Re: [Freesurfer] mkbrainmask error with libmeshclass.so

[Corinna Bauer]

actually, on closer look, adding those lines to the FSL config did not fix
the problem. However, if I call bet2 by typing fsl5.0-bet2, then it works.
I am not sure why, but to call anything from fsl I have to first put
fsl5.0- first.




On Tue, Apr 16, 2013 at 2:40 PM, Corinna Bauer  wrote:

> That's alright. I had to add these lines to my .bashrc file
> # get FSL config loaded
> if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then
>   . /usr/share/fsl/5.0/etc/fslconf/fsl.sh;
> fi
>
> but now, I get this error when running preproc-sess -per-run -fwhm 3
> -force -so up -surface self lhrh -s . -d . -fsd bold -rlf symm_runs
>
>  /usr/local/freesurfer/subjects/symmetry/functional
> mri_convert ERROR: could not determine file for
> /usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/mri/brainmask
> lindsay_functional/bold/006/tmp.bbregister.7574/fslregister/refvol.fslregister.nii
>
>
>
>
>
> On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve  > wrote:
>
>>  Hi Corinna, I hate to pass the buck, but I think you'll have to contact
>> the FSL people to get it sorted out.
>> doug
>>
>>
>>
>> On 4/16/13 9:31 AM, Corinna Bauer wrote:
>>
>> Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared
>> object file: No such file or directory.
>>
>>
>>
>> On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Corinna, if you just run bet2 at the command line, do you get the
>>> same error?
>>> doug
>>>
>>> On 04/12/2013 03:56 PM, Corinna Bauer wrote:
>>> > Hello all, when running preproc-sess, I got this error message:
>>> > ERROR: could not determine file for
>>> >
>>> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain
>>> > Try running mkbrainmask-sess with -per-run
>>> >
>>> > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d .
>>> > -fsd bold
>>> > m) and got the output below, which shows a problem with a shared
>>> library?
>>> >
>>> > Any suggestions?
>>> >
>>> > Corinna
>>> >
>>> > 
>>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test
>>> > Fri Apr 12 15:53:14 EDT 2013
>>> > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil
>>> > 1 -nerode 0
>>> > FSLMATHS fslmaths.fsl
>>> > Scratch Dir is /tmp/mkbrainmask_9634
>>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
>>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
>>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> > reading from template.nii.gz...
>>> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>>> > i_ras = (-0.996119, -0.0108587, 0.0873391)
>>> > j_ras = (0.000562893, 0.991553, 0.129698)
>>> > k_ras = (0.0880098, -0.129244, 0.9877)
>>> > writing to /tmp/mkbrainmask_9634/in.nii...
>>> > # -- Using FSL's BET to Extract Brain-- #
>>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>>> > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f
>>> 0.1
>>> > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries:
>>> > libmeshclass.so: cannot open shared object file: No such file or
>>> directory
>>> > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o
>>> > /tmp/mkbrainmask_9634/brain_mask.nii
>>> > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
>>> >
>>> > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
>>> > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>>> > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min
>>> > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii
>>> > sysname  Linux
>>> > hostname lotfi
>>> > machine  x86_64
>>> > user bauer
>>> >
>>> > input  /tmp/mkbrainmask_9634/brain_mask.nii
>>> > frame  0
>>> > nErode3d   0
>>> > nErode2d   0
>>> > output /tmp/mkbrainmask_9634/brain_mask.nii
>>> > Binarizing based on threshold
>>> > min0.01
>>> > max+infinity
>>> > binval1
>>> > binvalnot 0
>>> >
>>> >
>>> >
>>>  > ___
>>> > 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
>

Re: [Freesurfer] pial surface with FLAIR

[Nick Schmansky]

Veronica,

Can you send me the recon-all.log?  The one where it is getting hung
when you run this:

recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial

this should work, by importing the flair and then re-running the surface
creation code, but perhaps there is a dependency bug that was missed.

