Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

How to extract hippocampus from nu.mgz using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
by Hoang Gia Minh 29 Mar '23

29 Mar '23

External Email - Use Caution Dear experts, I am doing a Hippocampus segmentation task using Freesurfer. After I run the command: recon-all -i sub-ADNI002S0295_ses-M00_T1w.nii.gz -s S1 -hippocampal-subfields-T1 -all -openmp 80 in which sub-ADNI002S0295_ses-M00_T1w.nii.gz is my input MRI scan I received an MRI folder that included "nu.mgz, aseg.mgz, etc." However, file "lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz" is just a mask or label file of the hippocampus. I want to extract the hippocampus from the original scan (nu.mgz or orig.mgz) using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz. Is there any command or step that I can do? Thank you so much Best regards Minh -- *Hoang Gia Minh, MSc* *Research Assistant* Department of Biomedical Science and Engineering Gwangju Institute of Science and Technology (GIST) TEL: (+84)-38-521-3040 EMAIL: hoanggiaminh1996(a)gmail.com

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HPC Usage - Moving On from CentOS7
by Horn, Mitchell Jacob 29 Mar '23

29 Mar '23

Hi Dev team, I just wanted to let the community know that as many HPC systems are moving on from CentOS7, to be very cognizant of the potential need to reprocess their dataset. My institution is moving to Alma and there was in fact a difference (attaching table). All recons were done with subject bert, all with 7.2.0, no flags. [cid:image001.png@01D960C3.8FAB7CD0] Best, Mitch

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T2 Flair for GM/WM differentiation
by Michael Mc Laughlin 29 Mar '23

29 Mar '23

External Email - Use Caution Would it not be better if Freesurfer used T2 Flair MRI images for differentiation between grey matter and white matter than using T1, or at least using these as extra information. You can clearly see in these attached (inline) images that the contrast between GM and WM is better in the T2 image than the T1 [image: T2Flair.jpg] [image: T1SE.jpg] Michael McLaughlin, Dublin 18 Ireland

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Manual of Freesurfer to Learn the Software from Zero to advanced Level
by Ahsan Ali 29 Mar '23

29 Mar '23

External Email - Use Caution Dear Sir, I've been learning Freesurfer software for a long time but still, I couldn't understand its basics and how a freesurfer actually works. I am always searching all the terms from the freesurfer web page but not getting exactly how it works. It will be a great help from your side for me if you can provide me the manual of freesurfer. Such as how the folders are generated and in each folder (ex. MRI folder-auto.mgz, aparc+aseg.mgz files) file is getting generated. Thank You. Regards, Ahsan

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errors with running recon-all -autorecon1
by 张思敏 28 Mar '23

28 Mar '23

External Email - Use Caution TO: freesurfer(a)nmr.mgh.harvard.edu FROM: 1913191(a)mail.nankai.edu.cn SUBJECT: recon-all -autorecon1 error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Hello FreeSurfer Developers, I'm trying to run the command: recon-all -subjid <subname> -autorecon1. I'm getting the an error message and the error log reads as follows: error: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Then I run the command: recon-all -subjid <subname> -autorecon1. I get the same error as before. Finally, I run the command: tkregister2 --s subjid --fstal. But I am new to Freesurfer so I can't get the meaning of the output after running that command. How do I know if this is true？I‘ve attached the tkregister2.png and the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: MacOS release 10.15.7 (Catalina) 3) uname -a: Darwin zsilencedeMacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_644) recon-all.log: see attached 5) tkregister2.png: see attached

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Samseg lesion mask holes
by Evie Neylon 28 Mar '23

28 Mar '23

External Email - Use Caution Dear experts, I am running SAMSEG to segment MS lesions from T2 FLAIR scans. I wanted to create a lesion mask in order to obtain lesion volumes and lesion counts, so I used mri_binarize on seg.mgz to obtain all voxels with the value 99. However, upon visualising this mask I see that there are holes in the mask in regions that are quite clearly lesions based on the FLAIR image. I see in seg.mgz that these voxels are instead assigned incorrectly to a different tissue, as the lateral ventricle, for example. I wondered if this misassignation of tissue was due to the chosen threshold (0.3) so I added the --save-probabilties flag to look at the probability maps too, and I see that actually the probability map thresholded at 0.3 does not contain holes. The probability map actually seems more accurate in general and picks up on more of the hyperintensities. This is important for my desired outputs (i.e. accurate lesion counts/volumes). So I wondered if it was possible to explain a little why these holes might be occurring in the final segmentation but not the probability map? Would it be incorrect to derive the lesion mask from the probability map instead? Apologies I cannot attach the images of the data. TIA, Evie

