Re: [Freesurfer] Tracula_weighted dti metrics values

[Anastasia Yendiki]

Hi Karuna - I haven't seen this before. Can you check which version of 
freeview you have? Is it the one that came with freesurfer 5.3 or a newer 
version of freeview that you downloaded separately from the web site?


a.y

On Thu, 28 Jan 2016, Karuna Subra wrote:


HI Anastasia,

I'm new to tracula.  I was able to get the stats of each diffusion parameter 
for each tract, as shown
below.  However, when I try and use waypoint in freeview to display the mean 
paths, using the command here:

freeview -w 
/data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt

I get the below error.  Please let me know if you have any ideas as to what 
could be wrong here. 

Thanks very much.

Karuna

advaita.129> cd /data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/
advaita.130> ls *.path.mean.txt
fmajor_PP.avg33_mni_bbr.path.mean.txt  lh.cst_AS.avg33_mni_bbr.path.mean.txt  
rh.atr_PP.avg33_mni_bbr.path.mean.txt  rh.slfp_PP.avg33_mni_bbr.path.mean.txt
fminor_PP.avg33_mni_bbr.path.mean.txt  lh.ilf_AS.avg33_mni_bbr.path.mean.txt  
rh.cab_PP.avg33_mni_bbr.path.mean.txt  rh.slft_PP.avg33_mni_bbr.path.mean.txt
lh.atr_PP.avg33_mni_bbr.path.mean.txt  lh.slfp_PP.avg33_mni_bbr.path.mean.txt 
rh.ccg_PP.avg33_mni_bbr.path.mean.txt  rh.unc_AS.avg33_mni_bbr.path.mean.txt
lh.cab_PP.avg33_mni_bbr.path.mean.txt  lh.slft_PP.avg33_mni_bbr.path.mean.txt 
rh.cst_AS.avg33_mni_bbr.path.mean.txt
lh.ccg_PP.avg33_mni_bbr.path.mean.txt  lh.unc_AS.avg33_mni_bbr.path.mean.txt  
rh.ilf_AS.avg33_mni_bbr.path.mean.txt



advaita.131> freeview -w 
/data/bil-mb2/fMRI/CAST/all_freesurfer_subjectsdir/stats/*.path.mean.txt

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try
http://valgrind.org on linux or man libgmalloc on Apple to find memory 
corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision:
4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named advaita.radiology.ucsf.edu by 
karunas Thu Jan 28 21:33:23
2016
[0]PETSC ERROR: Libraries linked 
from/autofs/space/lyon_006/pubsw/Linux2-2.3-i386/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-
opt
[0]PETSC ERROR: Configure run at Mon Jun 16 12:09:46 2008
[0]PETSC ERROR: Configure options --with-debugging=0 --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0
--download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 
--with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0


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Re: [Freesurfer] tracula quality assessment dwi_motion.txt units

[Anastasia Yendiki]

That's correct!

On Wed, 27 Jan 2016, Ruth Carper wrote:


Anastasia,

Thanks for the quick reply.
And millimeters for the translation?


Ruth 

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Re: [Freesurfer] Wm correction

[maryam koochaki]

Hi Bruce,I uploaded yesterday.
best,
Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Friday, January 29, 2016 5:47 AM, Bruce Fischl 
 wrote:
 

 sure, let us know after you have uploaded it.

Bruce
On Fri, 29 Jan 2016, maryam 
koochaki wrote:

> Thanks, I also have another major problem with the subjects I am working on.
> Two of the subjects intend to freeze at #@# Fix Topology rh step while
> running reconstruction process.
> CORRECTING DEFECT 12 (vertices=29993, convex hull=7603)
> 
> I will upload one of the subjects to your ftp site, if you could take a look
> to see what is the defect.
> Really appreciate your help in advance,
> 
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
> 
> 
> 
> 
> On Thursday, January 28, 2016 5:51 PM, Bruce Fischl
>  wrote:
> 
> 
> Hi Maryam
> We are working hard to get it out, but it's not quite ready yet. We will
> make an announcement when we have a beta version
> Bruce
> 
> On Jan 28, 2016, at 8:25 PM, maryam koochaki 
> wrote:
>
>      Hi Bruce,
> How can I download version 6?
> 
> 
> Best,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
> 
> 
> On Thursday, January 28, 2016 5:55 AM, Bruce Fischl
>  wrote:
> 
> 
> Hi Maryam
> 
> have you look at the aseg? I suspect that it didn't properly handle
> the
> very large ventricles in this subject. Try manually editing it. V6
> handles this kind of thing significantly better
> 
> cheers
> Bruce
> On Thu, 28 Jan 2016, maryam
> koochaki wrote:
> 
> > Hi Bruce,
> > I am editing a brain with Freesurfer version 5.3. I have a issue in
> Lateral
> > Ventricle. As you can see in the image attached, the big part is
> excluded in
> > both hemisphere. I tried to fill it by editing wm volume but the
> problem
> > still exists.
> > Do you have any suggestion?
> > Thanks,
> > Maryam
> >  
> >
> >
> >
> >
> >
> >
> >
> >
> >
> 
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Re: [Freesurfer] HSF in 5.3

[Alan Francis]

Works beautifully - Thanks so much Eugenio. Have a great weekend.