Nick


On Tue, 2013-04-16 at 09:27 -0400, Bruce Fischl wrote:
> ok, then I don't see what's going wrong. Nick: any thoughts?
> 
> On Tue, 16 Apr 
> 2013, Popescu, Veronica wrote:
> 
> >
> > Dear Bruce,
> > I ran the follwing:
> > autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all.
> > And my file was indeed a 3D T1 scan.
> > Thank you very much!
> > Best wishes,
> > Veronica
> >
> > -Original Message-
> > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> > Sent: Tuesday, 16 April, 2013 15:02
> > To: Popescu, Veronica
> > Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu'
> > Subject: RE: [Freesurfer] pial surface with FLAIR
> >
> > Hi Veronica
> >
> > what recon-all command lines did you run? You did run it with a T1 first, 
> > right?
> >
> > Bruce
> > On Tue, 16 Apr 2013, Popescu, Veronica wrote:
> >
> >> Hi, Christopher!
> >> Best of luck to you all in these difficult times!
> >> Thank you very much for your advice. I'll try this as well.
> >> Best wishes,
> >> Veronica
> >>
> >> -Original Message-
> >> From: Watson, Christopher
> >> [mailto:christopher.wat...@childrens.harvard.edu]
> >> Sent: Tuesday, 16 April, 2013 07:15
> >> To: Bruce Fischl; Popescu, Veronica
> >> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> >> Subject: RE: [Freesurfer] pial surface with FLAIR
> >>
> >> Hi Veronica,
> >> Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
> >> And then, when you do the remaining recon-all steps:
> >>
> >> recon-all -autorecon3 -s $SUBJECT -FLAIRpial
> >>
> >> It has worked for me. (And worked very well! No edits necessary for
> >> the pial surface!) 
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu
> >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> >> [fis...@nmr.mgh.harvard.edu]
> >> Sent: Monday, April 15, 2013 12:31 PM
> >> To: Popescu, Veronica
> >> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> >> Subject: Re: [Freesurfer] pial surface with FLAIR
> >>
> >> Hi Veronica,
> >>
> >> we haven't seen that before. Can you upload your subject including the 
> >> FLAIR and we'll take a look?
> >>
> >> thanks
> >> Bruce
> >>
> >> On Mon, 15 Apr 2013, Popescu, Veronica wrote:
> >>
> >>>
> >>> Dear all,
> >>>
> >>> I have already run the FreeSurfer 5.2 -all, and I would like to
> >>> improve the pial surface recongition using the FLAIR. From the
> >>> $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the 
> >>> following syntax:
> >>>
> >>> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
> >>>
> >>> It starts running but then it hangs, I never get an output. The FLAIR
> >>> file is in nifti format.
> >>>
> >>> I am not sure what I am doing wrong: it is the syntax? Should I first
> >>> convert the FLAIR file to .mgz?
> >>>
> >>> Thank you in advance for the help!
> >>>
> >>> Veronica Popescu, MD, MSc
> >>> Department of Radiology & Nuclear Medicine VU University Medical
> >>> Center Amsterdam, The Netherlands
> >>>
> >>>
> >>
> >>
> >>
> >
> >
> > 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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> 
> 


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Re: [Freesurfer] mkbrainmask error with libmeshclass.so

[Corinna Bauer]

That's alright. I had to add these lines to my .bashrc file
# get FSL config loaded
if [ -f /usr/share/fsl/5.0/etc/fslconf/fsl.sh ]; then
  . /usr/share/fsl/5.0/etc/fslconf/fsl.sh;
fi

but now, I get this error when running preproc-sess -per-run -fwhm 3 -force
-so up -surface self lhrh -s . -d . -fsd bold -rlf symm_runs

 /usr/local/freesurfer/subjects/symmetry/functional
mri_convert ERROR: could not determine file for
/usr/local/freesurfer/subjects/symmetry/functional/lindsay_functional/mri/brainmask
lindsay_functional/bold/006/tmp.bbregister.7574/fslregister/refvol.fslregister.nii





On Tue, Apr 16, 2013 at 12:07 PM, Douglas Greve
wrote:

>  Hi Corinna, I hate to pass the buck, but I think you'll have to contact
> the FSL people to get it sorted out.
> doug
>
>
>
> On 4/16/13 9:31 AM, Corinna Bauer wrote:
>
> Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared
> object file: No such file or directory.
>
>
>
> On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Corinna, if you just run bet2 at the command line, do you get the
>> same error?
>> doug
>>
>> On 04/12/2013 03:56 PM, Corinna Bauer wrote:
>> > Hello all, when running preproc-sess, I got this error message:
>> > ERROR: could not determine file for
>> >
>> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain
>> > Try running mkbrainmask-sess with -per-run
>> >
>> > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d .
>> > -fsd bold
>> > m) and got the output below, which shows a problem with a shared
>> library?
>> >
>> > Any suggestions?
>> >
>> > Corinna
>> >
>> > 
>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test
>> > Fri Apr 12 15:53:14 EDT 2013
>> > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil
>> > 1 -nerode 0
>> > FSLMATHS fslmaths.fsl
>> > Scratch Dir is /tmp/mkbrainmask_9634
>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
>> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> > reading from template.nii.gz...
>> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> > i_ras = (-0.996119, -0.0108587, 0.0873391)
>> > j_ras = (0.000562893, 0.991553, 0.129698)
>> > k_ras = (0.0880098, -0.129244, 0.9877)
>> > writing to /tmp/mkbrainmask_9634/in.nii...
>> > # -- Using FSL's BET to Extract Brain-- #
>> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>> > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f
>> 0.1
>> > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries:
>> > libmeshclass.so: cannot open shared object file: No such file or
>> directory
>> > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o
>> > /tmp/mkbrainmask_9634/brain_mask.nii
>> > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
>> >
>> > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
>> > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
>> > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min
>> > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii
>> > sysname  Linux
>> > hostname lotfi
>> > machine  x86_64
>> > user bauer
>> >
>> > input  /tmp/mkbrainmask_9634/brain_mask.nii
>> > frame  0
>> > nErode3d   0
>> > nErode2d   0
>> > output /tmp/mkbrainmask_9634/brain_mask.nii
>> > Binarizing based on threshold
>> > min0.01
>> > max+infinity
>> > binval1
>> > binvalnot 0
>> >
>> >
>> >
>>  > ___
>> > 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.
>>
>>
>
>
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Re: [Freesurfer] QDEC questions

[Tudor Popescu]

Thanks Nick, (and thanks Doug too for the answer to question 2.)

