Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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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Coordinate Transformation
by Hye Bin Yoo 04 May '20

04 May '20

External Email - Use Caution Dear Freesurfer Developers, How are you? We have been using Freesurfer Freeview for localizing implanted electrodes for human brains, and the coordinate system of choice was "Talairach". However, we are trying to utilize MNI152 coordinate system for advanced analyses. How could we transform between the coordinate systems between Talairach and MNI152 using Freesurfer commands? We do realize there are formulae available, but we would like to make sure WHAT coordinates Freeview is actually referring to. For your information, please find the attached picture. The red squares are on RAS and Talairach, and we assume these correspond to MNI305 and Talairach in MNI space, respectively. Is there an internal formulae we can utilize to obtain the RAS values given Talairach coordinates only? Thank you very much for your help in advance!

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longitudinal trac-all -path exited with error
by Zeng, Qi 04 May '20

04 May '20

External Email - Use Caution Hi, My trac-all -path exited with error after trying to load BEDPOST parameter samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong with my bedpostX from trac-all -bedp? Should I run bedpostX separately again without trac-all. Though my last step '-bedp' didn't prompt 'finished without error' log message as preproc did, expected files were created. BTW, which log script should I look into? the one follows SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the trac-all -path log. Thank you so much! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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recon-all and fMRI coordinates mismatch
by Peled, Noam 04 May '20

04 May '20

Hello, After running recon-all on a patient, the resulting T1.mgz coordinates system turned to be LIA. Can I guarantee the recon-all output will be in RAS? I also would like to run FS-FAST on this patient's fMRI task dataset, which is in LSA. Any recommendation what should I do to make sure both are in the same coordinates system (I preferred RAS)? Thanks, Noam

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Hippocampus subfields ROI
by Muhammad Naveed Iqbal Qureshi 04 May '20

04 May '20

External Email - Use Caution Hi FreeSurfer experts, I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I can see in the hipposubfields.lh.T1.v21.stats and lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and tail volumes of each subfield. May I know what is the file name containing the corresponding separate 21 head and tail ROIs? I can only find full subfield in all the ROI files. Thank you. Regards, Naveed

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Re: [Freesurfer] Longitudinal Hippocampal Subfields Module, existed with errors
by Zeng, Qi 04 May '20

04 May '20

External Email - Use Caution Hi Eugenio, Thank you so much for the prompt reply ! Here attached the log file. The files generated: SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1 Best, Qi On Wed, Apr 29, 2020 at 5:22 PM Zeng, Qi <qi.zeng(a)icahn.mssm.edu> wrote: > Hi Eugenio, > > Thank you so much for the prompt reply ! > Here attached the output error and log file. > The files generated: > SUBJ/SUBJ_base/tmp/hippoSF_T1_long.v21_left > SUBJ/SUBJ_base/scripts/long-hippocampal-subfields-T1 > > Best, > Qi > > On Wed, Apr 29, 2020 at 3:23 PM Iglesias Gonzalez, Juan E. < > JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote: > >> Dear Qi, >> >> The correct syntax is that of your First try, but I’m very surprised you >> got that error, as we fixed this a while ago… Can you please send me the >> complete output? >> >> 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 "Zeng, Qi" >> <qi.zeng(a)icahn.mssm.edu> >> *Reply-To: *Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> *Date: *Wednesday, April 29, 2020 at 04:44 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> *Subject: *[Freesurfer] Longitudinal Hippocampal Subfields Module, >> existed with errors >> >> >> >> * External Email - Use Caution * >> >> Hi, >> >> I am trying to use the longitudinal pipeline of the “hippocampal >> subfields and nuclei of amygdala”. Keep getting error messages when running >> it longitudinal but with no error message running it cross-sectional. I >> want to know if there is any way to fix the error and to run a longitudinal >> pipeline successfully. >> >> I am using Freesurfer/dev and matlab_runtime/2014b. >> >> I got two timepoints for each subject and finished recon-all longitudinal >> with no errors. >> >> 1) First Try >> >> segmentHA_T1_long.sh SUBJ_base >> >> >> run for about 15 mins and exited with error message: >> >> “Error using kvlGEMSMatlab >> >> >> /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327: >> >> itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search >> direction is not a descent direction! >> >> Error in kvlStepOptimizer (line 11) >> >> Error in SegmentSubfieldsT1Longitudinal” >> >> >> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 >> generated. >> >> >> >> 2) Second Try >> >> segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base >> >> segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base >> >> >> run for about 16 mins, most successful but a few with errors: >> >> “Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)” >> >> Or >> >> >> >> >> “Open file failed because file >> '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' >> has invalid content. Details: 'file is closed.failbit is set.' >> >> The file >> >> >> "/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m" >> >> cannot be executed. >> >> Error in segmentSubjectT1_autoEstimateAlveusML (line 538)” >> >> >> >> >> successful done subject or hemisphere generated >> mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21. >> >> >> >> 3) Third Try cross-sectional >> >> segmentHA_T1.sh SUBJ1_timepoint1 >> >> segmentHA_T1.sh SUBJ1_timepoint2 >> >> >> run for about 15 mins, all successful with no errors: >> >> >> all subjects have mri/lh.amygNucVolumes-T1.v21 and >> mri/lh.hippoSfVolumes-T1.v21 generated. >> >> >> >> Manual inspection with freeview, it seems fine with all successful >> longitudinal and cross sectional subfield segmentation outputs mgz. >> >> >> >> I wonder if I can fix first try and second try errors so that >> longitudinal output can be generated. >> >> >> >> Thank you for your help! >> >> Best, >> >> Qi >> >> >> >> -- >> >> >> >> Ph.D. candidate >> >> Icahn School of Medicine at Mount Sinai >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Ph.D. candidate > Icahn School of Medicine at Mount Sinai > > -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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Recon-all exited WITH errors
by Mason Wells 04 May '20

04 May '20

External Email - Use Caution Hi Experts, I appear to be having some issues with recon-all. I ran the command from a bash script (see attached), and it appears to work fine for the left hemisphere as the correct files are in the surf folder. However, there are no right hemisphere surf files. I have attached the log and error log for PPT01 and PPT02. Any advice on as to why this has happened would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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