Freesurfer February 2023

freesurfer@nmr.mgh.harvard.edu

85 participants
122 discussions

mri_robust_register --minsize
by Proulx, Jean Sebastien 06 Mar '23

06 Mar '23

Hello, I am trying to register a full volume to a single slice, and I follow example 3 of mri_robust_register's help. I get the following error: Input image is smaller than min dimension: 1 < 16 Input dimensions (after conformalizing) MOV: 64 64 64 Input dimensions (after conformalizing) DST: 64 64 1 Specify larger minimum ... This error stays after adding --minsize 1 or --minsize, despite mri_robust_register recognizing the flag, as suggested by this terminal output: --minsize: Smallest dimension > 0 . Registration ran ok when replacing the single-slice with a 40-slice volume. Any idea on what is going on here? Thanks a lot for the good work and Have a good day! Sebastien

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Visualizing transparent surface with non transparent annotations
by Leonardo Tozzi 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Experts, I would like to use Freeview to achieve the following. I would like to visualize a transparent brain surface, with only some annotations visible. In other words, I would like the surface to be transparent, but the annotations I choose to visualize to not be transparent. Is there a way to achieve this? Thank you, Leonardo Tozzi, MD, PhD Director of Computational Neuroscience & Neuroimaging Program Stanford Center for Precision Mental Health and Wellness Stanford University ltozzi(a)stanford.edu<mailto:ltozzi@stanford.edu> | (650) 5615738 Connect with us! [signature_1075933358]<https://secure-web.cisco.com/10OmKEEhtSQzpfvnfJVDeLBEHHi9OqaBVJ9LAvZsQvsNWt…> [signature_1282923475] <http://secure-web.cisco.com/1I3hXNj6irLn6oQYZFgxz73In-4_EGzX-NMOPCnUJP3yv02…> [signature_911042299] <https://secure-web.cisco.com/10-8-bEWGWgfQnDhesaI2ZU2QywWqHHyTXTPc8TI7RfrgI…>

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infant freesurfer - input and output questions
by Inga Harting 06 Mar '23