It must indeed have been a disk-space issue, as running the -qcache again,
after clearing up some space, produced all the expected .mgh files

If I can follow up on two of my previous questions:

3) Not sure I understand your answer. So it seems discrete variables, such
as gender, cannot be taken as covariates or nuisance variables, only as
factors. But users might want to take some discrete variables as
covariates, rather than as factors, as I might not be interested in their
direct effect on the brain measure but simply want to parcel out the
variance that they contribute. Are you suggesting that they should be taken
as factors even if they aren't of interest?

4) Does the ideal value of FWHM depend on the blob size in the sense that
if one expects small blobs in the results (how small?), then one should use
small FWHMs in QDEC, and large FWHMs if expecting large blobs?

I apologise for the amount of questions I keep asking, but I have a few
more:

A) When trying repeated analyses (designs) in QDEC, do I need to delete the
output files of previous analyses, and/or restart QDEC every time? Or are
the results of each analysis displayed correctly independently of
previously-made analyses in the same QDEC session? I'm asking because I see
that, once the "Set using FDR" button is pressed, the corrected t threshold
remains in use for subsequent analyses, but after restarting QDEC and
redoing the last analysis, the t threshold is no longer the same

B) Must all QDEC analyses always be done for the two hemispheres
separately? Is there no analysis that can be done on the whole brain, such
that the t-value thresholds are FDR-corrected at the whole-brain level?

C) I would like to extract the cortical thickness of several cortical ROIs
including the IPS, IFG and SPL; I didn’t know whether the Desikan-Killiany
or the Destrieux atlas would be more appropriate, but I tried the command
given 
here,
hoping to obtain a table with the thickness of all ROIs from the
parcelation corresponding to the Destrieux atlas. However, although the
command results in the message " lh.aparc.a2009.thickness.table", I found
no such file anywhere in my $SUBJECTS_DIR

D) How should a regression-type analysis be made in QDEC, i.e. one where I
have a continuous predictor such as behavioural score, whose correlation
with the brain measure (cortical thickness) I want to compare between my
two groups? Because of QDEC's preference for discrete variables as factors,
it seems that only ANOVA-type analyses can be done (i.e. effect of discrete
factor(s) on brain measure), rather than regression-type (i.e. correlation
between continuous factor and brain measure)

E) The average brain with inflated cortex that results are projected on –
is this the same average that is normally used in most papers, or does the
inflating algorithm differ? And is the colour-coding the same (dark gray =
sulci, light gray = gyri)?


On 15 April 2013 23:52, Nick Schmansky  wrote:

> Tudor,
>
> In the recon-all.log, it has this line:
> ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
>
> but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
> correctly, so this indicates to me that it might have run out of disk
> space.  is that the case?
>
> to answer the others:
> 2. not sure
> 3. you can select discrete can a regular variate along with your main
> variate.  'nuisance' variates are like any other.
> 4. depends on the expected 'blob' size
> 5. the selection of fwhm in qdec corresponds directly with the values
> selected by qcache (they are one-to-one related, ie the 10mm fwhm values
> created by qcache are used by the 10mm fwhm selection in qdec).
>
> Nick
>
>
>
> On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
> > Dear experts,
> >
> > Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
> > misbehaving, and so after running a first whole-brain group cortical
> > thickness analysis on my structural data, I have some questions:
> >
> > 1. After running recon-all with the –qcache flag (i.e. presmoothing),
> > files of the type lh.thickness.*.mgh were created for all 38 subjects
> > (19 in each group), however files of the type rh.thickness.*.mgh were
> > not created for 5 out of the 19 subjects of the first group. Log files
> > recon-all-status.log and recon-all.log (attached, for one of those 5
> > subjects) both mention that the process ran on Mar22nd ended with
> > errors, although I can't quite see what that was
> >
> >
> >
> > 2. When I take age as a continuous factor (covariate), the list of
> > clusters in my results look dramatically different from the clusters
> > that I get for the same contrast ran without the covariate. Why is
> > that, given that normally adding a covariate very rarely changes the
> > results by a great

Re: [Freesurfer] recon-all -autorecon2 bug?

[Miklos Argyelan]

Hi Doug, You mean autorecon1? Yes I did, ran without problem, and it seems
I have all the output files from autorecon2 as well. Miklos
--
argyelan, miklos


On Tue, Apr 16, 2013 at 1:06 PM, Douglas N Greve
wrote:

> Hi Miklos, did you run all the steps that go before autorecon2?
> doug
>
>
>
>
> On 04/16/2013 12:23 PM, Miklos Argyelan wrote:
> > Hi,
> >
> > I have recently installed Freesurfer on a new computer, and downloaded
> > the latest version of Freesurfer (centos 64 bit) and when ran:
> >
> > recon-all -subject test001 -autorecon2
> >
> > I got the following error message:
> >
> > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> > cwd
> > cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
> > mri/norm.mgz --empty --brainmask mri/brainmask.mgz
> > --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in
> > mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv
> > --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab
> > /usr/local/freesurfer/ASegStatsLUT.txt --subject test001
> > sysname  Linux
> > hostname mikbox
> > machine  x86_64
> > user amiklos
> > UseRobust  0
> > atlas_icv (eTIV) = 1444225 mm^3(det: 1.348893 )
> >
> *mghRead(/home/amiklos/nethome/work/METHODS/FS/subjects/test001/mri/ribbon.mgz,
> > -1): could not open file*
> >
> > I am not sure but the bug seems that autorecon2 tries to run SegStats
> > too early (supposed to be in autorecon3).
> >
> > Maybe this is the error in recon-all:
> > case "-autorecon2":
> >   set DoGCAReg = 1;
> >   set DoCARegInv   = 1;
> >   set DoRemoveNeck = 1;
> >   set DoSkullLTA   = 1;
> >   set DoCANormalize= 1;
> >   set DoCAReg  = 1;
> >   set DoCALabel= 1;
> > *set DoSegStats   = 1;*
> >   set DoNormalization2 = 1;
> >   set DoMaskBFS= 1;
> >   set DoSegmentation   = 1;
> >   set DoFill   = 1;
> >   set DoTessellate = 1;
> >   set DoSmooth1= 1;
> >   set DoInflate1   = 1;
> >   set DoQSphere= 1;
> >   set DoFix= 1;
> >   set DoSmooth2= 1;
> >   set DoInflate2   = 1;
> >   set DoWhiteSurfs = 1;
> >   set DoCurvStats  = 1;
> >   breaksw
> >
> > Could some expert verify please that this is indeed the problem and I
> > can change the 1 to zero, or am I completely off?
> >
> > Miklos
> >
> >
> >
> > ___
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> > 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
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Re: [Freesurfer] recon-all -autorecon2 bug?

[Douglas N Greve]

Hi Miklos, did you run all the steps that go before autorecon2?
doug




On 04/16/2013 12:23 PM, Miklos Argyelan wrote:
> Hi,
>
> I have recently installed Freesurfer on a new computer, and downloaded 
> the latest version of Freesurfer (centos 64 bit) and when ran:
>
> recon-all -subject test001 -autorecon2
>
> I got the following error message:
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> cwd
> cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
> mri/norm.mgz --empty --brainmask mri/brainmask.mgz 
> --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in 
> mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv 
> --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab 
> /usr/local/freesurfer/ASegStatsLUT.txt --subject test001
> sysname  Linux
> hostname mikbox
> machine  x86_64
> user amiklos
> UseRobust  0
> atlas_icv (eTIV) = 1444225 mm^3(det: 1.348893 )
> *mghRead(/home/amiklos/nethome/work/METHODS/FS/subjects/test001/mri/ribbon.mgz,
>  
> -1): could not open file*
>
> I am not sure but the bug seems that autorecon2 tries to run SegStats 
> too early (supposed to be in autorecon3).
>
> Maybe this is the error in recon-all:
> case "-autorecon2":
>   set DoGCAReg = 1;
>   set DoCARegInv   = 1;
>   set DoRemoveNeck = 1;
>   set DoSkullLTA   = 1;
>   set DoCANormalize= 1;
>   set DoCAReg  = 1;
>   set DoCALabel= 1;
> *set DoSegStats   = 1;*
>   set DoNormalization2 = 1;
>   set DoMaskBFS= 1;
>   set DoSegmentation   = 1;
>   set DoFill   = 1;
>   set DoTessellate = 1;
>   set DoSmooth1= 1;
>   set DoInflate1   = 1;
>   set DoQSphere= 1;
>   set DoFix= 1;
>   set DoSmooth2= 1;
>   set DoInflate2   = 1;
>   set DoWhiteSurfs = 1;
>   set DoCurvStats  = 1;
>   breaksw
>
> Could some expert verify please that this is indeed the problem and I 
> can change the 1 to zero, or am I completely off?
>
> Miklos
>
>
>
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[Freesurfer] recon-all -autorecon2 bug?

[Miklos Argyelan]

Hi,

I have recently installed Freesurfer on a new computer, and downloaded the
latest version of Freesurfer (centos 64 bit) and when ran:

recon-all -subject test001 -autorecon2

I got the following error message:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
--excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
--surf-ctx-vol --totalgray --euler --ctab
/usr/local/freesurfer/ASegStatsLUT.txt --subject test001
sysname  Linux
hostname mikbox
machine  x86_64
user amiklos
UseRobust  0
atlas_icv (eTIV) = 1444225 mm^3(det: 1.348893 )
*mghRead(/home/amiklos/nethome/work/METHODS/FS/subjects/test001/mri/ribbon.mgz,
-1): could not open file*

I am not sure but the bug seems that autorecon2 tries to run SegStats too
early (supposed to be in autorecon3).

Maybe this is the error in recon-all:
case "-autorecon2":
  set DoGCAReg = 1;
  set DoCARegInv   = 1;
  set DoRemoveNeck = 1;
  set DoSkullLTA   = 1;
  set DoCANormalize= 1;
  set DoCAReg  = 1;
  set DoCALabel= 1;
 * set DoSegStats   = 1;*
  set DoNormalization2 = 1;
  set DoMaskBFS= 1;
  set DoSegmentation   = 1;
  set DoFill   = 1;
  set DoTessellate = 1;
  set DoSmooth1= 1;
  set DoInflate1   = 1;
  set DoQSphere= 1;
  set DoFix= 1;
  set DoSmooth2= 1;
  set DoInflate2   = 1;
  set DoWhiteSurfs = 1;
  set DoCurvStats  = 1;
  breaksw

Could some expert verify please that this is indeed the problem and I can
change the 1 to zero, or am I completely off?