On Fri, Jan 29, 2016 at 10:33 AM, Eugenio Iglesias 
wrote:

> Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID
> of the analysis:
>
> quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt
>
> Let me know if it doesn't work!
>
> Cheers,
>
> /Eugenio
>
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Alan Francis" 
> *To: *"Eugenio Iglesias" , "Freesurfer support list" <
> freesurfer@nmr.mgh.harvard.edu>
> *Sent: *Friday, January 29, 2016 4:17:06 PM
>
> *Subject: *Re: HSF in 5.3
>
> Hi Eugenio:
>
> Here is the list of files in the 'mri' directory of a given subject:
>
> afrancis-mac:HSF afrancis$ cd Smoke_d004/
> afrancis-mac:Smoke_d004 afrancis$ cd mri
> afrancis-mac:mri afrancis$ ls -la
> total 93464
> drwxrwxr-x  47 afrancis  staff  1598 Dec 23 01:05 .
> drwxr-xr-x  13 afrancis  staff   442 Dec 22 13:14 ..
> -rw-r--r--@  1 afrancis  staff  6148 Dec 18 15:11 .DS_Store
> -rwxrw-rw-   1 afrancis  staff 0 Dec  8 16:52 .xdebug_mris_calc
> -rw-rw-r--   1 afrancis  staff   5497095 Dec 22 13:25 T1.mgz
> -rw-rw-r--   1 afrancis  staff387540 Dec 22 23:27 aparc+aseg.mgz
> -rw-rw-r--   1 afrancis  staff418008 Dec 22 23:29 aparc.a2009s+aseg.mgz
> -rw-rw-r--   1 afrancis  staff223392 Dec 22 17:35 aseg.auto.mgz
> -rw-rw-r--   1 afrancis  staff  1545 Dec 22 17:06
> aseg.auto_noCCseg.label_intensities.txt
> -rw-rw-r--   1 afrancis  staff222988 Dec 22 17:34 aseg.auto_noCCseg.mgz
> -rw-rw-r--   1 afrancis  staff328176 Dec 22 23:29 aseg.mgz
> -rw-rw-r--   1 afrancis  staff223419 Dec 22 23:25
> aseg.presurf.hypos.mgz
> -rw-rw-r--   1 afrancis  staff223392 Dec 22 17:35 aseg.presurf.mgz
> -rw-rw-r--   1 afrancis  staff   1245108 Dec 22 17:39 brain.finalsurfs.mgz
> -rw-rw-r--   1 afrancis  staff   1245108 Dec 22 17:39 brain.mgz
> -rw-rw-r--   1 afrancis  staff   1248043 Dec 22 13:43 brainmask.auto.mgz
> -rw-rw-r--   1 afrancis  staff   1248043 Dec 22 13:43 brainmask.mgz
> -rw-rw-r--   1 afrancis  staff482728 Dec 22 14:08 ctrl_pts.mgz
> -rw-rw-r--   1 afrancis  staff129128 Dec 22 17:43 filled.mgz
> -rw-rw-r--   1 afrancis  staff 69210 Dec 23 00:36
> lh.hippoSfLabels-T1.v10.T1space.mgz
> -rw-rw-r--   1 afrancis  staff 66085 Dec 23 00:36
> lh.hippoSfLabels-T1.v10.mgz
> -rw-rw-r--   1 afrancis  staff   286 Dec 23 00:36
> lh.hippoSfVolumes-T1.v10.txt
> -rw-rw-r--   1 afrancis  staff107428 Dec 22 23:13 lh.ribbon.mgz
> -rw-rw-r--   1 afrancis  staff 20564 Dec 22 13:51
> mri_nu_correct.mni.log
> -rw-rw-r--   1 afrancis  staff 17647 Dec 22 13:22
> mri_nu_correct.mni.log.bak
> -rw-rw-r--   1 afrancis  staff   1314015 Dec 22 14:08 norm.mgz
> -rw-rw-r--   1 afrancis  staff   3901730 Dec 22 13:51 nu.mgz
> -rw-rw-r--   1 afrancis  staff   2735369 Dec 22 16:29 nu_noneck.mgz
> drwxrwxr-x   3 afrancis  staff   102 Dec  8 15:38 orig
> -rw-rw-r--   1 afrancis  staff   6690110 Dec 22 13:14 orig.mgz
> -rw-rw-r--   1 afrancis  staff   6922353 Dec 22 13:22 orig_nu.mgz
> -rwxrw-r--   1 afrancis  staff  10717567 Dec 22 13:14 rawavg.mgz
> -rw-rw-r--   1 afrancis  staff 69132 Dec 23 01:05
> rh.hippoSfLabels-T1.v10.T1space.mgz
> -rw-rw-r--   1 afrancis  staff 62976 Dec 23 01:05
> rh.hippoSfLabels-T1.v10.mgz
> -rw-rw-r--   1 afrancis  staff   286 Dec 23 01:05
> rh.hippoSfVolumes-T1.v10.txt
> -rw-rw-r--   1 afrancis  staff109623 Dec 22 23:13 rh.ribbon.mgz
> -rw-rw-r--   1 afrancis  staff203963 Dec 22 23:13 ribbon.mgz
> -rw-rw-r--   1 afrancis  staff   119 Dec 22 17:40 segment.dat
> -rw-rw-r--   1 afrancis  staff  1545 Dec 22 15:02
> talairach.label_intensities.txt
> -rw-rw-r--   1 afrancis  staff   214 Dec 22 14:05 talairach.log
> -rw-rw-r--   1 afrancis  staff   214 Dec 22 13:42
> talairach_with_skull.log
> -rw-rw-r--   1 afrancis  staff   214 Dec 22 16:51
> talairach_with_skull_2.log
> drwxrwxr-x  13 afrancis  staff   442 Dec 22 17:35 transforms
> -rw-rw-r--   1 afrancis  staff382039 Dec 22 17:42 wm.asegedit.mgz
> -rw-rw-r--   1 afrancis  staff382750 Dec 22 17:42 wm.mgz
> -rw-rw-r--   1 afrancis  staff415355 Dec 22 17:41 wm.seg.mgz
> -rw-rw-r--   1 afrancis  staff435034 Dec 22 23:39 wmparc.mgz
>
> thank you,
>
> Alan
>
>
> On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias 
> wrote:
>
>> Hi Alan,
>> can you please list the files in the mri directory of any of the subjects
>> and send me the output?
>> Cheers,
>> Eugenio
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> --
>> *From: *"Alan Francis" 
>> *To: *"Eugenio Iglesias" 
>> *Cc: *"Freesurfer support list" 
>> *Sent: *Thursday, January 28, 2016 9:18:

