Freesurfer

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Re: [Freesurfer] fcseed-config
by shahin＠nmr.mgh.harvard.edu 31 Jul '18

31 Jul '18

Your problem solved?

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Surface editing: recon-all exited with errors
by Rockers, Elijah D. 31 Jul '18

31 Jul '18

External Email - Use Caution Hello. I manually edited the brainmask.mgz file for three subjects. This was done to prevent the pial surface from extending into non-cortical areas, in particular the soft-tissue near the brain stem, and some cerebellar areas. Usually this type of editing (just removing voxels from brianmask.mgz) doesn't give me any trouble, and I use the command recon-all -make all -subjid <subject_id> -sd <subject_dir> to then rebuild the surfaces. However, the tail of the log shows that the pipeline exited with errors, with a few commands near the end related to curvstats and jacobian_white failing. The new surfaces seem to look fine in freeview. The edits to brainmask were registered correctly, but I'm still concerned that the errors might affect an mri_glmfit analysis. This is true for all three subjects I edited, which seems odd, and I'm not sure what would be causing this. Below is a pastebin showing the relevant errors. The rest of the pipeline seems to execute without errors. I could send entire log if necessary. <https://pastebin.com/b4JX04AT>https://pastebin.com/raw/b4JX04AT Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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A Help Request for Random Parcellation
by Maedeh Khalilian 31 Jul '18

31 Jul '18

External Email - Use Caution Dear Dr.Bruce Fischle; Thank you very much for all help you have given me so far,I would like to know if it is possible to access the algorithms(or any specific parts of them) that run FreeSurfer and I also would like to know if I can do a random parcellation by FreeSurfer. Thanks in advance. Kind regards; Maedeh;

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Mixed Block Event-related Design Optseq Question
by Yu Han 30 Jul '18

30 Jul '18

External Email - Use Caution Hello Experts, I am wondering if any of you are aware of any commands of optseq for a mixed design? We are specifically not sure how to specify block duration. It seems like optseq is designed for event related design according to the help page, but I checked some community blogs and it looks like there should be some commands for mixed block event related design. There are four blocks of 6 images each. 1) Surprise/Embarrassment faces 2) Happy/Sad faces 3) Identify gender of faces 4) Match shapes We planned to have the Match shapes blocks to interleave all other blocks. Thank you in advance! Best, Yu optseq2 --ntp 160 --tr 2 --psdwin 0 20 2 --ev disgustingPic 2 20 --ev attractivePic 2 15 --ev neutalPic 2 30 --evc 1 -1 0 --nkeep 3 --o IAPS --tnullmin 2 --tnullmax 8 --nsearch 1000

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Main surface not adjusting after voxels removed from wm.mgz and autorecon2-wm
by Matthew Peverill 30 Jul '18

30 Jul '18

External Email - Use Caution Hi all, I'm trying to get recon-all to adjust white matter boundary after making a deletion from wm.mgz. What I'm finding is that, apparently in only some of my brains, the surface doesn't seem to get adjusted. Here is T1.mgz with the edit overlay to show where I have made a deletion (in this case, because there is a hyper-intensity on the surface of the middle temporal gyrus which is getting read as WM): [image: image.png] and here is wm.mgz: [image: image.png] (adjacent slices have been similarly edited). I've tried a few recon-all commands, but the one I expected to work was: recon-all -s 1062_1 -autorecon2-wm -autorecon3 -gca-dir (gcadir) -gca (gca volume) -gca-skull (gca-withskull volume) -3T -mprage -nowmsa -xopts-overwrite -expert ../expert.opts (expert opts just has "mri_segment -wlo 92") recon-all outputs no errors, and both surf/lh.white and surf/rh.white show that they have been modified in the filesystem. I'm happy to attach log files if it would be helpful. Thank you, -Matt -- Matthew Peverill mrpeverill(a)gmail.com

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Atlases in FreeSurfer
by Yaakub, Siti Nurbaya 30 Jul '18

