Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

Hippocampal subfield segmentation error
by Md. Mamun Al-Amin 18 Sep '17

18 Sep '17

Dear Experts I have been experiencing a problem while running the following command *segmentHA_T1.sh subject_name* The program exits with the following error "MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args" The log file is attached herewith. I have reinstalled Matlab R2012 runtime. However, still I am experiencing same problem. Looking for a solution. I would appreciate your suggestion. -- Kind regards Md. Mamun Al-Amin ------------------------------ PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072

2 4

labels used by freesurfer
by Benjamin Luerweg 18 Sep '17

18 Sep '17

dear fs community, as a kind of a freesurfer greenhorn i would kindly ask you to help me out with identifying the different labels used by freesurfer. after using mri segstats most of the labels seem to be describing thereselfs in proper way. what i don’t understand are for example the different volume values showing up inside the console after entering the segstat command. VentChorVol what does this label explain? CSFVol why is this volume differing to the one within the segstat file? and finally i would really love to know how to calculate a correct brain to liquor ratio?! kind regards, ben

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Saving results in volume space
by Martin Juneja 18 Sep '17

18 Sep '17

Hi experts, I have three questions. I would really appreciate any help. (1). I ran following commands to estimate relationships between LGI and Behav data: mris_preproc --fsgd Behav.fsgd --target fsaverage --hemi lh --meas pial_lgi --out lh.Behav_LGI.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.Behav_LGI.mgh --fwhm 10 --cortex --tval lh.Behav_LGI.10.mgh mri_glmfit --y lh.Behav_LGI.10.mgh --fsgd Behav.fsgd dods --C Corr-Behav-cor1.mtx --surf fsaverage lh --cortex --glmdir lh.Behav_LGI_P.glmdir --eres-save mri_glmfit-sim_nonortho --glmdir lh.Behav_LGI_P.glmdir --sim perm 2000 1.3 permcsd --sim-sign pos --cwpvalthresh .05 --perm-resid --overwrite Finally, cluster summary gives me one clusters with peak at the fusiform gyrus as following: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -4.045 10153 32101.81 -36.5 -39.5 -15.1 0.00050 0.00000 0.00100 64731 -106698.82 fusiform As you can see number of voxels is 64731, so I when I viewed the results in FreeView, its showing me a big cluster, almost all over the brain (please see attached screen shot). Could you please tell me why I am getting these sort of results, and how can I fix this? If I change cluster forming threshold from 1.3 to 3, would that work? I wanted to make sure before I re-run the analysis because mri_glmfit-sim_nonortho command takes about a day to finish. (2). How can I save output cluster e.g. fusiform gyrus in above example in NIFTI MNI volume space so that I can use this cluster for functional connectivity analysis? (3). If I want to use fusiform gyrus from standard FreeSurfer parcellation rather than from my results, how can I save that in standard MNI volume space? Thank you so much !

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hippocampus subfields in longitudinal dataset
by Lara Foland-Ross 18 Sep '17

18 Sep '17

Hello Freesurfer experts, I have a longitudinal data set already processed in the longitudinal pipeline of v5.3. I'd now like to use the hippocampus subfield commands available in 6.0. I'm wondering whether I will arrive at the same result using either of the following two approaches: 1. run "recon-all -s ${subjTp} -hippocampal-subfields-T1" separately on the time1 and time 2 longitudinal scans 2. run longHippoSubfieldsT1.sh Thanks in advance, Lara

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R: Re: R: Re: FS-FAST longitudinal analyis
by stdp82＠virgilio.it 18 Sep '17

18 Sep '17

My apologies for the trivial question. Anyway, the web page reports information for cortical thickness analysis. I understand it. No information I found on fs-fast longitudinal analysis. Thus, when I run fs-fast longitudinal analysis, the steps 1-5 should be performed? Or they are only for morphometry? Many thanks >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 18-set-2017 20.03 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: FS-FAST longitudinal analyis > >I don't understand what you don't understand. Isn't the web page clear >enough? Are those 5 steps on the web page? > > >On 09/18/2017 02:20 AM, stdp82(a)virgilio.it wrote: >> Thanks, but I not understand if the follow step that you suggested me >> should be used also for FS-FAST analysis. >> >> Specifically, I'm refferring to: >> >> 1Sample each individual's surface onto the average surface. >> 2Compute the difference between each of the pairs in the average >> surface space. >> 3Concatenate the differences into one file. >> 4Smooth on the surface (optional) >> 5Perform analysis with mri_glmfit on this file >> >> Importantly, should I create the two fsgd files as reported in the web >> page and below? Or only the second is due? >> >> One is: >> GroupDescriptorFile 1 >> Class Main >> Input subject1 Main >> Input subject1match Main >> Input subject2 Main >> Input subject2match Main >> Input subject3 Main >> Input subject3match Main >> Input subject3 Main >> Input subject3match Main >> >> the other is: >> GroupDescriptorFile 1 >> Class Main >> Variables Age >> Input subject1pair Main 30 >> Input subject2pair Main 40 >> Input subject3pair Main 50 >> Input subject4pair Main 60 >> >> Thanks >> >> Regards >> >> >> Stefano >> >> ----Messaggio originale---- >> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >> Data: 18-set-2017 0.13 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: Re: [Freesurfer] FS-FAST longitudinal analyis >> >> That looks correct. You can also checkout the instructions here: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis >> >> >> On 9/17/17 6:07 PM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> >>> I'm not sure that the files reported below are correct to assess >>> the longitudinal difference between T1 and T2. >>> Please, could you check it? The result which I have obtained bu >>> running mri_glmfit is too strange. >>> Thanks >>> Best regards >>> Stefano >>> >>> 1) PAIRWISE.fsgd file >>> ------------------- >>> GroupDescriptorFile 1 >>> Class subj1 >>> Class subj2 >>> ... >>> Class subjN >>> Variables TP1-vs-TP2 >>> Input subj1_tp1 subj1 1 >>> Input subj1_tp2 subj1 -1 >>> Input subj2_tp1 subj2 1 >>> Input subj2_tp2 subj2 -1 >>> ... >>> Input subjN_tp1 subjN 1 >>> Input subjN_tp2 subjN -1 >>> ---------------------------- >>> >>> 2) mean.mtx >>> 1 1 ... 1 0 >>> ------------------------------ >>> 3) tp-effect.mtx >>> 0 0 ... 0 1 >>> ------------------------------ >>> 4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz --wls >>> cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd >>> PAIRWISE.fsgd doss --C mean.mtx --C tp-effect.mtx >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