Re: [Freesurfer] Reading values from overlays with PETcoreg

[Pradeep]

It worked! Thank you!
mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
gtmseg.mgz --reg output.lta --replace-file seg.replace251.list --rescale
251 --mgx 0.01 --o gtmpvcRcc.output

On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve  wrote:

> The problem is that --default-seg-merge merges the CC with WM, so you
> can't use that option, which means that you'll have to specify the rest
> of the default seg merge manually. You can do this with more --replace
> args or you can create a file. If you've been able to run mri_gtmpvc
> without the current replace, then it will create a replacement file in
> the aux folder. Get that, remove the 251 entry, and change the 252-255
> entries to point to 251
>
> On 01/29/2016 02:12 PM, Pradeep wrote:
> > Unfortunately, that did not fix the problem.
> >
> > Here is what I did
> > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors
> > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg  # no errors
> >
> > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251
> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o
> > gtmpvcrcc.output
> > Loading input t12pet.nii.gz
> >   done loading input 1 frames
> > ERROR: item 251 appears as both source and target seg id in
> > replacement list
> >
> > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> > cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri
> > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251
> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o
> > gtmpvcrcc.output
> > sysname  Linux
> > hostname
> > machine  x86_64
> > user
> > vgthresh   0.001000
> > nReplace   22
> > 0. 0. 0. 0. 0. 0.
> > 9 avail.processors, using 9
> > Creating output directory gtmpvcrcc.output
> > Loading seg for gtm gtmseg.mgz
> > Loading seg ctab gtmseg.ctab
> > Reading gtmseg.lta
> > Replacing 22
> > ERROR: CheckSegTissueType() no entry for seg 192
> > Failed tissue type check
> >
> > Thank you for looking into this,
> > Pradeep
> >
> >
> > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > I think I see the problem. When you run gtmseg, you need to add
> > --keep-cc. You can rerun it using the previous command line, but add
> > --keep-cc and --no-xcerseg. The second option tells it not to redo
> the
> > extracerebral segmentation (which won't change with CC)
> >
> > On 01/29/2016 11:21 AM, Pradeep wrote:
> > > Thank you for the response.
> > >
> > > Here is my full command log with error
> > >
> > >
> > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
> > >
> > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> > > gtmpvccc.output
> > > Loading input t12pet.nii.gz
> > >   done loading input 1 frames
> > >
> > > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> > > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> > > cd /analysis/software_test/fs6pvc/**/mri
> > > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> > > gtmpvccc.output
> > > sysname  Linux
> > > hostname server
> > > machine  x86_64
> > > user user
> > > vgthresh   0.001000
> > > nReplace   18
> > > 0. 0. 0. 0. 0. 0.
> > > 9 avail.processors, using 9
> > > Creating output directory gtmpvccc.output
> > > Loading seg for gtm gtmseg.mgz
> > > Loading seg ctab gtmseg.ctab
> > > Reading gtmseg.lta
> > > Replacing 18
> > > ERROR: CheckSegTissueType() no entry for seg 192
> > > Failed tissue type check
> > >
> > >
> > > Thanks,
> > > Pradeep
> > >
> > >
> > > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > >
> > >
> > > On 01/28/2016 06:50 PM, Pradeep wrote:
> > > > Hello Doug,
> > > >
> > > > I have used the gtmseg with --keep-cc flag and the
> > > corresponding ctab
> > > > files showed the labels but the mri_gtmpvc step failed.
> > > > 
> > > > Loading seg for gtm gtmseg.mgz
> > > > Loading seg ctab gtmseg.ctab
> > > > Reading gtmseg.lta
> > > > Replacing 18
> > > > ERROR: CheckSegTissueType() no entry for seg 192
> > > > Failed tissue type check
> > > > 
> > > What is your mri_gtmpvc command line? What is the rest of
> > the terminal
>

Re: [Freesurfer] Reading values from overlays with PETcoreg

[Douglas N Greve]

The problem is that --default-seg-merge merges the CC with WM, so you 
can't use that option, which means that you'll have to specify the rest 
of the default seg merge manually. You can do this with more --replace 
args or you can create a file. If you've been able to run mri_gtmpvc 
without the current replace, then it will create a replacement file in 
the aux folder. Get that, remove the 251 entry, and change the 252-255 
entries to point to 251

