Freesurfer May 2020

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freesurfer 7.0.0 in a virtual machine...
by Gonzalo Rojas Costa 07 May '20

07 May '20

External Email - Use Caution Hi: How can install freesurfer 7.0.0 in a virtual machine ? Sincerely, Gonzalo Rojas Costa

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recon-all-rms error < 2.00
by jiahui 06 May '20

06 May '20

External Email - Use Caution Hello FreeSurfer Developers, I run the recon-all -all command:this true error?how to resolve this problem? ERROR: 245/300: dt: 0.9000, rms radial error=134. 782, avgs=0 250/300: dt: 0.9000, rms radial error=134. 022, avgs=0 255/300: dt: 0.9000, rms radial error=133.265, avgs=0 260/300: dt: 0.9000, rMS radial error=132.513, avgs=0 265/300: dt: 0.9000, rms radial error=131. 766, avgs=0 270/300: dt: 0.9000, rmS radial error=131. 022 , avgs=0 275/300: dt: 0.9000, rMS radial error=130 .283, avgs=o 280/300: dt: 0.9000, rMS radial error=129.548, avgs0 285/300: dt: 0.9000, rmS radial error=128.817 , avgs=0 290/300: dt: 0.9000, rms radial error=128 .090, avgs=0 295/300: dt: 0.9000, rMS radial error=127 .367 , avgs=0 300/300: dt: 0.9000, rMs radial error=126.648, avgs=0 final distance error %24.71 pass 1: epoch 1 of 3 starting distance error %19.14 pass 1: epoch 2 of 3 starting distance error %19.08 starting distance error X19.04 final distance error %19.04 pass 1: epoch 1 of 3 starting distance error %19.50 pass 1: epoch 2 of 3 starting distance error %19.45 starting distance error %19. 41 final distance error %19.43 recon-all -s 100034 finished without error at 2020# 05A 05E 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

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Hippocampus Subfields Segmentation
by Muhammad Naveed Iqbal Qureshi 06 May '20

06 May '20

External Email - Use Caution Hi FreeSurfer experts, I preprocess my data with FreeSurfer v 6. After it I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I get the following output: # Hippocampal subfield volumes as created by segmentHA_T1.sh 1 1 0 618.413010 Hippocampal_tail 2 2 0 308.580548 subiculum-body 3 3 0 112.098146 CA1-body 4 4 0 146.657166 subiculum-head 5 5 0 202.046082 hippocampal-fissure 6 6 0 144.323840 presubiculum-head 7 7 0 513.572092 CA1-head 8 8 0 207.825661 presubiculum-body 9 9 0 75.481830 parasubiculum 10 10 0 332.502880 molecular_layer_HP-head 11 11 0 230.190313 molecular_layer_HP-body 12 12 0 174.264695 GC-ML-DG-head 13 13 0 76.776264 CA3-body 14 14 0 163.024711 GC-ML-DG-body 15 15 0 150.412851 CA4-head 16 16 0 150.002992 CA4-body 17 17 0 85.262570 fimbria 18 18 0 149.769932 CA3-head 19 19 0 61.819269 HATA 20 20 0 1333.761205 Whole_hippocampal_body 21 21 0 1748.804555 Whole_hippocampal_head 22 22 0 3700.978770 Whole_hippocampus I can see in the hipposubfields.lh.T1.v21.stats and lh.hippoSfVolumes-T1.v21.txt files with separate information for the head and tail volumes of each subfield. May I know what is the file name containing the corresponding separate head and tail ROIs that were use to calculate the above mentioned volumes? I can only find full subfield in all the ROI files. Thank you. Regards, Naveed

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mean for a bash script from mris_calc.
by Knut J Bjuland 06 May '20

06 May '20

External Email - Use Caution Dear Freesurfer experts, I have tried to use mris_calc to calculate mean and std and export the variable to bash with this command, mean=$(mris_calc mghfile std), but the array is not stored in mean. Is there any other way to calculate, mean and use it in a bash script apart from using matlab? Best regards Knut Jørgen Bjuland