Miklos
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Re: [Freesurfer] A problem while doing retinotopy by freesurfer

[Douglas Greve]

Hi Yufeng, it cannot handle only a single run. You must have both polar 
and eccen. You can "fool" it by copying your polar run into another run 
and calling it eccen.
doug
ps. Please remember to send email to the list and not to me personally. 
Thanks!



On 4/16/13 11:02 AM, yuf...@mail.ustc.edu.cn wrote:
> Hi Doug,
>   Thank you for your patient. I am doing retinotopy analysis by using 
> freesurfer 5.1 with the help of the webside 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . 
> And my problem is as followed while doing
> selxavg3-sess -s Sess01 -a fmcpr.sm5.self.lh.nii.gz
> My mmkanalysis-sess code is as followed:
> mmkanalysis-sess -fsd bold -stc odd -surface self lh -fwhm 5 -retinotopy 32 
> -paradigm rtopy.par -analysis fmcpr.sm5.self.lh.nii.gz -TR 2
>
> Error information
> Saving X matrix to 
> /usr/local/freesurfer/stable5/retinotopy_002/Sess01/bold/fmcpr.odd.sm5.fsaverage.lh.nii.gz/Xtmp.mat
> ??? Error using ==> svd
> Input to SVD must not contain NaN or Inf.
>
> Error in ==> cond at 40
> s = svd(A);
>
> Error in ==> fast_selxavg3 at 254
>XCond = cond(XtX);
>   
>>> --
> ERROR: fast_selxavg3() failed\n
>   
>   I just have one run and the rtopy.par is
> stimtype polar
>
> direction neg
>   
> I attach the analysis.info and Xtmp.mat on the email. Thanks very much.
>   
>Yours Yufeng
>   
> 

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Re: [Freesurfer] QDEC questions

[Douglas Greve]

For #2, it is hard to say without seeing the design. I would not say 
that covariates should not change the results (otherwise one would not 
add them), especially age. If you have a balanced design, then one would 
hope that adding age would reduce the residual noise and show more of an 
effect. But if you have a very narrow age range, then "age" can look 
like a constant which would be colinear with the actual group 
designations and so reduce activation.
doug



On 4/15/13 5:52 PM, Nick Schmansky wrote:
> Tudor,
>
> In the recon-all.log, it has this line:
> ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
>
> but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
> correctly, so this indicates to me that it might have run out of disk
> space.  is that the case?
>
> to answer the others:
> 2. not sure
> 3. you can select discrete can a regular variate along with your main
> variate.  'nuisance' variates are like any other.
> 4. depends on the expected 'blob' size
> 5. the selection of fwhm in qdec corresponds directly with the values
> selected by qcache (they are one-to-one related, ie the 10mm fwhm values
> created by qcache are used by the 10mm fwhm selection in qdec).
>
> Nick
>
>
>
> On Mon, 2013-04-15 at 18:38 +0200, Tudor Popescu wrote:
>> Dear experts,
>>
>> Upgrading to 5.2.0 stopped QDEC (specifically, mri_concat) from
>> misbehaving, and so after running a first whole-brain group cortical
>> thickness analysis on my structural data, I have some questions:
>>
>> 1. After running recon-all with the –qcache flag (i.e. presmoothing),
>> files of the type lh.thickness.*.mgh were created for all 38 subjects
>> (19 in each group), however files of the type rh.thickness.*.mgh were
>> not created for 5 out of the 19 subjects of the first group. Log files
>> recon-all-status.log and recon-all.log (attached, for one of those 5
>> subjects) both mention that the process ran on Mar22nd ended with
>> errors, although I can't quite see what that was
>>
>>
>>
>> 2. When I take age as a continuous factor (covariate), the list of
>> clusters in my results look dramatically different from the clusters
>> that I get for the same contrast ran without the covariate. Why is
>> that, given that normally adding a covariate very rarely changes the
>> results by a great deal? Also in my case, I had quite a narrow (and
>> well-balanced between the groups) age range!
>>
>>   
>>
>> 3. I know that discrete factors cannot be taken as nuisance factors,
>> but it seems they also can't be taken as covariates. How does one,
>> then, control for the effects of e.g. gender in a group comparison?
>>
>>
>> 4. When should values other than 10 be used for the FWHM parameter of
>> the smoothing?
>>
>>
>> 5. How come QDEC allows you to set the FWHM parameter, when in fact it
>> is also set in the qcache stage of recon-all, which precedes QDEC?
>>
>>
>> Many thanks in advance!!
>>
>> Tudor
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Re: [Freesurfer] mkbrainmask error with libmeshclass.so

[Douglas Greve]

Hi Corinna, I hate to pass the buck, but I think you'll have to contact 
the FSL people to get it sorted out.

doug


On 4/16/13 9:31 AM, Corinna Bauer wrote:
Yes, if I just type bet2 I still get: libmeshclass.so: cannot open 
shared object file: No such file or directory.