On 01/29/2016 02:12 PM, Pradeep wrote:
> Unfortunately, that did not fix the problem.
>
> Here is what I did
> 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors
> 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg  # no errors
>
> 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg 
> gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 
> --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o 
> gtmpvcrcc.output
> Loading input t12pet.nii.gz
>   done loading input 1 frames
> ERROR: item 251 appears as both source and target seg id in 
> replacement list
>
> $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri
> mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg 
> gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 
> --replace 253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o 
> gtmpvcrcc.output
> sysname  Linux
> hostname
> machine  x86_64
> user
> vgthresh   0.001000
> nReplace   22
> 0. 0. 0. 0. 0. 0.
> 9 avail.processors, using 9
> Creating output directory gtmpvcrcc.output
> Loading seg for gtm gtmseg.mgz
> Loading seg ctab gtmseg.ctab
> Reading gtmseg.lta
> Replacing 22
> ERROR: CheckSegTissueType() no entry for seg 192
> Failed tissue type check
>
> Thank you for looking into this,
> Pradeep
>
>
> On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I think I see the problem. When you run gtmseg, you need to add
> --keep-cc. You can rerun it using the previous command line, but add
> --keep-cc and --no-xcerseg. The second option tells it not to redo the
> extracerebral segmentation (which won't change with CC)
>
> On 01/29/2016 11:21 AM, Pradeep wrote:
> > Thank you for the response.
> >
> > Here is my full command log with error
> >
> >
> > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
> >
> > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> > gtmpvccc.output
> > Loading input t12pet.nii.gz
> >   done loading input 1 frames
> >
> > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> > cd /analysis/software_test/fs6pvc/**/mri
> > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> > gtmpvccc.output
> > sysname  Linux
> > hostname server
> > machine  x86_64
> > user user
> > vgthresh   0.001000
> > nReplace   18
> > 0. 0. 0. 0. 0. 0.
> > 9 avail.processors, using 9
> > Creating output directory gtmpvccc.output
> > Loading seg for gtm gtmseg.mgz
> > Loading seg ctab gtmseg.ctab
> > Reading gtmseg.lta
> > Replacing 18
> > ERROR: CheckSegTissueType() no entry for seg 192
> > Failed tissue type check
> >
> >
> > Thanks,
> > Pradeep
> >
> >
> > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> >
> > On 01/28/2016 06:50 PM, Pradeep wrote:
> > > Hello Doug,
> > >
> > > I have used the gtmseg with --keep-cc flag and the
> > corresponding ctab
> > > files showed the labels but the mri_gtmpvc step failed.
> > > 
> > > Loading seg for gtm gtmseg.mgz
> > > Loading seg ctab gtmseg.ctab
> > > Reading gtmseg.lta
> > > Replacing 18
> > > ERROR: CheckSegTissueType() no entry for seg 192
> > > Failed tissue type check
> > > 
> > What is your mri_gtmpvc command line? What is the rest of
> the terminal
> > output?
> > > My objective is to use the combination of all CC's as a
> reference
> > > region and obtain the PVC results, which would be listed in
> > gtm.stats.dat
> > It will be best to combine them when running mri_gtmpvc using
> > --replace,
> > eg, --replace 252 251 --replace 253 251 --replace 254 251
> > --replace 255 251
> > this will cause all segments of the CC to appear to be a single
> > 

Re: [Freesurfer] Reading values from overlays with PETcoreg

[Pradeep]

Unfortunately, that did not fix the problem.

Here is what I did
1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors
2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg  # no errors

3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace
253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output
Loading input t12pet.nii.gz
  done loading input 1 frames
ERROR: item 251 appears as both source and target seg id in replacement list

$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri
mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
gtmseg.mgz --reg output.lta --default-seg-merge --replace 252 251 --replace
253 251 --replace 254 251 --replace 255 251 --mgx 0.01 --o gtmpvcrcc.output
sysname  Linux
hostname
machine  x86_64
user
vgthresh   0.001000
nReplace   22
0. 0. 0. 0. 0. 0.
9 avail.processors, using 9
Creating output directory gtmpvcrcc.output
Loading seg for gtm gtmseg.mgz
Loading seg ctab gtmseg.ctab
Reading gtmseg.lta
Replacing 22
ERROR: CheckSegTissueType() no entry for seg 192
Failed tissue type check

Thank you for looking into this,
Pradeep


On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve  wrote:

> I think I see the problem. When you run gtmseg, you need to add
> --keep-cc. You can rerun it using the previous command line, but add
> --keep-cc and --no-xcerseg. The second option tells it not to redo the
> extracerebral segmentation (which won't change with CC)
>
> On 01/29/2016 11:21 AM, Pradeep wrote:
> > Thank you for the response.
> >
> > Here is my full command log with error
> >
> >
> > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
> >
> > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> > gtmpvccc.output
> > Loading input t12pet.nii.gz
> >   done loading input 1 frames
> >
> > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> > cd /analysis/software_test/fs6pvc/**/mri
> > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
> > gtmpvccc.output
> > sysname  Linux
> > hostname server
> > machine  x86_64
> > user user
> > vgthresh   0.001000
> > nReplace   18
> > 0. 0. 0. 0. 0. 0.
> > 9 avail.processors, using 9
> > Creating output directory gtmpvccc.output
> > Loading seg for gtm gtmseg.mgz
> > Loading seg ctab gtmseg.ctab
> > Reading gtmseg.lta
> > Replacing 18
> > ERROR: CheckSegTissueType() no entry for seg 192
> > Failed tissue type check
> >
> >
> > Thanks,
> > Pradeep
> >
> >
> > On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> >
> > On 01/28/2016 06:50 PM, Pradeep wrote:
> > > Hello Doug,
> > >
> > > I have used the gtmseg with --keep-cc  flag and the
> > corresponding ctab
> > > files showed the labels but the mri_gtmpvc step failed.
> > > 
> > > Loading seg for gtm gtmseg.mgz
> > > Loading seg ctab gtmseg.ctab
> > > Reading gtmseg.lta
> > > Replacing 18
> > > ERROR: CheckSegTissueType() no entry for seg 192
> > > Failed tissue type check
> > > 
> > What is your mri_gtmpvc command line? What is the rest of the
> terminal
> > output?
> > > My objective is to use the combination of all CC's as a reference
> > > region and obtain the PVC results, which would be listed in
> > gtm.stats.dat
> > It will be best to combine them when running mri_gtmpvc using
> > --replace,
> > eg, --replace 252 251 --replace 253 251 --replace 254 251
> > --replace 255 251
> > this will cause all segments of the CC to appear to be a single
> > segment
> > (251).
> > >
> > > Also, I read in the previous email discussions that the default
> > > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR
> with
> > > another ROI as a reference region,
> > > would it be OK take a ratio of the ROI's in gtm.stats.dat table.
> > Yes, or you can spec the new region, eg --rescale 251
> > >
> > > Thanks,
> > > Pradeep
> > >
> > > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > >
> > > If you want to use partial volume correction, then you are
> > better off
> > > using mri_gtmpvc with the bbr registration, something like
> > >
> > > 1. To start, run
> > >
> > > gtmseg --s subject
> > >
> > > This will take a couple of hours and produces some files needed
> > > for GTM
> > 

