Re: [Freesurfer] Pial surface volume
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 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 > 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 >> wrote: >> > Hi Bruce, >> > Thank you for your replies. >> > Cheers >> > >> > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl >> 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 < >> fis...@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.ramez...@gmail.com> >> > wrote: >> > > > >> > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl >> >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@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@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] R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
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" >Data: 18-set-2017 23.03 >A: >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, std...@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" >>> Data: 18-set-2017 20.03 >>> A: >>> 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, std...@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" Data: 18-set-2017 0.13 A: 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, std...@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@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] R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
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" >Data: 18-set-2017 23.03 >A: >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, std...@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" >>> Data: 18-set-2017 20.03 >>> A: >>> 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, std...@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" Data: 18-set-2017 0.13 A: 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, std...@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
Re: [Freesurfer] Pial surface volume
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 wrote: > > On Tue, Sep 19, 2017 at 11:51 AM Fereshte > 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 >> 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 >>> 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 wrote: > Hi Bruce, > Thank you for your replies. > Cheers > > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl < fis...@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 < fis...@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.ramez...@gmail.com> > wrote: > > > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl >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@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@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
[Freesurfer] Error: nifti1Read(): unsupported slice timing pattern 5
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@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] error in dev version for quantifyHAsubregions.sh
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 ${prefix} which is how the subfields file
names end. Obviously, can flip suffix and prefix throughout so it is more
intuitive. Seems to work fine after this adjustment.
Josh
--
Joshua C. Gray, PhD
Psychology Instructor
Center for Deployment Psychology
Work: (301) 816-4768
www.deploymentpsych.org
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] error in dev version for quantifyHAsubregions.sh
Realized in my tooling around I had flipped T1 and hippoSf in my command.
Here is how the adjustment needs to be made for:
quantifyHAsubregions.sh hippoSf -
leftVolFile="$resultsDirectory/$subjectName/mri/lh.${*prefix*}Volumes-${*suffix*}.v20.txt"
rightVolFile="$resultsDirectory/$subjectName/mri/rh.${*prefix*}Volumes-${*suffix*}.v20.txt"
On Tue, Sep 19, 2017 at 9:23 AM, Josh Gray wrote:
> Hello,
>
> I found a small bug in recent dev version bin quantifyHAsubregions.sh:
> leftVolFile="$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
>
--
Joshua C. Gray, PhD
Psychology Instructor
Center for Deployment Psychology
Work: (301) 816-4768
www.deploymentpsych.org
___
Freesurfer mailing list
Freesurfer@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.
Re: [Freesurfer] Pial surface volume
Hi Fereshte mris_volumes computes and prints the volume of the interior of a closed surface (a single number). It does not fill the interior. For that, use mris_fill cheers Bruce On Tue, 19 Sep 2017, Fereshte wrote: 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 wrote: On Tue, Sep 19, 2017 at 11:51 AM Fereshte 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 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 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 wrote: > Hi Bruce, > Thank you for your replies. > Cheers > > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl 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 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 > wrote: > > > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl > 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@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. > > > > > > > > >
Re: [Freesurfer] Freeview aborts under centos6
Dear Andrew, after the System admin executed your proposed commands, it stays the same, Freeview aborts. Is there anything else we could try? Thank you and best wishes, Markus 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew : > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup the shared objects > mv libvtkverdict.so libvtkverdict.so.bk > mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk > # link them to 5.6 > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6 > > then do you get the same error from freeview? > > -Andrew > > On Sep 15, 2017, at 12:10 PM, Markus Gschwind > wrote: > > Dear Andrew, > > The command gives this result: > > [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< >> $LD_LIBRARY_PATH) | grep libvtkverdict.so >> /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0- >> openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory >> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: >> duplicate hwcap 1 nosegneg >> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: >> duplicate hwcap 1 nosegneg >> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6. >> 32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg >> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: >> duplicate hwcap 1 nosegneg >> /sbin/ldconfig: Path `/usr/lib64' given more than once >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not >> a symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is >> not a symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 >> is not a symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is >> not a symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not >> a symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not >> a symbolic link >> libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is >> not a symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a >> symbolic link >> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/ >> 5.3.0-centos6_x86_64/lib/vtk/lib/v
