Freesurfer September 2017

freesurfer@nmr.mgh.harvard.edu

109 participants
199 discussions

Re: [Freesurfer] Pial surface volume
by Fereshte 20 Sep '17

20 Sep '17

Dear Professor Bruce I'm just trying to convert lh.pial surface to the volume with the down below command but the output doesn't make any sense ( lh.voulme contains zero). Could you please help? Mris_volume topo_defect_after/surf/rh.pial Thank you! On Tue, Sep 19, 2017 at 1:11 PM Fereshte <fereshte.ramezani(a)gmail.com> wrote: > > On Tue, Sep 19, 2017 at 11:51 AM Fereshte <fereshte.ramezani(a)gmail.com> > wrote: > >> I changed the FreeSurfer version to 6 and now i could find it. >> Thank you! >> Cheers >> >> On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve <greve(a)nmr.mgh.harvard.edu> >> wrote: >> >>> Is it not in $FREESURFER_HOME/bin ? What version are you using? >>> >>> On 9/16/17 12:05 PM, Fereshte wrote: >>> >>> Well i did ask if it was possible to obtain the volume of Pial surface >>> and here's the response; >>> >>> "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" >>> >>> I can't see mris_volume in FreeSurfer commands. >>> >>> On Sat, Sep 16, 2017 at 8:09 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>>> sorry, can you clarify what your question is? >>>> >>>> On Sat, 16 Sep 2017, Fereshte >>>> wrote: >>>> >>>> > Dear FreeSurfer developers >>>> > I couldn't find the mentioned mris_volume in the commands. Shall i >>>> use mri_vol2surf or something? >>>> > Looking forward to hearing from you! >>>> > On Tue, Sep 5, 2017 at 9:46 AM Fereshte <fereshte.ramezani(a)gmail.com> >>>> wrote: >>>> > Hi Bruce, >>>> > Thank you for your replies. >>>> > Cheers >>>> > >>>> > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl < >>>> fischl(a)nmr.mgh.harvard.edu> wrote: >>>> > Hi Fereshte >>>> > >>>> > the algorithm is documented in the recon1 1999 NeuroImage and >>>> 2000 PNAS >>>> > papers >>>> > >>>> > cheers >>>> > Bruce >>>> > On Mon, 4 Sep 2017, Fereshte wrote: >>>> > >>>> > > What's the algorithm used to expand inner cortical boundary ( >>>> to achieve the >>>> > outer cortical boundary >>>> > > in pial surface) in FreeSurfer? >>>> > > On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl < >>>> fischl(a)nmr.mgh.harvard.edu> wrote: >>>> > > it will give the interior volume of whatever surface >>>> you give it as a >>>> > > command line argument. >>>> > > >>>> > > On Mon, 4 Sep 2017, Fereshte >>>> > > wrote: >>>> > > >>>> > > > 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. >>>> > > > >>>> > > > >>>> > > >_______________________________________________ >>>> > > 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 >>>> > >>>> > >>>> > 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 >>>> >>>> >>>> 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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 >>> >>> >>> 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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morphing ?h.cortex.patch.flat to sample subject
by Peled, Noam 20 Sep '17

20 Sep '17

Hey all I'm trying to morph the fsaverage flat patch (?h.cortex.patch.flat) to the freesurfer sample subject, and getting the following error: mri_surf2surf --srcsubject fsaverage --srcsurfval lh.cortex.patch.flat --trgsubject sample --trgsurfval lh.cortex.patch.sample.flat --hemi lh ERROR: could not determine type of lh.cortex.patch.sample.flat mris_convert also didn't work: mri_surf2surf --srcsubject fsaverage --srcsurfval lh.cortex.patch.flat --trgsubject sample --trgsurfval lh.cortex.patch.sample.flat --hemi lh ERROR: could not determine type of lh.cortex.patch.sample.flat [thibault:surf] (nmr-stable53-env) mris_convert lh.cortex.patch.flat lh.cortex.patch.flat.asc mrisFindNeighbors: lh.cortex.patch.flat: face[0].v[0] = 0, but face 0 not in vertex 0 face list I could read it using the python code in pyCortex: https://github.com/gallantlab/pycortex/blob/00cc7dadd16149ac7f6fe38621c95c4… And after that save it as a freesurfer surface: https://github.com/gallantlab/pycortex/blob/00cc7dadd16149ac7f6fe38621c95c4… But even after that mri_surf2surf couldn't determine the type. Any ideas? Thanks, Noam

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Freeview aborts under centos6
by Markus Gschwind 19 Sep '17

19 Sep '17

Hi experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$ freeview Abort When running freeview.bin it complains about a libraries error: [gschwind@login1 ~]$ freeview.bin freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory I searched the archives and found this info to be given, [gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0 I then integrated this into bashrc export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 however, the problem persists. Any help is highly appreciated! Thanks you! Markus

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

19 Sep '17

Thanks which is the command line for computation of (cesvar1+cesvar2)/2? >----Messaggio originale---- >Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 19-set-2017 17.25 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: FS-FAST longitudinal analyis > >Don't do the subtraction on cesvar. Instead compute cesvar = >(cesvar1+cesvar2)/2 > > >On 9/19/17 4:17 AM, stdp82(a)virgilio.it wrote: >> 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 >>> >> _______________________________________________ >> 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 >

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

19 Sep '17

>From what I understand while going through, previous archives, a patch for mri_convert will do. Unless there is another way to solve the problem with mri_convert. Date: Tue, 19 Sep 2017 11:28:52 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Error: nifti1Read(): unsupported slice timing pattern 5 To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <528a2fe4-289f-a3d0-9525-aae876983f7c(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" which file do you need? On 9/19/17 9:11 AM, Jyothirmayi Vadlamudi wrote: > 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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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

1 1

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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Freesurfer September 2017