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Re: [Freesurfer] UnicodeEncodeError while running the recon-all
by fsbuild 27 Mar '23

27 Mar '23

External Email - Use Caution Looks like python3 tries to write/process a string into a file when running the res-config script and fails to translate something to a utf-8 character. If your locale says you are using UTF-8, e.g., $ locale LANG="en_US.UTF-8" LC_COLLATE="en_US.UTF-8" LC_CTYPE="en_US.UTF-8" LC_MESSAGES="en_US.UTF-8" LC_MONETARY="en_US.UTF-8" LC_NUMERIC="en_US.UTF-8" LC_TIME="en_US.UTF-8" LC_ALL= - then it should work to use this grep command to find files with non-UTF8 characters in them, e.g. $ grep -axvq '.*’ file.txt The -q will prevent displaying the non-utf8 characters which might screw up your terminal session. This thread gives some examples of when that error occurs and how to unmangle the string,https://secure-web.cisco.com/1K3cgYD2bSzKyvPVJ_FeWPCrJhQSWfAKprwIwga… - R. On Mar 27, 2023, at 22:14, David Lau <drlauci(a)gmail.com> wrote:        External Email - Use Caution        Hi,I tried to run Freesurfer (macOS-7.1.1) to the command line and the terminal replied, "DavidLaus-MacBook-Air:local davidlau$ recon-all -i /Users/davidlau/Desktop/testing/1RAS.nii -subject /Users/davidlau/Desktop/testing/$d doneTraceback (most recent call last):  File "/Users/davidlau/Documents/freesurfer/python/scripts/rca-config", line 143, in <module>    file.write(arg + '\n')UnicodeEncodeError: 'utf-8' codec can't encode character '\udcc3' in position 0: surrogates not allowedERROR: could not configure recon-all parameters"A similar question has been retrieved from the mail list (20 Jul 2020) by Molly and Andrew replied that there might be a non-unicode character accidentlly passed to the command line and recommended manually typing out the recon-all command. I've tried this several times but the same error message popped out. Any suggestions would be much appreciated.David_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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UnicodeEncodeError while running the recon-all
by David Lau 27 Mar '23

27 Mar '23

External Email - Use Caution Hi, I tried to run Freesurfer (macOS-7.1.1) to the command line and the terminal replied, "DavidLaus-MacBook-Air:local davidlau$ recon-all -i /Users/davidlau/Desktop/testing/1RAS.nii -subject /Users/davidlau/Desktop/testing/$d done Traceback (most recent call last): File "/Users/davidlau/Documents/freesurfer/python/scripts/rca-config", line 143, in <module> file.write(arg + '\n') UnicodeEncodeError: 'utf-8' codec can't encode character '\udcc3' in position 0: surrogates not allowed ERROR: could not configure recon-all parameters" A similar question has been retrieved from the mail list (20 Jul 2020) by Molly and Andrew replied that there might be a non-unicode character accidentlly passed to the command line and recommended manually typing out the recon-all command. I've tried this several times but the same error message popped out. Any suggestions would be much appreciated. David

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mri_convert mosaic dicoms
by John Anderson 27 Mar '23

27 Mar '23

External Email - Use Caution Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails even when using this latest dev version. To resolve this issue, I attempted to use the --nslices-override option. It seems working, however, I am unsure if I used it correctly, and I was not able to find any relevant examples or guidance on how to use this option in the FreeSurfer documentation or other websites. n=({-1..7}) unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log for i in $(cat dicomdir.sumfile | awk '{print $2}'); do n=$(($n + 1)) mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n done Thanks for guidance, John

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Using the Desterieux Cortical Atlas to Extract PET SUVs
by Bues, Hannah Francesca 27 Mar '23

27 Mar '23

Good afternoon all, I was hoping to get some advice on how to approach this. Any and all feedback is much appreciated. My group has been using FSL’s Feat to run analyses for our PET-MR project. Part of what we need to do next is create masks using fslmaths that overlay the significant clusters in the zstat images with different brain regions. We then extract standard uptake values (SUVs) from the clusters in each region for each subject so that we can graph them. The issue is that the Atlas in FSL is the Harvard-Oxford Cortical Structural Atlas, which has a broader parcellation of the cingulate cortex then we would like to use (just anterior/posterior). Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer? I would really appreciate the help. Best, Hannah -- Hannah Bues (she/her) Clinical Research Coordinator - VanElzakker Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School 149 13th Street, Charlestown, MA 02129 Office: (617) 726-8120

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Freesurfer March 2023