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh

[Douglas N Greve]

Hi Erik, please remember to include previous correspondence. Can you 
upload the file for me?

https://gate.nmr.mgh.harvard.edu/filedrop2


On 01/29/2016 02:17 AM, Erik Lindberg wrote:
> Dear Bruce and Freesurfer,
>
> Yes, that is what I am saying! This what appears in the commandprompt 
> when running the command:
>
> input  cache.th13.abs.sig.cluster.mgh
> frame  0
> nErode3d   0
> nErode2d   0
> output thresholded.mgh
> Binarizing based on threshold
> min1.3
> max+infinity
> binval1
> binvalnot 0
> Found 12485 values in range
> Counting number of voxels
> Found 12485 voxels in final mask
> mri_binarize done
>
> Yet nothing is visible when I open the thresholded surface in tksurfer.
>
>
> previous:
>
> what was the command line and screen output of the binarization? And are
> you saying that pre-binarization you have locations that are above
> threshold, but they are set to 0 anyway?
>
>
>
> ___
> 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.

Re: [Freesurfer] Reading values from overlays with PETcoreg

[Douglas N Greve]

I think I see the problem. When you run gtmseg, you need to add 
--keep-cc. You can rerun it using the previous command line, but add 
--keep-cc and --no-xcerseg. The second option tells it not to redo the 
extracerebral segmentation (which won't change with CC)

On 01/29/2016 11:21 AM, Pradeep wrote:
> Thank you for the response.
>
> Here is my full command log with error
>
>
> $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
>
> $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg 
> gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o 
> gtmpvccc.output
> Loading input t12pet.nii.gz
>   done loading input 1 frames
>
> $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> cd /analysis/software_test/fs6pvc/**/mri
> mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg 
> gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o 
> gtmpvccc.output
> sysname  Linux
> hostname server
> machine  x86_64
> user user
> vgthresh   0.001000
> nReplace   18
> 0. 0. 0. 0. 0. 0.
> 9 avail.processors, using 9
> Creating output directory gtmpvccc.output
> Loading seg for gtm gtmseg.mgz
> Loading seg ctab gtmseg.ctab
> Reading gtmseg.lta
> Replacing 18
> ERROR: CheckSegTissueType() no entry for seg 192
> Failed tissue type check
>
>
> Thanks,
> Pradeep
>
>
> On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
>
> On 01/28/2016 06:50 PM, Pradeep wrote:
> > Hello Doug,
> >
> > I have used the gtmseg with --keep-cc  flag and the
> corresponding ctab
> > files showed the labels but the mri_gtmpvc step failed.
> > 
> > Loading seg for gtm gtmseg.mgz
> > Loading seg ctab gtmseg.ctab
> > Reading gtmseg.lta
> > Replacing 18
> > ERROR: CheckSegTissueType() no entry for seg 192
> > Failed tissue type check
> > 
> What is your mri_gtmpvc command line? What is the rest of the terminal
> output?
> > My objective is to use the combination of all CC's as a reference
> > region and obtain the PVC results, which would be listed in
> gtm.stats.dat
> It will be best to combine them when running mri_gtmpvc using
> --replace,
> eg, --replace 252 251 --replace 253 251 --replace 254 251
> --replace 255 251
> this will cause all segments of the CC to appear to be a single
> segment
> (251).
> >
> > Also, I read in the previous email discussions that the default
> > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with
> > another ROI as a reference region,
> > would it be OK take a ratio of the ROI's in gtm.stats.dat table.
> Yes, or you can spec the new region, eg --rescale 251
> >
> > Thanks,
> > Pradeep
> >
> > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > If you want to use partial volume correction, then you are
> better off
> > using mri_gtmpvc with the bbr registration, something like
> >
> > 1. To start, run
> >
> > gtmseg --s subject
> >
> > This will take a couple of hours and produces some files needed
> > for GTM
> > PVC (which is used for GTM, MG, RBV).
> >
> > 2. You'd then register the PET to the anatomical with bbregister
> > (probably with --t2 weighting). Make sure to save the output
> as an LTA
> > (--lta). I usually use the mean TAC as the input. You can do
> this in
> > parallel with #1.
> >
> > 3. You'd then run mri_gtmpvc, something like
> >
> > mri_gtmpvc --i pet.nii.gz --psf PSF --auto-mask PSF+2 .01 --seg
> > gtmseg.mgz
> > --reg reg.lta --default-seg-merge  --o gtmpvc.output
> >
> > PSF is the point-spread FWHM of the scanner; reg.lta is the
> > registration from #2. By default, this will scale by pons.
> The output
> > will be gtm.stats.dat and gtm.nii.gz. They both basically
> have the
> > same information. gtm.stats.dat is an easy to read text
> file. Where
> > each row is an ROI, something like:
> >
> > 9   17 Left-Hippocampus subcort_gm   473
> > 174.0831.406   0.1216
> >
> > 9 = nineth row
> > 17 = index for RO
> > Left-Hippocampus = name of ROI
> > subcort_gm = tissue class
> > 473 = number of PET voxels in the ROI
> > 174 = variance reduction factor for ROI (based on GLM/SGTM)
> > 1.406 = PVC uptake of ROI relative to Pons
> > 0.1216 = resdiual varaince across voxels in the ROI
> >
> > gtm.nii.gz is a nifti file with each "voxel" being an ROI.
> The value
> > is the PVC uptake 