Re: [Freesurfer] R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
yes On 9/19/17 3:22 AM, std...@virgilio.it wrote: > 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" >> Data: 18-set-2017 23.03 >> A: >> 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, std...@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" Data: 18-set-2017 20.03 A: 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, std...@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" > Data: 18-set-2017 0.13 > A: > 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, std...@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@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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, std...@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" >> Data: 18-set-2017 23.03 >> A: >> 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, std...@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" Data: 18-set-2017 20.03 A: 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, std...@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" > Data: 18-set-2017 0.13 > A: > 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, std...@virgilio.it wrote: >> Hi list, >> >>>
Re: [Freesurfer] Error: nifti1Read(): unsupported slice timing pattern 5
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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Strange looking dtifit_FA.nii.gz in FreeView
Hi Linnea, I don't see any issue in the screenshots you sent. I couldn't find freeview_T207_dtifit_FA.nii.gz.png in the attachment, either. Also your second screenshot is comparing FA image with a b0 image, which will look somewhat inversed. Best, Ruopeng On 09/19/2017 09:17 AM, Linnea Marie Dramdal Borg wrote: Hi, We have run TRACULA on a couple hundred subjects and the quality control shows that most of them are OK, but in a few subjects the dtifit_FA.nii.gz images look strange in FreeView. The image intensities appear reversed in FreeView (see freeview_T207_dtifit_FA.nii.gz.png) but look normal in Fslview (see Fslview_T207_dtifit_FA.nii.gz.png). T205 is an example of a subject that looks normal also in FreeView (see fslview-freeview_T205_dtifit_FA.nii.gz.png), as most of our subjects' dtifit_FA images do. 207's dwi_orig image looks fine in FreeView (see freeview_T207_dwi_orig.nii.gz.png) as do all its L1,L2,L3,V1,V2,V3 etc. images. I'm puzzled as to what has happened here. Since the image looks fine in Fslview I'm inclined to think this is a FreeView issue? Thank you, Linnea Marie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Error: nifti1Read(): unsupported slice timing pattern 5
>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 Subject: Re: [Freesurfer] Error: nifti1Read(): unsupported slice timing pattern 5 To: freesurfer@nmr.mgh.harvard.edu Message-ID: <528a2fe4-289f-a3d0-9525-aae876983...@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@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Error: nifti1Read(): unsupported slice timing pattern 5
try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_convert.v53 On 09/19/2017 12:12 PM, Jyothirmayi Vadlamudi wrote: > >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 > Subject: Re: [Freesurfer] Error: nifti1Read(): unsupported slice > timing pattern 5 > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <528a2fe4-289f-a3d0-9525-aae876983...@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@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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] R: Re: R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
Thanks which is the command line for computation of (cesvar1+cesvar2)/2? >Messaggio originale >Da: "Douglas Greve" >Data: 19-set-2017 17.25 >A: >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, std...@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" >>> Data: 18-set-2017 23.03 >>> A: >>> 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, std...@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" > Data: 18-set-2017 20.03 > A: > 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, std...@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: "Dougl
Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
fscalc, which is a general math program for volumes On 09/19/2017 12:34 PM, std...@virgilio.it wrote: > Thanks > which is the command line for computation of (cesvar1+cesvar2)/2? > > >> Messaggio originale >> Da: "Douglas Greve" >> Data: 19-set-2017 17.25 >> A: >> 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, std...@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" Data: 18-set-2017 23.03 A: 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, std...@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" >> Data: 18-set-2017 20.03 >> A: >> 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, std...@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 subject1
Re: [Freesurfer] Freeview aborts under centos6
Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall of vtk might work, because those shared objects that we distribute are usually sym-linked Can you also send the fs buildstamp? You can get this by running the command ‘bugr’ after sourcing freesurfer Andrew On Sep 19, 2017, at 11:02 AM, Markus Gschwind mailto:markus.gschw...@gmail.com>> wrote: Dear Andrew, after the System admin executed your proposed commands, it stays the same, Freeview aborts. Is there anything else we could try? Thank you and best wishes, Markus 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew mailto:ahoo...@mgh.harvard.edu>>: Hm okay thanks - I’m curious what happens when you run: cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6 then do you get the same error from freeview? -Andrew On Sep 15, 2017, at 12:10 PM, Markus Gschwind mailto:markus.gschw...@gmail.com>> wrote: Dear Andrew, The command gives this result: [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: duplicate hwcap 1 nosegneg /sbin/ldconfig: Path `/usr/lib64' given more than once /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig: /opt/ebsofts/Co