30 Jul '18

External Email - Use Caution Hello, I’m working on a comparison of atlas and segmentation methods. One of the atlas sets I’m using is the subset of Neuromorphometrics data from the MICCAI 2012 Grand Challenge and Workshop on Multi-Atlas Labeling. From what I understand, the “general segmentation” of the brains for this atlas was defined by the MGH Center for Morphometric Analysis, while the cortical segmentation is similar to the DKT atlas available in FreeSurfer. I have 2 questions about the atlases used in FreeSurfer: 1. Is this MGH sub-cortical segmentation protocol similar to that used in the default FreeSurfer sub-cortical segmentation? 2. Would it be possible to have more information about the atlas subjects used in both the FreeSurfer cortical (DK & DKT atlases) and sub-cortical segmentation and are these manual labels available for download? The only description I could find on the sub-cortical atlas was from Fischl et al. 2002, but I don’t think this is the atlas set used in the most current FreeSurfer version. Thank you and best wishes, Siti -- Siti Nurbaya Yaakub, Ph.D. Research Associate School of Biomedical Engineering and Imaging Sciences King’s College London St. Thomas’ Hospital London SE1 7EH

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hippocampal subfields segmentation error
by 오진영 30 Jul '18

30 Jul '18

External Email - Use Caution Hello, freesurfer experts I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala by using "segmentSF_T1.sh" command. I have downloaded the newest development version(freesurfer v.6.0) and license, as well as the required matlab runtime. However, I am getting the following error: mv: rename volumesAmygdala.txt to /Users/mnd_mac/Desktop/JY_surf er/T1_data/Jinyoung_T1/Jinyoung_test/mri/lh.hippoSfVolumes-T1.amygdala.v10.txt: No such file or directory and I have no idea how to find the text file and solve this problem out. If you have any idea or recommends, please send me the e-mail back. Thanks! Jinyoung

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"A question about mris_divide_parcellation"
by Maedeh Khalilian 29 Jul '18

29 Jul '18

External Email - Use Caution Dear Dr.Bruce Fischl Thx for replying. You told me that inequality of the subregions depends on the code I ran. First off I ran the command: recon-all -subject test -i data_00.nii -all "data_00.nii" is a raw MR image. Then, I ran this command: mris_divide_parcellation test lh aparc.annot splitfile.txt lh.aparc.split And splitfile is a 2-column file I myself made based on the FreeSurFerColorLUT.txt's content according to the description in "mris_divide_parcellation --help". And that's it I would be grateful if you could help me. Kind regards;

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A Question about mris_divide_parcellation
by Maedeh Khalilian 28 Jul '18

28 Jul '18

External Email - Use Caution Dear experts; By using "recon-all", I have parcellated an MR image and by using "mris_divide_parcellation" i have subdivided the result into specific regions,(each region has been divided into 10 subregions), the question I have is that are these subregions equal sized? Are they equal sized within the whole cortex or within each region? In other words,if i have 340 regions par hemisphere,are they all equal sized or not? How can check and get it?

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Re: [Freesurfer] no register.dat file for mri_label2vol
by Ayzenberg, Vladislav 27 Jul '18

27 Jul '18

External Email - Use Caution Greetings, I am trying to convert a surface label (e.g., lh.V1_exvivo.thresh.label) into a volume to use as an ROI mask. I have played around with the mri_label2vol command, but I can't seem to get it to work. Here is the command I am using: mri_label2vol --label lh.V1_exvivo.thresh.label --temp T1.mgz --reg register.dat --fillthresh .3 --proj frac 0 1 .1 --subject sub1 --hemi lh --o V1Test.nii.gz The issue I believe is that I don't have seem to have a register.dat file. However, I'm not sure how to generate the relevant registration file since the surface label I'm using is already in subject space. The label that I need was created when I used recon-all to generate surfaces from my anatomical image. If it is relevant, my original anatomical image is a skull stripped T1 generated using FSL which I then converted to .mgz. Does anyone have any insight? Thank you! Vlad ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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