Re: [Freesurfer] fast_selxavg3 error when Octave is used

[Douglas N Greve]

Does octave now have a version of textread? I looked over my notes and 
saw that it did not support it at one point, which I apparently forgot 
and put it into the code. Can't do much about your space issue

On 01/29/2016 11:37 AM, m.abouelya...@gmail.com wrote:
>
> Okaii, so I fixed that last issue by changing the version of octave 
> installed then I found I needed to install FSL also. Problem is… now 
> the virtual machine drive has run out of space…
>
> Sent from Mail  for 
> Windows 10
>
>
> *From: *m.abouelya...@gmail.com 
> *Sent: *Friday, January 29, 2016 12:01 PM
> *To: *Douglas Greve 
> *Subject: *RE: [Freesurfer] fast_selxavg3 error when Octave is used
>
> Are there any other paths that I need to add? because now I get 
> another error
>
> Extension format = nii.gz
>
> error: `textread' undefined near line 210 column 17
>
> error: evaluating argument list element number 1
>
> error: evaluating argument list element number 1
>
> error: called from:
>
> error: /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m at line 
> 210, column 10
>
> error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 
> 53, column 9
>
>
> *From: *Douglas Greve 
> *Sent: *Friday, January 29, 2016 11:41 AM
> *To: *m.abouelya...@gmail.com ; free 
> surfer 
> *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used
>
> yes
>
> On 1/28/16 9:31 PM, m.abouelya...@gmail.com 
>  wrote:
>
> I am running on the virtual machine where I don’t have MATLAB so I
> installed Octave…
>
> Maybe I should include the folder into the Octave path?
>
>
> *From: *Douglas Greve 
> *Sent: *Friday, January 29, 2016 11:27 AM
> *To: *m.abouelya...@gmail.com ;
> freesurfer@nmr.mgh.harvard.edu 
> *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is used
>
> Is that directory in your matlab path? does it run properly in matlab?
>
> On 1/28/16 8:36 PM, m.abouelya...@gmail.com
>  wrote:
>
> Yes, it exists in the location you mentioned…
>
>
> *From: *Douglas N Greve 
> *Sent: *Friday, January 29, 2016 2:27 AM
> *To: *freesurfer@nmr.mgh.harvard.edu
> 
> *Subject: *Re: [Freesurfer] fast_selxavg3 error when Octave is
> used
>
> Does fast_fileexists.m exist in $FREESURFER_HOME/fsfast/toolbox ?
>
> On 01/28/2016 07:16 AM, m.abouelya...@gmail.com
>  wrote:
>
> >
>
> > Since I am a windows user I got the Virtualbox version of
> FreeSurfer
>
> > and to use fs fast, I installed Octave on the virtual
> machine, I set
>
> > the environment variables and then when I run the command
>
> >
>
> > selxavg3-sess -analysis rtopy.lh -sf sessid
>
> >
>
> > which runs a retinotopy analysis, I get the following error:
>
> >
>
> > sxa3pwd = /usr/local/freesurfer/projects/retinotopy_xxx
>
> >
>
> > sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess
> -analysis
>
> > rtopy.lh -sf sessid
>
> >
>
> > error: `fast_fileexists' undefined near line 5 column 4
>
> >
>
> > --
>
> >
>
> > ERROR: fast_selxavg3() failed\n
>
> >
>
> > Any idea of the cause of this error and how to run around?
>
> >
>
> > Thank you,
>
> >
>
> >
>
> >
>
> > ___
>
> > 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.

[Freesurfer] Statistical analyses with QDEC

[Francesco Cardinale]

Dear Freesurfer experts,
I have some questions about statistical analyses.

How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX 
version, and its tool QDEC to compare cortical thickness between two groups. I 
would like to use age and sex as nuisance factors. No problem with the age, but 
I don’t see the sex in the list of usable variables if I code it as a 
categorical variable (male / female). On the opposite, If I code it as numbers 
(male = 1, female = 2) I can use it, but how can I declare that it is a factor 
and not a continuous numerical variable? I don’t want that “female” affects the 
fitting of the GLM with a value that means “male” * 2. 
What about the use of other morphometric properties as nuisance factors? For 
example, how could I use sulcality or LGI as nuisance factors? Is it possible 
to use more than one scalar simultaneously?
Similarly to question 2, is it possible to use home-made *.mgh scalars as a 
nuisance factors? How?
Do the command-line tools allow such analyses better than QDEC? Related to my 
questions, which features do they add?
In this field of interest, are there any major advantages coming with 
Freesurfer 6.0?
Thanks a lot and best regards

Cico___
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] Reading values from overlays with PETcoreg

[Pradeep]

Thank you for the response.

