Freesurfer January 2023

freesurfer@nmr.mgh.harvard.edu

87 participants
111 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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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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PETsurfer: PVC without psf of the scanner
by Federica Di Antonio 08 May '23

08 May '23

External Email - Use Caution Dear experts, Few weeks ago i wrote to this mailing list but I didn't receive any answer, so I'll try again: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output If I put psf to 0, there is no PVC, and the same happens if I don’t put that flag at all.t all Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user? I apologize for the repetition, Thanks for your patience, Federica

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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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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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7.3.2-patch issues - thalamic segmentation
by Katie Rose Jobson 24 Feb '23

24 Feb '23

External Email - Use Caution Hi FS experts, I am attempting to implement the patch on version 7.3.2 for issues with thalamic segmentation. I followed the instructions found here: https://secure-web.cisco.com/1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHP… and placed the scripts in their designated directories. However, I received the same error as before. The output indicates that the core.py script is located in the '$FREESURFER/python/packages/freesurfer/subregions/' directory, as opposed to the directory I was instructed to put the core.py script in ('$FREESURFER/python/packages/gems/subregions/'). Should I replace the core.py script within '$FREESURFER/python/packages/freesurfer/subregions/'? Or is there another course of action that I can do that may solve this issue? Here is the exact error, if that is at all helpful: Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' Thank you in advance for your help! Best Wishes, Katie -- Katie Jobson, M.S. | Personal Website<https://secure-web.cisco.com/1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athV…> Ph.D. Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjV…> Department of Psychology and Neuroscience | Temple University

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FS FAST
by Justin Oh 13 Feb '23

13 Feb '23

External Email - Use Caution Dear Freesurfer team, I am new to freesurfer and I'm working on learning how to pre process and analyze resting state fMRI. It's my understanding that MATLAB and FSL have to run in the background from what I took away from online tutorials. Is there a specific program within MATLAB that is necessary or will purchasing the basic student package from MATLAB be sufficient? Thank you for your time! -Justin Oh

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Freesurfer January 2023