06 Mar '23

External Email - Use Caution Hello, I'm new to infant freesurfer. I was initially relieved when a first run of a test patient went through after I created mprage.nii.gz using mri_convert. 1. Today I wanted to rerun it, but it gives me an error message although the "original" file mprage.nii.gz is sitting unchanged right there in the directory (ERROR: must have the input file in home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz!). Could you help me find my error? I've copied the output on my screen below. 2. I wanted to look at the results using freeview and following along the lines of FS tutorial on FS output. However there is no T1.mgz in /mri and brainmask.mgz is referred to norm.mgz which is empty. Does this indicate the analysis went through but didn't work? 3. Is there a tutorial for infant freesurfer which I've missed and which might answer (some of) my questions? Best, Inga. -- Inga Harting private email: inga.harting(a)gmx.de Dpt. Neuroradiology Heidelberg University Medical Center INF400, 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de -- error for infant_revon_all-- inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ pwd /home/inga/Inga/Daten/test/pmd2-0 inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ ls -la insgesamt 33808 drwxrwxrwx 11 inga inga 4096 Oct 19 12:10 . drwxrwxr-x 10 inga inga 4096 Oct 19 12:10 .. drwxrwxrwx 2 inga inga 4096 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.218 drwxrwxrwx 2 inga inga 36864 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.219 drwxrwxrwx 2 inga inga 12288 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.223 drwxrwxrwx 2 inga inga 16384 Apr 6 2019 1.2.840.113619.2.322.2807.4236267.23758.1434086473.224 drwxrwxrwx 2 inga inga 12288 Apr 6 2019 1.2.840.113619.2.5.181722182500.1102.1434102017.91 drwxrwxrwx 2 inga inga 32768 Apr 6 2019 1.2.840.113619.2.80.4248871915.7044.1434101403.1.4.2 drwxrwxrwx 2 inga inga 40960 Apr 6 2019 1.2.840.113619.2.80.4248871915.7044.1434101419.123.4.2 drwxrwxrwx 2 inga inga 36864 Apr 6 2019 1.2.840.113619.2.80.4248871915.8240.1434101490.1.4.2 drwxrwxr-x 7 inga inga 4096 Oct 19 11:44 iFS_output_2022-10-05 -rw-rw-r-- 1 inga inga 34372241 Oct 5 14:36 mprage.nii.gz -rw-rw-r-- 1 inga inga 1350 Oct 5 10:39 scan.log inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ infant_recon_all --s pmd2-0 --age 4 InfantReconAll scripts DIR /usr/local/freesurfer/bin PWD /home/inga/Inga/Daten/test/pmd2-0 ERROR: must have the input file in home/inga/Inga/Daten/test/pmd2-0/mprage.nii.gz! inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0$ -- output from infant freesurfer /mri (result of first run) -- inga@XPS-15-9510:~/Inga/Daten/test/pmd2-0/iFS_output_2022-10-05/mri$ ls -la insgesamt 4824 drwxrwxr-x 3 inga inga 4096 Oct 5 15:44 . drwxrwxr-x 7 inga inga 4096 Oct 19 11:44 .. -rw-rw-r-- 1 inga inga 232837 Oct 5 15:44 aparc+aseg.mgz -rw-rw-r-- 1 inga inga 39 Oct 5 15:44 aseg.count.txt -rw-rw-r-- 1 inga inga 186355 Oct 5 15:44 aseg.mgz -rw-rw-r-- 1 inga inga 186080 Oct 5 15:44 aseg.nii.gz -rw-rw-r-- 1 inga inga 186355 Oct 5 15:44 aseg.presurf.mgz -rw-rw-r-- 1 inga inga 606165 Oct 5 15:44 brain.finalsurfs.mgz lrwxrwxrwx 1 inga inga 8 Oct 5 15:44 brainmask.mgz -> norm.mgz lrwxrwxrwx 1 inga inga 11 Oct 5 15:44 brainmask.nii.gz -> norm.nii.gz lrwxrwxrwx 1 inga inga 8 Oct 5 15:44 brain.mgz -> norm.mgz lrwxrwxrwx 1 inga inga 11 Oct 5 15:44 brain.nii.gz -> norm.nii.gz -rw-rw-r-- 1 inga inga 102107 Oct 5 15:44 filled.mgz -rw-rw-r-- 1 inga inga 1000069 Oct 5 15:44 lh.dpial.ribbon.mgz -rw-rw-r-- 1 inga inga 598075 Oct 5 15:44 lh.dwhite.ribbon.mgz -rw-rw-r-- 1 inga inga 53037 Oct 5 15:44 lh.ribbon.mgz -rw-rw-r-- 1 inga inga 0 Oct 18 19:08 norm.mgz -rw-rw-r-- 1 inga inga 0 Oct 18 19:08 norm.nii.gz -rw-rw-r-- 1 inga inga 1011650 Oct 5 15:44 rh.dpial.ribbon.mgz -rw-rw-r-- 1 inga inga 372114 Oct 5 15:44 rh.dwhite.ribbon.mgz -rw-rw-r-- 1 inga inga 54091 Oct 5 15:44 rh.ribbon.mgz -rw-rw-r-- 1 inga inga 93026 Oct 5 15:44 ribbon.mgz drwxrwxr-x 2 inga inga 4096 Oct 5 15:44 transforms -rw-rw-r-- 1 inga inga 62243 Oct 5 15:44 wm.mgz --

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infant Freesurfer - subcortical/white matter segmentation
by Inga Harting 06 Mar '23

06 Mar '23

External Email - Use Caution Hello experts, I've begun using infantFS for neonates and I'am interested in the subcortical segmentation. I noticed that the internal capsule is delineated in the manseg-tsubj2subj.NIFTYREG volumes (irrespective of the template's having gmwm or not), but that ist lost after mri_label_fusion when the thalamus has suddenly increased, swallowing PLIC and corona radiata, the basal ganglia have also expanded and the corpus of the caudate nucleus is large and pushed upwards. Is there a way to preserve the subcortical anatomy? Would labelling e.g. capsula interna help? Is there a way to include 2D T2axial to help with gmwm contrast? Best regards, Inga. -- Dr.med. Inga Harting Dpt. Neuroradiology Heidelberg University Medical Center INF 400 69120 Heidelberg inga.harting(a)med.uni-heidelberg.de Mühltalstr. 124b 69121 Heidelberg inga.harting(a)gmx.de

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Infant freesurfer issue
by Sayre, Christopher 06 Mar '23

06 Mar '23

External Email - Use Caution Hello all, I am having an issue when trying to run infant_recon_all. The error that I am getting is /opt/apps/software/FreeSurfer.7.2.0-centos7_x86_64/bin/atlassubjects.csh No such file or directory. I have searched through the bin folder xç xfor the atlassubjects.csh and indeed it does not exist. I have looked at the github for FreeSurfer and I was able to find the file under the infant folder. Am I missing something here or can anyone offer anything that would assist me in resolving this error? Thanks, Chris Sayre