Here is my full command log with error


$gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc

$ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
gtmpvccc.output
Loading input t12pet.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
cd /analysis/software_test/fs6pvc/**/mri
mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
gtmseg.mgz --reg output.lta --default-seg-merge --mgx 0.01 --o
gtmpvccc.output
sysname  Linux
hostname server
machine  x86_64
user user
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
9 avail.processors, using 9
Creating output directory gtmpvccc.output
Loading seg for gtm gtmseg.mgz
Loading seg ctab gtmseg.ctab
Reading gtmseg.lta
Replacing 18
ERROR: CheckSegTissueType() no entry for seg 192
Failed tissue type check


Thanks,
Pradeep


On Thu, Jan 28, 2016 at 5:34 PM, Douglas N Greve 
wrote:

>
>
> On 01/28/2016 06:50 PM, Pradeep wrote:
> > Hello Doug,
> >
> > I have used the gtmseg with --keep-cc  flag and the corresponding ctab
> > files showed the labels but the mri_gtmpvc step failed.
> > 
> > Loading seg for gtm gtmseg.mgz
> > Loading seg ctab gtmseg.ctab
> > Reading gtmseg.lta
> > Replacing 18
> > ERROR: CheckSegTissueType() no entry for seg 192
> > Failed tissue type check
> > 
> What is your mri_gtmpvc command line? What is the rest of the terminal
> output?
> > My objective is to use the combination of all CC's as a reference
> > region and obtain the PVC results, which would be listed in gtm.stats.dat
> It will be best to combine them when running mri_gtmpvc using --replace,
> eg, --replace 252 251 --replace 253 251 --replace 254 251 --replace 255 251
> this will cause all segments of the CC to appear to be a single segment
> (251).
> >
> > Also, I read in the previous email discussions that the default
> > ref-region Pons is 'PVC'ed'. So if I want to calculate the SUVR with
> > another ROI as a reference region,
> > would it be OK take a ratio of the ROI's in gtm.stats.dat table.
> Yes, or you can spec the new region, eg --rescale 251
> >
> > Thanks,
> > Pradeep
> >
> > On Mon, Jan 11, 2016 at 9:25 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > If you want to use partial volume correction, then you are better off
> > using mri_gtmpvc with the bbr registration, something like
> >
> > 1. To start, run
> >
> > gtmseg --s subject
> >
> > This will take a couple of hours and produces some files needed
> > for GTM
> > PVC (which is used for GTM, MG, RBV).
> >
> > 2. You'd then register the PET to the anatomical with bbregister
> > (probably with --t2 weighting). Make sure to save the output as an
> LTA
> > (--lta). I usually use the mean TAC as the input. You can do this in
> > parallel with #1.
> >
> > 3. You'd then run mri_gtmpvc, something like
> >
> > mri_gtmpvc --i pet.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
> > gtmseg.mgz
> > --reg reg.lta --default-seg-merge  --o gtmpvc.output
> >
> > PSF is the point-spread FWHM of the scanner; reg.lta is the
> > registration from #2. By default, this will scale by pons. The output
> > will be gtm.stats.dat and gtm.nii.gz. They both basically have the
> > same information. gtm.stats.dat is an easy to read text file. Where
> > each row is an ROI, something like:
> >
> > 9   17 Left-Hippocampussubcort_gm   473
> > 174.0831.406   0.1216
> >
> > 9 = nineth row
> > 17 = index for RO
> > Left-Hippocampus = name of ROI
> > subcort_gm = tissue class
> > 473 = number of PET voxels in the ROI
> > 174 = variance reduction factor for ROI (based on GLM/SGTM)
> > 1.406 = PVC uptake of ROI relative to Pons
> > 0.1216 = resdiual varaince across voxels in the ROI
> >
> > gtm.nii.gz is a nifti file with each "voxel" being an ROI. The value
> > is the PVC uptake of ROI relative to Pons. These can easily be
> > concatenated together (mri_concat) and used as input to mri_glmfit
> > for group analysis.
> >
> >
> >
> >
> > On 01/08/2016 04:22 AM, Benjamin Spurny wrote:
> > > Dear Freesurfer experts!
> > >
> > > I am currently working on PET analysis using FS
> > >
> > > I coregistered my PET with the processed MR using bbregister,
> > > transfered it to a surface using mri_vol2surf
> > > and now createt an overlay in freeview with the lh.inflated and
> > used the
> > > labels from the lh.aparc.a2009s.annot file.
> > >
> > > In freeview i get the corresponding BP value for each vertex now
> but
> > > is there a way to get a list of vertices with the corresponding
> > BP value
> > > and the corresponding ROI this vertex belongs to?
> > > Or is

Re: [Freesurfer] HSF in 5.3

[Eugenio Iglesias]

Got it! All you need to do is to replace Smoke_e024 by T1, which is the ID of 
the analysis: 

quantifyHippocampalSubfields.sh T1 Nicotine_HSF.txt 

Let me know if it doesn't work! 