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stats t test
by jiahui 06 May '20

06 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume average thickness.Can I use them from stats file to compare two groups (HC and diesease) through t test?1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c figure1.png: see attached

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recon-all-rms error < 2.00
by jiahui 06 May '20

06 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume, but for some of my subjects I get the following error when I run the recon-all -all command: ERROR: inflating to sphere (rms error < 2.00) final distance error(this is true error?) 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) recon-all.log and figure1.png: see attached

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Re: [Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim
by Xiaojiang Yang 05 May '20

05 May '20

External Email - Use Caution Hi Douglas, Not only vertex 10738. For all vertexes listed in the summary file, they all have a very big Max value (absolute) that is out of the visual range. Please see the video I grabbed from my screen: https://imgur.com/a/kkSO7sT *Thank you for your time to help this.* *Xiaojiang*

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Re: [Freesurfer] samseg with subfields
by Iglesias Gonzalez, Juan E. 05 May '20

05 May '20

Dear Sneha, We use cortical and white matter parcels in the hippocampal subfields, which is more reliable than using the whole white / gray matter to compute parameters. But it could be hacked, albeit it would be a bit less reliable. I’ll add this to the wishlist / to-do list (unfortunately it isn’t likely I’ll be able to look at it any time soon…) Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Sneha Pandya <snp2003(a)med.cornell.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, May 5, 2020 at 10:46 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] samseg with subfields External Email - Use Caution Dear experts, I want to revisit if anyone has ran subfield analysis just by running samseg? If it is possible is it as reliable as from running regular routine with “-all” recon-all flag? Thank you, Sneha From: Sneha Pandya Sent: Thursday, April 30, 2020 4:15 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: samseg with subfields Dear experts, Is it possible to run subfield analysis (hippcampal subfields, amygdalar, thalamic nuclei, and brainstem structures) when we only run samseg on our dataset? Thank you, Sneha

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sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim
by Xiaojiang Yang 05 May '20

05 May '20

External Email - Use Caution Hi FS developers, I have used mri_glmfit-sim to do multiple comparison like below: mri_glmfit-sim --glmdir lh.thickness.0.glmdir --cache 3 abs --cwp 0.05 --2spaces and in the lh.thickness.0.glmdir/group.diff directory, I got some output files, some of which were: cache.th30.abs.sig.cluster.summary cache.th30.abs.sig.cluster.mgh When I open the file cache.th30.abs.sig.cluster.summary, I see its content like below: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -7.090 10738 37.13 -4.6 48.8 -22.0 0.00020 0.00000 0.00040 75 -296.47 medialorbitofrontal 2 6.620 27279 32.15 -43.2 32.8 8.6 0.00060 0.00020 0.00100 35 148.52 parstriangularis 3 7.006 144024 25.30 -26.8 -69.9 -4.5 0.00300 0.00200 0.00400 40 172.77 lingual 4 -4.688 4845 23.24 -22.5 52.4 -12.6 0.00579 0.00440 0.00719 28 -99.88 rostralmiddlefrontal 5 5.796 123246 17.35 -25.1 33.2 26.4 0.04019 0.03666 0.04371 30 109.79 rostralmiddlefrontal My question is: what are the values of the Max column? I thing they are -log10(p), and the file cache.th30.abs.sig.cluster.mgh should also have this kind of values saved. But when I use freeview to view the lh.inflated surface with overlay file cache.th30.abs.sig.cluster.mgh, and use the "configure" button to configure the "Overlay" threshold, I cannot find the Max value of overlay displayed on the inflated surface. Could you please explain to me why I cannot see the Max values (shown in the summary file) as the overlay on the lh.inflated surface? BTW, in another experiment where I use mri_surfcluster to generate both summary file and overlay file, this problem does NOT exist. Thanks! Xiaojiang

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recon-all
by jiahui 05 May '20

05 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume, but for some of my subjects I get the following error when I run the recon-all -all command: ERROR: inflating to sphere (rms error < 2.00) final distance error I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) recon-all.log and figure1.png: see attached

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Freesurfer May 2020