Freesurfer October 2022

freesurfer@nmr.mgh.harvard.edu

89 participants
132 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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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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Fwd: mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 07 Feb '23

07 Feb '23

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Fusion of PET and T1 weighted
by Amar Shukla 12 Dec '22

12 Dec '22

External Email - Use Caution Dear Freesurfer Community. I want to do image fusion (PET+T1) = T' weighted image. Then I want to go for the feature extraction from this T1 modality which I will get from the fusion.So how i can go for this. Questions are: 1) Do I have to use PET Surfer for this? Does Pet Surfer support the fusion of the two different modality. 2) I am in the perception that I want PET+ T = T' , or does it justify the multimodality approach for the detection of disease. 3) If i extract features from the different modality and then i combine it. Can we say that this is the multimodality approach of Image Fusion. Please advise me and provide the approach or the tool which will help me for the multimodality. -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016

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A TRACULA Question
by Salar Dini, Elaheh 09 Dec '22

09 Dec '22

External Email - Use Caution Dear Anastasia, Thanks for your support in the past few months. I got an error message in -prep step: "Exception caught: itk::ExceptionObject (0x8a1e880) Location: "unknown" File: /home1/zs24/sandbox/build/ITKv5-install/include/ITK-5.0/itkSmoothingRecursiveGaussianImageFilter.hxx Line: 229 Description: itk::ERROR: SmoothingRecursiveGaussianImageFilter(0x8a1dd00): The number of pixels along dimension 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed. ConvertTransformFile 3 /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras file /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat does not exist . Linux ursapet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Oct 20 23:31:04 EDT 2022" I am attaching a log file too. Do you have a guess why this happened and how we can address it? One possibility is that we don't have all the dMRI sequence slices (like 300 out of 1600 are missing). Thanks for your time and help, Ela

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Re: [Freesurfer] Issue with rotation during longitudinal base creation
by Huang, Yujing 22 Nov '22

22 Nov '22

Hi Nathan, Can you confirm that the error was from mri_robust_template? Not sure what your command line options. I think these options ‘—inittp <>’, ‘--fixtp’, ‘—seed <>’ might help. Best, Yujing -------- Forwarded Message -------- Subject: [Freesurfer] Issue with rotation during longitudinal base creation Date: Wed, 12 Oct 2022 16:54:29 +0000 From: Nathan Kindred (PGR) <N.Kindred1(a)newcastle.ac.uk><mailto:N.Kindred1@newcastle.ac.uk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Hi, I have been processing longitudinal data using the longitudinal processing stream but for some subjects I am having getting this error when creating the base: Input rotation's max deviation from rotation is: 0.000258493 MyMatrix::RotationMean input(s) not rotation What would be the best way to fix this? Best, Nathan

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Mapping the labels onto the aparc atlas
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 17 Nov '22

17 Nov '22

External Email - Use Caution Hi Freesurfer devs, We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the corresponding voxels that the labels identify as the mpm/vpnl. Can we reliably use the mpm.vpnl+aseg.mgz, and are the stats created from that file, or from the annot file? We are asking because we are using the mpm.vpnl+aseg.mgz as a mask for blood perfusion measurements. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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Freesurfer October 2022