On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Hi Corinna, if you just run bet2 at the command line, do you get the
same error?
doug

On 04/12/2013 03:56 PM, Corinna Bauer wrote:
> Hello all, when running preproc-sess, I got this error message:
> ERROR: could not determine file for
>
/usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain
> Try running mkbrainmask-sess with -per-run
>
> I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s .
-d .
> -fsd bold
> m) and got the output below, which shows a problem with a shared
library?
>
> Any suggestions?
>
> Corinna
>
> 
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test
> Fri Apr 12 15:53:14 EDT 2013
> mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1
-ndil
> 1 -nerode 0
> FSLMATHS fslmaths.fsl
> Scratch Dir is /tmp/mkbrainmask_9634
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
> mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from template.nii.gz...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.996119, -0.0108587, 0.0873391)
> j_ras = (0.000562893, 0.991553, 0.129698)
> k_ras = (0.0880098, -0.129244, 0.9877)
> writing to /tmp/mkbrainmask_9634/in.nii...
> # -- Using FSL's BET to Extract Brain-- #
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain
-m -f 0.1
> /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries:
> libmeshclass.so: cannot open shared object file: No such file or
directory
> mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o
> /tmp/mkbrainmask_9634/brain_mask.nii
> niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
>
> $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
> cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min
> .01 --o /tmp/mkbrainmask_9634/brain_mask.nii
> sysname  Linux
> hostname lotfi
> machine  x86_64
> user bauer
>
> input  /tmp/mkbrainmask_9634/brain_mask.nii
> frame  0
> nErode3d   0
> nErode2d   0
> output /tmp/mkbrainmask_9634/brain_mask.nii
> Binarizing based on threshold
> min0.01
> max+infinity
> binval1
> binvalnot 0
>
>
>
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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

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Re: [Freesurfer] 5.2 pial surfaces

[Yang, Daniel]

Dear Bruce,

Thanks so much again for improving it.

When looking at the pial surfaces, I noticed that sometimes the pial
surfaces and the main surfaces are entangled in 5.2 (but it seems less so
in 5.1).

Here are two slides
(https://dl.dropboxusercontent.com/u/65918007/FS%205.2.pptx) with this
version difference indicated by the yellow arrows.

If 5.2 can be improved to automatically disentangle these surfaces like in
5.1, that would be really really nice!!

Thanks!!
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454






On 4/16/13 10:44 AM, "Bruce Fischl"  wrote:

>glad to hear it
>Bruce
>On Tue, 16 Apr 2013, Yang, Daniel wrote:
>
>> Thanks so much for the improvement!
>>
>> I ran the new mris_make_surfaces and the pial surfaces look much better
>>in
>> FS 5.2!
>>
>> Here is the comparison slice if you're interested.
>>
>> https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>>
>>
>> Best,
>> Daniel
>>
>>
>
>
>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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Re: [Freesurfer] 5.2 pial surfaces

[Bruce Fischl]

glad to hear it
Bruce
On Tue, 16 Apr 2013, Yang, Daniel wrote:

> Thanks so much for the improvement!
>
> I ran the new mris_make_surfaces and the pial surfaces look much better in
> FS 5.2!
>
> Here is the comparison slice if you're interested.
>
> https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>
>
> Best,
> Daniel
>
>
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Re: [Freesurfer] 5.2 pial surfaces

[Yang, Daniel]

Thanks so much for the improvement!

I ran the new mris_make_surfaces and the pial surfaces look much better in
FS 5.2!

Here is the comparison slice if you're interested.

https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn


Best,
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454




>
>Date: Sat, 13 Apr 2013 22:36:32 -0400 (EDT)
>From: Bruce Fischl 
>Subject: [Freesurfer] 5.2 pial surfaces
>To: freesurfer@nmr.mgh.harvard.edu
>
>
>Hi All
>
>we've tracked down the problem with 5.2 pial surfaces that affects some
>types of acquisitions. We will be testing the fixed version this week and
>hope to release a corrected mris_make_surfaces in the near future. You
>should just be able to rerun autorecon2 I believe to update your surfaces
>and not the whole recon pipeline, but we'll make a more detailed
>announcement when we are ready with it. Anyone who has had problems with
>the 5.2 pial surfaces (or anyone else for that matter) is welcome to try
>it 
>out. Just let us know your hardware/software environment and we'll send
>you 
>a version.
>
>Sorry for the problems.
>
>cheers
>Bruce
>
>


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Re: [Freesurfer] mkbrainmask error with libmeshclass.so

[Corinna Bauer]

Yes, if I just type bet2 I still get: libmeshclass.so: cannot open shared
object file: No such file or directory.



On Fri, Apr 12, 2013 at 4:07 PM, Douglas N Greve
wrote:

> Hi Corinna, if you just run bet2 at the command line, do you get the
> same error?
> doug
>
> On 04/12/2013 03:56 PM, Corinna Bauer wrote:
> > Hello all, when running preproc-sess, I got this error message:
> > ERROR: could not determine file for
> >
> /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold/masks/brain
> > Try running mkbrainmask-sess with -per-run
> >
> > I then ran the mkbrainmask-sess as follows (kbrainmask-sess -s . -d .
> > -fsd bold
> > m) and got the output below, which shows a problem with a shared library?
> >
> > Any suggestions?
> >
> > Corinna
> >
> > 
> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test
> > Fri Apr 12 15:53:14 EDT 2013
> > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil
> > 1 -nerode 0
> > FSLMATHS fslmaths.fsl
> > Scratch Dir is /tmp/mkbrainmask_9634
> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
> > mri_convert template.nii.gz /tmp/mkbrainmask_9634/in.nii
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> > reading from template.nii.gz...
> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> > i_ras = (-0.996119, -0.0108587, 0.0873391)
> > j_ras = (0.000562893, 0.991553, 0.129698)
> > k_ras = (0.0880098, -0.129244, 0.9877)
> > writing to /tmp/mkbrainmask_9634/in.nii...
> > # -- Using FSL's BET to Extract Brain-- #
> > /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> > bet.fsl /tmp/mkbrainmask_9634/in.nii /tmp/mkbrainmask_9634/brain -m -f
> 0.1
> > /usr/share/fsl/5.0/bin/bet2: error while loading shared libraries:
> > libmeshclass.so: cannot open shared object file: No such file or
> directory
> > mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min .01 --o
> > /tmp/mkbrainmask_9634/brain_mask.nii
> > niiRead(): error opening file /tmp/mkbrainmask_9634/brain_mask.nii
> >
> > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
> > cwd /usr/local/freesurfer/subjects/symmetry/lindsay/first_test/bold
> > cmdline mri_binarize --i /tmp/mkbrainmask_9634/brain_mask.nii --min
> > .01 --o /tmp/mkbrainmask_9634/brain_mask.nii
> > sysname  Linux
> > hostname lotfi
> > machine  x86_64
> > user bauer
> >
> > input  /tmp/mkbrainmask_9634/brain_mask.nii
> > frame  0
> > nErode3d   0
> > nErode2d   0
> > output /tmp/mkbrainmask_9634/brain_mask.nii
> > Binarizing based on threshold
> > min0.01
> > max+infinity
> > binval1
> > binvalnot 0
> >
> >
> >
> > ___
> > 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
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>
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Re: [Freesurfer] pial surface with FLAIR

[Bruce Fischl]

ok, then I don't see what's going wrong. Nick: any thoughts?

On Tue, 16 Apr 
2013, Popescu, Veronica wrote:

>
> Dear Bruce,
> I ran the follwing:
> autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all.
> And my file was indeed a 3D T1 scan.
> Thank you very much!
> Best wishes,
> Veronica
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Tuesday, 16 April, 2013 15:02
> To: Popescu, Veronica
> Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu'
> Subject: RE: [Freesurfer] pial surface with FLAIR
>
> Hi Veronica
>
> what recon-all command lines did you run? You did run it with a T1 first, 
> right?
>
> Bruce
> On Tue, 16 Apr 2013, Popescu, Veronica wrote:
>
>> Hi, Christopher!
>> Best of luck to you all in these difficult times!
>> Thank you very much for your advice. I'll try this as well.
>> Best wishes,
>> Veronica
>>
>> -Original Message-
>> From: Watson, Christopher
>> [mailto:christopher.wat...@childrens.harvard.edu]
>> Sent: Tuesday, 16 April, 2013 07:15
>> To: Bruce Fischl; Popescu, Veronica
>> Cc: 'freesurfer@nmr.mgh.harvard.edu'
>> Subject: RE: [Freesurfer] pial surface with FLAIR
>>
>> Hi Veronica,
>> Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
>> And then, when you do the remaining recon-all steps:
>>
>> recon-all -autorecon3 -s $SUBJECT -FLAIRpial
>>
>> It has worked for me. (And worked very well! No edits necessary for
>> the pial surface!) 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, April 15, 2013 12:31 PM
>> To: Popescu, Veronica
>> Cc: 'freesurfer@nmr.mgh.harvard.edu'
>> Subject: Re: [Freesurfer] pial surface with FLAIR
>>
>> Hi Veronica,
>>
>> we haven't seen that before. Can you upload your subject including the FLAIR 
>> and we'll take a look?
>>
>> thanks
>> Bruce
>>
>> On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>>
>>>
>>> Dear all,
>>>
>>> I have already run the FreeSurfer 5.2 -all, and I would like to
>>> improve the pial surface recongition using the FLAIR. From the
>>> $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following 
>>> syntax:
>>>
>>> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>>>
>>> It starts running but then it hangs, I never get an output. The FLAIR
>>> file is in nifti format.
>>>
>>> I am not sure what I am doing wrong: it is the syntax? Should I first
>>> convert the FLAIR file to .mgz?
>>>
>>> Thank you in advance for the help!
>>>
>>> Veronica Popescu, MD, MSc
>>> Department of Radiology & Nuclear Medicine VU University Medical
>>> Center Amsterdam, The Netherlands
>>>
>>>
>>
>>
>>
>
>
> 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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Re: [Freesurfer] pial surface with FLAIR

[Popescu, Veronica]

Dear Bruce,
I ran the follwing: 
autorecon-all -cw256 -bigventricles -i $FILENAME -subjid $SUBJ_ID -all. 
And my file was indeed a 3D T1 scan. 
Thank you very much!
Best wishes,
Veronica

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Tuesday, 16 April, 2013 15:02
To: Popescu, Veronica
Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu'
Subject: RE: [Freesurfer] pial surface with FLAIR

Hi Veronica

what recon-all command lines did you run? You did run it with a T1 first, right?