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R: Re: FS-FAST longitudinal analyis
by stdp82＠virgilio.it 18 Sep '17

18 Sep '17

Thanks, but I not understand if the follow step that you suggested me should be used also for FS-FAST analysis. Specifically, I'm refferring to: 1Sample each individual's surface onto the average surface. 2Compute the difference between each of the pairs in the average surface space. 3Concatenate the differences into one file. 4Smooth on the surface (optional)5Perform analysis with mri_glmfit on this file Importantly, should I create the two fsgd files as reported in the web page and below? Or only the second is due? One is:GroupDescriptorFile 1Class MainInput subject1 MainInput subject1match MainInput subject2 MainInput subject2match MainInput subject3 MainInput subject3match MainInput subject3 MainInput subject3match Main the other is:GroupDescriptorFile 1Class MainVariables AgeInput subject1pair Main 30Input subject2pair Main 40Input subject3pair Main 50Input subject4pair Main 60 Thanks Regards Stefano ----Messaggio originale---- Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> Data: 18-set-2017 0.13 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] FS-FAST longitudinal analyis That looks correct. You can also checkout the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis On 9/17/17 6:07 PM, stdp82(a)virgilio.it wrote: Hi list, I'm not sure that the files reported below are correct to assess the longitudinal difference between T1 and T2. Please, could you check it? The result which I have obtained bu running mri_glmfit is too strange. Thanks Best regards Stefano 1) PAIRWISE.fsgd file ------------------- GroupDescriptorFile 1 Class subj1 Class subj2 ... Class subjN Variables TP1-vs-TP2 Input subj1_tp1 subj1 1 Input subj1_tp2 subj1 -1 Input subj2_tp1 subj2 1 Input subj2_tp2 subj2 -1 ... Input subjN_tp1 subjN 1 Input subjN_tp2 subjN -1 ---------------------------- 2) mean.mtx 1 1 ... 1 0 ------------------------------ 3) tp-effect.mtx 0 0 ... 0 1 ------------------------------ 4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd PAIRWISE.fsgd doss --C mean.mtx --C tp-effect.mtx _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Left & Right flip on asymmetric MNI template
by yskim 18 Sep '17

18 Sep '17

Dear Freesurfer experts,I recently received manually segmentated MR data that registered to ch2better MNI template. However, I have been informed that this data has been registered in inverted form, and I could not simply flip left and right because ch2better MNI template was asymmetric.To solve this problem, I first used the LeftRightReversal method of freesurfer, but this method did not properly reflect the left-right different structure of the asymmetric template.How can I flip registered data successfully with reflecting asymmetric MNI template structure? Thank you for your help and information. - yskim

2 1

FreeSurfer6 on Ubuntu
by Fereshte 18 Sep '17

18 Sep '17

Dear FreeSurfer Developers Is FreeSurfer 6 available on Ubunto? If so, does it work properly? Thank you!

2 1

FS-FAST longitudinal analyis
by stdp82＠virgilio.it 17 Sep '17

17 Sep '17

Hi list, I'm not sure that the files reported below are correct to assess the longitudinal difference between T1 and T2.Please, could you check it? The result which I have obtained bu running mri_glmfit is too strange.ThanksBest regardsStefano 1) PAIRWISE.fsgd file-------------------GroupDescriptorFile 1Class subj1Class subj2...Class subjNVariables TP1-vs-TP2Input subj1_tp1 subj1 1Input subj1_tp2 subj1 -1Input subj2_tp1 subj2 1Input subj2_tp2 subj2 -1...Input subjN_tp1 subjN 1Input subjN_tp2 subjN -1---------------------------- 2) mean.mtx1 1 ... 1 0------------------------------3) tp-effect.mtx0 0 ... 0 1------------------------------4) mri_glmfit --glmdir PAIRWISE --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd PAIRWISE.fsgd doss --C mean.mtx --C tp-effect.mtx

2 1

Multiple comparison, color maps and contrast
by miracle ozzoude 17 Sep '17

17 Sep '17

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Freesurfer September 2017