Freesurfer August 2024

freesurfer@nmr.mgh.harvard.edu

43 participants
58 discussions

Extracting cortical thickness from a sphere with different coordinates for different participants.
by Michel, Léa 26 Aug '24

26 Aug '24

External Email - Use Caution Hi everyone, I'm working on a dataset where T1 scans were taken before the patients went under surgery. During the procedure, a small, non-pathological brain tissue sample was resected from the temporal cortex. The sample, extracted 4cm from the anterior pole within the middle temporal gyrus (Brodmann area 21), measured 1-1.5 cm in diameter. My goal is to extract the MRI-derived cortical thickness from that tissue on the T1 scan. My first step was creating a sphere as my ROI with the coordinates that I decided by participants (through looking at fsleyes). The problem now is that I'm unsure on how to extract the cortical thickness from that ROI for each participant. Do I need to register my ROI into the inflated template? If you have any ideas or codes to solve that issue, please let me know. Here the script that I used to get the sphere: # choose radius radius=20 # in mm # replace with image of your subject subj_image='/Project_2.5/MRI/Subject_103/Scan103.nii.gz' # NB, these are not MNI coordinates, but coordinates in the so called voxel space # change to the coordinates you are interested in coordinate_x=70 coordinate_y=53 coordinate_z=32 ## do not change anything below fslmaths ${subj_image} -mul 0 -add 1 -roi ${coordinate_x} 1 ${coordinate_y} 1 ${coordinate_z} 1 0 1 _tmp_point -odt float fslmaths _tmp_point -kernel sphere ${radius} -fmean spherical_roi_r${radius} -odt float rm -f _tmp_point.nii.gz fsleyes ${subj_image} spherical_roi_r${radius}.nii.gz & Thank you for your help, Lea __________________________________________________________ Léa C. Michel PhD Student Lifespan Cognitive Dynamics Lab - www.rogierkievit.com<http://www.rogierkievit.com/> Affiliation: Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Cognitive Neuroscience Department, Nijmegen, The Netherlands Email: Lea.Michel(a)radboudumc.nl Website: https://leacmichel.github.io/ Twitter: @LeaCMichel<https://twitter.com/LeaCMichel> De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kopiëren en verspreiden van deze e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaande schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 80262783. The content of this message is intended solely for the addressee. No rights can be derived from this message or its attachments. If you are not the intended recipient, we kindly request you to delete the message and inform the sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, without a written consent from the sender. Radboud university medical center is registered with the Dutch Chamber of Commerce trade register with number 80262783.

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Freesurfer Longitudinal analysis
by De Giorgi, Sara 23 Aug '24

23 Aug '24

Hi all, Could it be a problem in FreeSurfer longitudinal analysis if I use two different sequences (T1 MP2RAGE and T1 MPRAGE) for different time points/follow-ups? Thanks for the support, Sara

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Longitudinal base processing error
by Nelson, Eric (Campus) 23 Aug '24

23 Aug '24

External Email - Use Caution Hello all, I am using the longitudinal pipeline and keep getting the following error when generating the base for one of our subjects. I have 3 timepoints I am including. I have checked the nu.mgz and orig.mgz files for both the base and each time point. Everything looks fine with the exception of the nu.mgz for timepoint 1 (which is a solid white and looks like a mask). Could this be the problem? I have re-run recon-all for that cross sectional subject, but the image remains the same. Attached the full recon-all.log from the base output. 3d normalization pass 1 of 2 error: MRInormFindControlPoints: could not find enough control points error: MRInormFindControlPoints failed @#@FSTIME 2024:08:16:18:05:30 mri_normalize N 10 e 10.45 S 0.04 U 10.40 P 99% M 434992 F 0 R 10859 W 0 c 4 w 11 I 0 O 0 L 1.14 0.90 0.57 @#@FSLOADPOST 2024:08:16:18:05:40 mri_normalize N 10 1.19 0.92 0.58 Linux c0235 3.10.0-1160.24.1.el7.x86_64 #1 SMP Thu Mar 25 21:21:56 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Best, Eric Nelson, Ph.D. | Postdoctoral Fellow Department of Psychiatry and Behavioral Neurobiology School of Medicine UAB | The University of Alabama at Birmingham

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Recon-all -all for many MRI sequences?
by 김유진 23 Aug '24

23 Aug '24

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pial surface correction doesn't work
by Atena Akbari 22 Aug '24

22 Aug '24

External Email - Use Caution Dear Freesurfer team, I edited my "brainmask.mgz" file to remove some voxels related to non-brain areas and then re-ran the recon-all with this command: Recon-all -s subjid -autorecon-pial -hires However, when I checked my pial surface it seems like it hasn't been corrected for (please see the attached photo with blue arrows). I greatly appreciate your help on this matter. Thank you very much. Atena

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TRACULA with multi-shell DWI
by Fromm, Anna 22 Aug '24