[Freesurfer] Freeview Versions
Dear Freesurfer Experts, My apologies if I missed this information elsewhere on the website, but could not find any info. about it. There appear to be two Freeview versions, both from 2017 (released one day apart), for which the screenshots are attached. I was wondering if you could let me know what the difference is between the two. I do use one of them on the cluster and one locally- might that account for the difference in versions? If there are other processing differences that I should be aware of, please let me know. Thank you for all of your help and information. - Arkadiy [cid:image001.png@01D33153.34FF4EB0] ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Freeview aborts under centos6
Hi Andrew, Thank you! Here is the output of bugr > [gschwind@login1 ~]$ bugr > Cut-and-paste the following info into your FreeSurfer problem report: > - > FREESURFER_HOME: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64 > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > RedHat release: CentOS release 6.9 (Final) > Kernel info: Linux 2.6.32-696.1.1.el6.x86_64 x86_64 > - I'll tell the system admin to reinstall your new vtk libraries. I'll come back to you. Thanks again, Markus 2017-09-19 19:56 GMT+02:00 Hoopes, Andrew : > Hi Markus, okay - I'll directly send you a tar of the vtk library. A > reinstall of vtk might work, because those shared objects that we > distribute are usually sym-linked > > Can you also send the fs buildstamp? You can get this by running the > command ‘bugr’ after sourcing freesurfer > > Andrew > > > On Sep 19, 2017, at 11:02 AM, Markus Gschwind > wrote: > > Dear Andrew, > > after the System admin executed your proposed commands, it stays the same, > Freeview aborts. > > Is there anything else we could try? > > Thank you and best wishes, > > Markus > > 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew : > >> Hm okay thanks - I’m curious what happens when you run: >> >> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 >> # backup the shared objects >> mv libvtkverdict.so libvtkverdict.so.bk >> mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk >> # link them to 5.6 >> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so >> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6 >> >> then do you get the same error from freeview? >> >> -Andrew >> >> On Sep 15, 2017, at 12:10 PM, Markus Gschwind >> wrote: >> >> Dear Andrew, >> >> The command gives this result: >> >> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< >>> $LD_LIBRARY_PATH) | grep libvtkverdict.so >>> /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjd >>> k-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory >>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: >>> duplicate hwcap 1 nosegneg >>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: >>> duplicate hwcap 1 nosegneg >>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.3 >>> 2-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg >>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: >>> duplicate hwcap 1 nosegneg >>> /sbin/ldconfig: Path `/usr/lib64' given more than once >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not >>> a symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is >>> not a symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 >>> is not a symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is >>> not a symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not >>> a symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a >>> symbolic link >>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5 >>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkComm
[Freesurfer] morphing ?h.cortex.patch.flat to sample subject
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/00cc7dadd16149ac7f6fe38621c95c43c4b71cad/cortex/freesurfer.py#L189 And after that save it as a freesurfer surface: https://github.com/gallantlab/pycortex/blob/00cc7dadd16149ac7f6fe38621c95c43c4b71cad/cortex/freesurfer.py#L167 But even after that mri_surf2surf couldn't determine the type. Any ideas? Thanks, Noam ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] Pial surface volume
Does it give the exact volume ( the volume which the surface was made from) or it gives an approximation of the volume? ( the toolboxes I've already worked with for such a purpose; give poor approximations). Thank you! On Tue, Sep 19, 2017 at 6:40 PM Bruce Fischl wrote: > Hi Fereshte > > mris_volumes computes and prints the volume of the interior of a closed > surface (a single number). It does not fill the interior. For that, use > mris_fill > > cheers > Bruce > On Tue, 19 Sep 2017, Fereshte wrote: > > > 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 > wrote: > > > > On Tue, Sep 19, 2017 at 11:51 AM Fereshte < > fereshte.ramez...@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 > 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 > > > 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 > >wrote: > > > Hi Bruce, > > > Thank you for your replies. > > > Cheers > > > > > > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl > >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 > >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 > > > > > wrote: > > > > > > > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce > > Fischl > > >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@nmr.mgh.harvard.edu > > > > > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > The information in this e-
[Freesurfer] Mris_volume
Dear FreeSurfer Developers Using "mris_volume surface_file_name " now i can't see any output files and 381271.851642 is shown in the command terminal, i have no idea what the problem is. Could you please help? Thank you! ___ Freesurfer mailing list Freesurfer@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.