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Re: [Freesurfer] Infant Freesurfer - manual edits
by Kang, Jee Won 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer experts, Hello, I have started experimenting with Infant Freesurfer (version 4a14499), and we have run into a problem with very poor segmentation of the thalamus in one of our subjects. Is there a way to incorporate manual edits, as in adult Freesurfer, to improve the segmentation? From this post: https://secure-web.cisco.com/1A3X8CGDC9HIB1-7GzN2d3Jhl_jxtbWw34-Ck5nrUNk5fV…, it looks like the option to make manual edits was a feature in the works, but I am not sure if that is still the case. I am guessing it would be inadvisable to re-run the infant data after making edits (to wm or aseg.presurf) in adult Freesurfer? Thank you for your advice on this! Sincerely, Jee Won

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cvs clarifications with petsurfer
by Federica Di Antonio 06 Mar '23

06 Mar '23

External Email - Use Caution Dear Freesurfer experts, I'm using PETsurfer. I've done the standard pipeline for all my subjects, using the cvs registration. I was wondering (maybe it's very stupid) when the standard pipeline "uses" the cvs resulting files (except for subcortical volume-based analysis and final resampling). Moreover, when I obtain a resampled file (like subctxgm.cvs.2mm.sm00.nii.gz ) should I process it with freesurfer? Sorry for my english, maybe what I ask is not very clear, but I hope you can help me. Thank you so much for your time and kindness! Sincerely, Federica

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Samseg cortex parcellation
by Stepanov, Valentin 06 Mar '23

06 Mar '23

External Email - Use Caution Hello, I hope this email finds you well. I am using Samseg for the MS patients' data and am very impressed with its performance in terms of lesions segmentation along with posteriors and probability maps saving. Also, compared to freesurfer, it has a remarkably better quality of cortical gray matter segmentation, particularly in subjects with juxta/intracortical lesions. However, to my knowledge, it does not allow doing a cortex parcellation. I used it with the —recon option, but in that case, the output (aparc+aseg.mgz) is identical or very close to those freesurfer provides and commonly has some segmentation errors, whereas seg.mgz saved in samseg directory demonstrates significantly better segmentation. I wonder if there is any way to run cortex parcellation using exact samseg seg.mgz output? I have attached a couple of images demonstrating the difference of segmentation output for freesurfer and samseg. Thank you, Best regards Valentin Valentin Stepanov Postdoctoral Fellow Center for Biomedical imaging Department of Radiology NYU Grossman School of Medicine 660 1st Avenue, office 212 New York, NY 10016

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Re: [Freesurfer] -pctsurfcon --fsvol default
by Antonio #30 06 Mar '23

06 Mar '23

External Email - Use Caution Hello again, I would like to ask one last thing. How can the class averages computed from csdbase.y.ocn.dat not match the gamma.mgh values in the cluster? e.g. How can gamma show +29 in a vertex that is part of the significantly positive cluster in an A-B contrast, while the average of all values taken from csdbase.y.ocn.dat referring to class A in that same cluster is lower than that of class B (average of values of input y for class A = 20.367; average for class B = 20.401)? Are the values in csdbase.y.ocn.dat not corrected by the variables chosen as covariates? Thanks again! Antonio Bonifanti Il giorno mer 15 feb 2023 alle ore 18:36 Antonio #30 < toni.bonif2511(a)gmail.com> ha scritto: > Hi, > > 1. I was wondering why the --fsvol argument in -pctsurfcon takes > rawavg.mgz by default, when most literature on grey/white contrast tends to > compute it from nu.mgz. > Is the intensity-corrected volume to be preferred in all cases or was > there a reason for choosing rawavg as a default while writing the script? > > 2. I would also like to ask whether or not you believe the values of > smoothing kernels seen in literature for grey-white contrast (which often > are over 20mm) to be adequate for such a measure. > > 3. As a final note, would you say it is appropriate, from a statistical > standpoint, to compare the results of group analyses conducted on the two > hemispheres with different covariates? (e.g. with mean left cortical > thickness and mean right cortical thickness rather than mean whole cortical > thickness) > > Thank you for your time! > > Antonio Bonifanti >

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WMH in aparc+aseg
by Alberto Del Cerro Leon 06 Mar '23

06 Mar '23

External Email - Use Caution Hello FS team! I am using the volumetric data of WMH obtained during the recon-all in the apar+aseg.mgz file. Where I could find the description of the method throught it is segmented? I find the Automated Labeling of Neuroanatomical Structures in the Human Brain but the label WMH doesn't figure on that. Thanks in advance

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Freesurfer February 2023