22 Aug '24

External Email - Use Caution Hey, I am currently analyzing HARDI DWI data, with the following bvals: 0 2500 2500 1000 1800 1800 2500 1800 1800 1000 2500 1000 1000 2500 2500 1000 1000 0 1800 2500 2500 2500 1800 2500 2500 2500 1000 1800 1800 2500 1000 1800 1000 2500 0 2500 2500 1000 1800 2500 2500 2500 1800 2500 1800 1000 1800 2500 1000 1000 1800 0 2500 2500 2500 2500 1800 1800 2500 1800 2500 1800 1800 1800 2500 1800 2500 1000 0 1800 2500 2500 1800 2500 2500 1800 2500 1000 1000 1800 2500 2500 1800 2500 2500 0 1800 2500 2500 2500 2500 1000 1800 2500 2500 2500 2500 2500 1800 1800 1800 1800 0 2500 1800 2500 1800 1800 2500 1800 2500 2500 2500 2500 1000 2500 2500 1800 1000 0 1000 2500 2500 2500 1800 2500 1800 1800 I wanted to know whether it is possible/ or whether it makes sense to run the TRACULA pipeline on multi-shell DWI data. I got some results, but I don't know whether they are really valid because TRACULA is supposed to work with single-shell data, correct? Thank you in advance! Best Anna

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PetSurfer: PET SUVR analysis
by WONG Wan Wa 21 Aug '24

21 Aug '24

External Email - Use Caution Hi FS experts, I want to do PET SUVR analysis using PetSurfer. When determining the FWHM of the PSF of the scanner, is it the same value for Siemens (Biograph40_mCT vs. Biograph128_mCT) or (Biograph64_Vision 600 vs. Biograph128_Vision 600 Edge)? We also have data collected with GE scanner. Are we able to use the ComBat to do harmonization for all calculated SUVR values across different sites/scanners with the use of same tracer (e.g. PiB)? Thanks, Angel

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How to change mri_convert --conform to use another flag while running recon-all
by Jeiran Choupan 21 Aug '24

21 Aug '24

External Email - Use Caution Dear Freesurfer support team, I noticed that the interpolation setting used within the first few steps of recon-all within the “mri_convert INPUT OUTPUT —conform” is reducing the data quality for data that has a rectangular field of view. I need to use the `mri_convert` with another flag setting, and I was wondering if there’s a way to smoothly do this. This command is used twice within the recon-all. And I only need to change the second time it is used. The first time is to rename/convert the original file to “mri/orig/001.mgz”, and the second time, is when "/mri/rawavg.mgz “ will be converted to “mri/orig.mgz” using “—conform”. I only need to change the second time it is used, and I need to use the flag “--resample_type cubic “. Any help is much appreciated Kind regards, Jeiran Jeiran Choupan, PhD, MSCS Assistant Professor of Research Neurology Laboratory of Neuro Imaging USC Stevens Neuroimaging and Informatics Institute Keck School of Medicine University of Southern California 2025 Zonal Ave, Los Angeles, CA 90033, USA (323) 44-BRAIN [image001.png] [image002.png]

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PetSurfer: how to convert nopvc.nii.gz to a format like gtm.stats.dat?
by WONG Wan Wa 21 Aug '24

21 Aug '24

External Email - Use Caution Hi experts, As stated in the subject, how to convert "nopvc.nii.gz" generated by "mri_gtmpvc" to a format like "gtm.stats.dat"? Moreover, how to consolidate all "gtm.stats.dat"'s PVC uptake values of ROIs from different subjects in one spreadsheet? Is there any existing command to do that? Thanks, Angel

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Re: [Freesurfer] Ubuntu 24.04 compatibility? (libc6 < 2.36, libncurses5)
by fsbuild 16 Aug '24

16 Aug '24

External Email - Use Caution  We are aware that changes to the system libraries in Ubuntu 24 prevent installing packages, e.g., freesurfer, that otherwise install in Ubuntu 22.   The plan is to start development builds of Freesurfer on Ubuntu 24 after this years point release of Freesurfer.   Ubuntu 22.04 LTS was made generally available in April of 2022 with the standard 5 year support cycle from Canonical. - R. On Aug 16, 2024, at 18:36, Hunter Buchanan <hunter.buchanan(a)lscg.ucsb.edu> wrote:        External Email - Use Caution        Hi all! Do we know if a version of Freesurfer compatible with Ubuntu 24.04 is planned for the near future? Attempting to install the 22.04 .deb file on 24.04 shows that dependency libncurses5 is unavailable (manually installing a previous version may fix this) and that libc6 < 2.36 is required, though 2.39 is already installed (this is the tough one). If a 24.04 compatible release is not expected in the near future, do we know of any temporary fixes to get Freesurfer working? Or are we SOL on new servers for now? Thanks in advance!_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer August 2024