '23

20 Jul '23

External Email - Use Caution Hi all, I am running freesurfer 7.3.2 for segmentation of T1 data. It seems like still using the old skull stripping tools by default. How should we change it to using synthstrip? (Question 1) Also, is it a good idea to also turn on the --no-csf flag for cortex and subcortical segmentation? (Question 2) If using synthstrip, do we still need the -T2 option for better treatment of dura regions? (Question 3) Thank you. Best, Ruifeng

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Obliqueness in the input images for recon-all
by Ruifeng Dong 20 Jul '23

20 Jul '23

External Email - Use Caution Dear all, We acquired the images (sagittal, 176*256*256) with obliqueness, because we tried to match the prescription with the subject's head positioning. Then, the obliqueness is shown in the header of the image. We used this image in recon-all. After mri_convert --conform, Freesurfer reoriented the image to RSP and then changed to 256*256*256 FOV. As a result, in orig.mgz, the image is tilted. Wouldn't this make it harder for Freesurfer to register with the template? Why does Freesurfer do this? Does it only expect input images with no obliqueness, i.e. anatomical coordinates and physical coordinates are always aligned? Thank you! Best, Ruifeng

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Generate Stats File for fornix.mgz in T1 weighted MRI ?
by Ahsan Ali 20 Jul '23

20 Jul '23

External Email - Use Caution Dear Sir/Madam, I hope you are doing well. I'm having a ADNI T1 weighted MRI database. I have run the recon-all command successfully and got a couple of default stats files in the stats folder. Then fornix.mgz is estimated using command "mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto_CCseg.mgz -f folder_name" successfully. Now what can be done to generate the stats for only fornix.mgz? I've been struggling with this for a long time, please help me with this. I'm using linux-ubuntu. [image: IMG-20230526-WA0000.jpg] With Regards Ahsan --------------------------------------------- Ahsan Ali Ph.D Scholar Department of Applied Mechanics and Biomedical Engineering (AMBE) Indian Institute of Technology Madras Chennai-600036, Tamil Nadu, INDIA Mob.:- +91-8899605552

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Pial and White surface maps are not found
by Varun Chandran 20 Jul '23

20 Jul '23

External Email - Use Caution Hi FS experts, It's been a few years, I used FS tools for cortical surface reconstruction. Now, when I used the freesurfer 7.2 version to perform cortical surface reconstruction on the T1-weighted structural MRI data, I was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light on this issue? command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache thanks, best, Varun -- Varun Arunachalam Chandran, PhD Postdoctoral Research Associate, Faculty of biology, medicine and health, School of health sciences, University of Manchester, United Kingdom. https://secure-web.cisco.com/1cnuenNM09eOjp8mrBzh-QGzKlgQQ0c8Rw7bNumyV-qFdk…

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Specifying certain surface regions for viewing in Freeview via command line
by Gavette, Levi William 20 Jul '23

20 Jul '23

External Email - Use Caution Hi FreeSurfer community, I am interested in specifying a region via command line from aparc.a2009s.annot and having only it displayed on the fsaverage surface (and no others). Ideally, this would be specified in the command line for loading Freeview so that I can iterate for multiple regions and then save each in a screenshot quickly. I know that it is possible within the Freeview GUI, but I am hoping that there may be command line functionality (have not found it so far in the documentation). Please let me know if it or a similar solution exists! Thanks, Levi

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Question about mri_convert --conform
by ruifeng14＠gmail.com 20 Jul '23

20 Jul '23

External Email - Use Caution Hi all, My input 001.mgz has data type short, but converted to unsigned byte. The plot shows the intensity of thee two images. How is the data conversion done? Thanks. Best, Ruifeng

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Tracula statistics outputs for version 7.2
by King-Wai Chu 18 Jul '23

18 Jul '23

External Email - Use Caution Hi, Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt, I have 2 more questions. Since my previous 3 questions still have not been answered, I'm including them here so that they are all in one place. The 2 new questions are 4) and 5), my previous 3 questions are appended after. 4) I have noticed that the averages of AD, RD, MD and FA in pathstats.byvoxel.txt are exactly the same as the *_Avg_Center in pathstats.overall.txt. According to the tutorial, *_Avg_Center in pathstats.overall.txt is the "average over highest-probability path only" and the AD, RD, MD and FA in pathstats.byvoxel.txt is the value at the "position on the maximum a posteriori path". Does it mean that "highest-probability path only" and "position on the maximum a posteriori path" are the same or one of them should be changed to the other one? 5) Are the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg in pathstats.byvoxel.txt suppose to match *_Avg(average over the entire support of the path distribution) in pathstats.overall.txt? When I removed the duplicate points in pathstats.byvoxel.txt, the averages of AD_Avg, RD_Avg, MD_Avg and FA_Avg come very close to the value of *_Avg in pathstats.overall.txt I don't think I can calculate the averages by including the duplicate points in 4) but removing them in 5). Either including them in both or not at all. Questions from my previous email. 1) There are duplicate points in pathstats.byvoxel.txt, is it normal? I didn't try it on all 42 tractcs. For the few I've looked at, they all have duplicate points. I used the default setting in the config file to run trac-all. 2) When I do along-tract statistical analysis, sig.mgh and z.mgh are 1D files. When embed the sig.mgh and z.mgh statistical maps from the analysis into the template .trk (*.display.trk, which is 3D), it seems to me that sig.mgh and z.mgh don't have enough information to give *.display.trk the voxel values for the *.overlay.trk. There is no one-to-one voxel corresponding between sig.mgh and *.display.trk. What am I missing? Or what's the embedding process do? 3) When I convert .trk(*.overlay.trk, for example) to nii.gz or ascii using dmri_trk2trk or mri_convert the voxel values of the .trk file don't get converted into the .nii.gz or ascii file, only the x,y,z coordinates are converted. Is there a way to get the voxels values of the .trk file when converting to .nii.gz or ascii format? Thanks, King-Wai -- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468

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Freesurfer June 2023