Bruce
On Tue, 16 Apr 2013, Popescu, Veronica wrote:

> Hi, Christopher!
> Best of luck to you all in these difficult times!
> Thank you very much for your advice. I'll try this as well.
> Best wishes,
> Veronica
>
> -Original Message-
> From: Watson, Christopher 
> [mailto:christopher.wat...@childrens.harvard.edu]
> Sent: Tuesday, 16 April, 2013 07:15
> To: Bruce Fischl; Popescu, Veronica
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: RE: [Freesurfer] pial surface with FLAIR
>
> Hi Veronica,
> Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
> And then, when you do the remaining recon-all steps:
>
> recon-all -autorecon3 -s $SUBJECT -FLAIRpial
>
> It has worked for me. (And worked very well! No edits necessary for 
> the pial surface!) 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, April 15, 2013 12:31 PM
> To: Popescu, Veronica
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] pial surface with FLAIR
>
> Hi Veronica,
>
> we haven't seen that before. Can you upload your subject including the FLAIR 
> and we'll take a look?
>
> thanks
> Bruce
>
> On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>
>>
>> Dear all,
>>
>> I have already run the FreeSurfer 5.2 -all, and I would like to 
>> improve the pial surface recongition using the FLAIR. From the 
>> $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following 
>> syntax:
>>
>> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>>
>> It starts running but then it hangs, I never get an output. The FLAIR 
>> file is in nifti format.
>>
>> I am not sure what I am doing wrong: it is the syntax? Should I first 
>> convert the FLAIR file to .mgz?
>>
>> Thank you in advance for the help!
>>
>> Veronica Popescu, MD, MSc
>> Department of Radiology & Nuclear Medicine VU University Medical 
>> Center Amsterdam, The Netherlands
>>
>>
>
>
>


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 
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Re: [Freesurfer] pial surface with FLAIR

[Bruce Fischl]

Hi Veronica

what recon-all command lines did you run? You did run it with a T1 first, 
right?

Bruce
On Tue, 16 Apr 2013, Popescu, Veronica wrote:

> Hi, Christopher!
> Best of luck to you all in these difficult times!
> Thank you very much for your advice. I'll try this as well.
> Best wishes,
> Veronica
>
> -Original Message-
> From: Watson, Christopher [mailto:christopher.wat...@childrens.harvard.edu]
> Sent: Tuesday, 16 April, 2013 07:15
> To: Bruce Fischl; Popescu, Veronica
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: RE: [Freesurfer] pial surface with FLAIR
>
> Hi Veronica,
> Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
> And then, when you do the remaining recon-all steps:
>
> recon-all -autorecon3 -s $SUBJECT -FLAIRpial
>
> It has worked for me. (And worked very well! No edits necessary for the pial 
> surface!) 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, April 15, 2013 12:31 PM
> To: Popescu, Veronica
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] pial surface with FLAIR
>
> Hi Veronica,
>
> we haven't seen that before. Can you upload your subject including the FLAIR 
> and we'll take a look?
>
> thanks
> Bruce
>
> On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>
>>
>> Dear all,
>>
>> I have already run the FreeSurfer 5.2 -all, and I would like to
>> improve the pial surface recongition using the FLAIR. From the
>> $SUBJECTS_DIR (where I have also placed the FLAIR file) I use the following 
>> syntax:
>>
>> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>>
>> It starts running but then it hangs, I never get an output. The FLAIR
>> file is in nifti format.
>>
>> I am not sure what I am doing wrong: it is the syntax? Should I first
>> convert the FLAIR file to .mgz?
>>
>> Thank you in advance for the help!
>>
>> Veronica Popescu, MD, MSc
>> Department of Radiology & Nuclear Medicine VU University Medical
>> Center Amsterdam, The Netherlands
>>
>>
>
>
>
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] pial surface with FLAIR

[Bruce Fischl]

you shouldn't be running the initial recon with a flair volume though, 
are you? That would utterly fail I would think
Bruce
On Tue, 16 Apr 2013, Watson, 
Christopher wrote:

> Hi Veronica,
> Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
> And then, when you do the remaining recon-all steps:
>
> recon-all -autorecon3 -s $SUBJECT -FLAIRpial
>
> It has worked for me. (And worked very well! No edits necessary for the pial 
> surface!)
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, April 15, 2013 12:31 PM
> To: Popescu, Veronica
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] pial surface with FLAIR
>
> Hi Veronica,
>
> we haven't seen that before. Can you upload your subject including the
> FLAIR and we'll take a look?
>
> thanks
> Bruce
>
> On Mon, 15 Apr 2013, Popescu, Veronica wrote:
>
>>
>> Dear all,
>>
>> I have already run the FreeSurfer 5.2 -all, and I would like to improve the
>> pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
>> have also placed the FLAIR file) I use the following syntax:
>>
>> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>>
>> It starts running but then it hangs, I never get an output. The FLAIR file
>> is in nifti format.
>>
>> I am not sure what I am doing wrong: it is the syntax? Should I first
>> convert the FLAIR file to .mgz?
>>
>> Thank you in advance for the help!
>>
>> Veronica Popescu, MD, MSc
>> Department of Radiology & Nuclear Medicine
>> VU University Medical Center
>> Amsterdam, The Netherlands
>>
>>
>
>
>
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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
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