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Error: nifti1Read(): unsupported slice timing pattern 5
by Jyothirmayi Vadlamudi 19 Sep '17

19 Sep '17

Hello Freesurfer users, I am trying to run recon -all basic pipeline on CentOS x86-64 - Freesurfer v5.1.0 . I face the similar error as reported earlier by other users. nifti1Read(): unsupported slice timing pattern 5 In the previous archives, there are links provided, which are currently not accessible or are dead links. Can I please have the correct file/link to avoid this error. Thank you, Jyothirmayi Vadlamudi University of Louvain (UcL) Belgium.

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R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
by stdp82＠virgilio.it 19 Sep '17

19 Sep '17

I have run 1) isxconcat-sess -sf sessid_LONG_tp1 -analysis fc.rhseed.surf.rh -contrast R_SEED -o LONG_tp1 isxconcat-sess -sf sessid_LONG_tp2 -analysis fc.rhseed.surf.rh -contrast R_SEED -o LONG_tp2 2) fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/ces.nii.gz -sub/ LONG_tp2/fc.rhseed. surf.rh/R_SEED/ces.nii.gz -o /LONG/fc.rhseed.surf.rh/ces.nii.gz fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/ces.nii.gz -sub /LONG_tp2/fc.rhseed. surf.rh/R_SEED/ces.nii.gz -o /LONG/fc.rhseed.surf.rh/ces.nii.gz fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/cesvar.nii.gz -sub /LONG_tp2/fc. rhseed.surf.rh/R_SEED/cesvar.nii.gz -o /LONG/fc.rhseed.surf.rh/cesvar.nii.gz fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/cesvar.nii.gz -sub /LONG_tp2/fc. rhseed.surf.rh/R_SEED/cesvar.nii.gz -o /LONG/fc.rhseed.surf.rh/cesvar.nii.gz 3) GroupDescriptorFile 1 Class Main Input subject1pair Main Input subject2pair Main Input subject3pair Main Input subject4pair Main Input subject5pair Main Input subject6pair Main Input subject7pair Main Input subject8pair Main Input subject9pair Main Input subject10pair Main mean.txt which contains 1 0 4) cd /LONG/fc.rhseed.surf.rh mri_glmfit --glmdir long --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --nii.gz --fsgd long.fsgd --C mean.mtx I have this error: Loading y from /LONG/fc.rhseed.surf.rh/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to long/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 149926 voxels in mask Saving mask to long/mask.nii.gz Reshaping mriglm->mask... search space = 74490.844410 ERROR: MRInormWeights: value less than or eq to 0. c=0, r=0, s=0, v=-0.00516849 >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 18-set-2017 23.03 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: FS-FAST longitudinal analyis > >oh, I see now. In fsfast, you would > >1. run isxconcat-sess on each time point separately (stacks all subjects >into one file) > >2. Compute the difference between the time points, eg, > >fscalc tp1.nii.gz sub tp2.nii.gz -o diff.nii.gz > >3. Then continue from "Create Second FSGD File" on the wiki. > >Don't smooth since that has probably been done when you ran the fsfast >analysis > > > >On 09/18/2017 04:58 PM, stdp82(a)virgilio.it wrote: >> 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. >>> >>> >> _______________________________________________ >> 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 >

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R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
by stdp82＠virgilio.it 19 Sep '17

19 Sep '17

Thanks. In the point 2) the tp1.gz and tp2.nii,gz are the ces.nii.gz that are computed using isxconcat-sess? >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 18-set-2017 23.03 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: FS-FAST longitudinal analyis > >oh, I see now. In fsfast, you would > >1. run isxconcat-sess on each time point separately (stacks all subjects >into one file) > >2. Compute the difference between the time points, eg, > >fscalc tp1.nii.gz sub tp2.nii.gz -o diff.nii.gz > >3. Then continue from "Create Second FSGD File" on the wiki. > >Don't smooth since that has probably been done when you ran the fsfast >analysis > > > >On 09/18/2017 04:58 PM, stdp82(a)virgilio.it wrote: >> 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. >>> >>> >> _______________________________________________ >> 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 >

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error in dev version for quantifyHAsubregions.sh
by Josh Gray 19 Sep '17

19 Sep '17

Hello, I found a small bug in recent dev version bin quantifyHAsubregions.sh: leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${suffix}.v20.txt" rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${suffix}.v20.txt" Should say leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${ *prefix*}.v20.txt" rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${ *prefix*}.v20.txt" because as specified "T1" is the ${prefix} which is how the subfields file names end. Obviously, can flip suffix and prefix throughout so it is more intuitive. Seems to work fine after this adjustment. Josh -- Joshua C. Gray, PhD Psychology Instructor Center for Deployment Psychology Work: (301) 816-4768 www.deploymentpsych.org

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Re: [Freesurfer] Pial surface volume
by Fereshte 19 Sep '17

19 Sep '17

Using the Pial surface; Does it mean mris_volume will give the inner cortical boundary of the surface and not the outer boundary? Sincerely, Fereshte Ramezani On Mon, Sep 4, 2017 at 9:53 PM Fereshte <fereshte.ramezani(a)gmail.com> wrote: > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > >> sure, mris_volume will give you the interior volume of any closed surface >> using the divergence formula. Note that this is *not* the volume of the >> ribbon but rather the volume of the entire interior >> >> cheers >> Bruce >> >> >> On Mon, 4 Sep 2017, Fereshte wrote: >> >> > Hello FreeSurfer developersIs it possible to have the volume of pial >> surface in FreeSurfer? >> > >> >_______________________________________________ >> 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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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

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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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