Cheers, 

/Eugenio 



Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Alan Francis"  
To: "Eugenio Iglesias" , "Freesurfer support list" 
 
Sent: Friday, January 29, 2016 4:17:06 PM 
Subject: Re: HSF in 5.3 

Hi Eugenio: 

Here is the list of files in the 'mri' directory of a given subject: 

afrancis-mac:HSF afrancis$ cd Smoke_d004/ 
afrancis-mac:Smoke_d004 afrancis$ cd mri 
afrancis-mac:mri afrancis$ ls -la 
total 93464 
drwxrwxr-x 47 afrancis staff 1598 Dec 23 01:05 . 
drwxr-xr-x 13 afrancis staff 442 Dec 22 13:14 .. 
-rw-r--r--@ 1 afrancis staff 6148 Dec 18 15:11 .DS_Store 
-rwxrw-rw- 1 afrancis staff 0 Dec 8 16:52 .xdebug_mris_calc 
-rw-rw-r-- 1 afrancis staff 5497095 Dec 22 13:25 T1.mgz 
-rw-rw-r-- 1 afrancis staff 387540 Dec 22 23:27 aparc+aseg.mgz 
-rw-rw-r-- 1 afrancis staff 418008 Dec 22 23:29 aparc.a2009s+aseg.mgz 
-rw-rw-r-- 1 afrancis staff 223392 Dec 22 17:35 aseg.auto.mgz 
-rw-rw-r-- 1 afrancis staff 1545 Dec 22 17:06 
aseg.auto_noCCseg.label_intensities.txt 
-rw-rw-r-- 1 afrancis staff 222988 Dec 22 17:34 aseg.auto_noCCseg.mgz 
-rw-rw-r-- 1 afrancis staff 328176 Dec 22 23:29 aseg.mgz 
-rw-rw-r-- 1 afrancis staff 223419 Dec 22 23:25 aseg.presurf.hypos.mgz 
-rw-rw-r-- 1 afrancis staff 223392 Dec 22 17:35 aseg.presurf.mgz 
-rw-rw-r-- 1 afrancis staff 1245108 Dec 22 17:39 brain.finalsurfs.mgz 
-rw-rw-r-- 1 afrancis staff 1245108 Dec 22 17:39 brain.mgz 
-rw-rw-r-- 1 afrancis staff 1248043 Dec 22 13:43 brainmask.auto.mgz 
-rw-rw-r-- 1 afrancis staff 1248043 Dec 22 13:43 brainmask.mgz 
-rw-rw-r-- 1 afrancis staff 482728 Dec 22 14:08 ctrl_pts.mgz 
-rw-rw-r-- 1 afrancis staff 129128 Dec 22 17:43 filled.mgz 
-rw-rw-r-- 1 afrancis staff 69210 Dec 23 00:36 
lh.hippoSfLabels-T1.v10.T1space.mgz 
-rw-rw-r-- 1 afrancis staff 66085 Dec 23 00:36 lh.hippoSfLabels-T1.v10.mgz 
-rw-rw-r-- 1 afrancis staff 286 Dec 23 00:36 lh.hippoSfVolumes-T1.v10.txt 
-rw-rw-r-- 1 afrancis staff 107428 Dec 22 23:13 lh.ribbon.mgz 
-rw-rw-r-- 1 afrancis staff 20564 Dec 22 13:51 mri_nu_correct.mni.log 
-rw-rw-r-- 1 afrancis staff 17647 Dec 22 13:22 mri_nu_correct.mni.log.bak 
-rw-rw-r-- 1 afrancis staff 1314015 Dec 22 14:08 norm.mgz 
-rw-rw-r-- 1 afrancis staff 3901730 Dec 22 13:51 nu.mgz 
-rw-rw-r-- 1 afrancis staff 2735369 Dec 22 16:29 nu_noneck.mgz 
drwxrwxr-x 3 afrancis staff 102 Dec 8 15:38 orig 
-rw-rw-r-- 1 afrancis staff 6690110 Dec 22 13:14 orig.mgz 
-rw-rw-r-- 1 afrancis staff 6922353 Dec 22 13:22 orig_nu.mgz 
-rwxrw-r-- 1 afrancis staff 10717567 Dec 22 13:14 rawavg.mgz 
-rw-rw-r-- 1 afrancis staff 69132 Dec 23 01:05 
rh.hippoSfLabels-T1.v10.T1space.mgz 
-rw-rw-r-- 1 afrancis staff 62976 Dec 23 01:05 rh.hippoSfLabels-T1.v10.mgz 
-rw-rw-r-- 1 afrancis staff 286 Dec 23 01:05 rh.hippoSfVolumes-T1.v10.txt 
-rw-rw-r-- 1 afrancis staff 109623 Dec 22 23:13 rh.ribbon.mgz 
-rw-rw-r-- 1 afrancis staff 203963 Dec 22 23:13 ribbon.mgz 
-rw-rw-r-- 1 afrancis staff 119 Dec 22 17:40 segment.dat 
-rw-rw-r-- 1 afrancis staff 1545 Dec 22 15:02 talairach.label_intensities.txt 
-rw-rw-r-- 1 afrancis staff 214 Dec 22 14:05 talairach.log 
-rw-rw-r-- 1 afrancis staff 214 Dec 22 13:42 talairach_with_skull.log 
-rw-rw-r-- 1 afrancis staff 214 Dec 22 16:51 talairach_with_skull_2.log 
drwxrwxr-x 13 afrancis staff 442 Dec 22 17:35 transforms 
-rw-rw-r-- 1 afrancis staff 382039 Dec 22 17:42 wm.asegedit.mgz 
-rw-rw-r-- 1 afrancis staff 382750 Dec 22 17:42 wm.mgz 
-rw-rw-r-- 1 afrancis staff 415355 Dec 22 17:41 wm.seg.mgz 
-rw-rw-r-- 1 afrancis staff 435034 Dec 22 23:39 wmparc.mgz 

thank you, 

Alan 


On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: 



Hi Alan, 
can you please list the files in the mri directory of any of the subjects and 
send me the output? 
Cheers, 
Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Alan Francis" < alandarkene...@gmail.com > 
To: "Eugenio Iglesias" < e.igles...@bcbl.eu > 
Cc: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > 
Sent: Thursday, January 28, 2016 9:18:46 PM 
Subject: Re: HSF in 5.3 

Hi Eugenio: 

As you advised, I ran the following command: 

afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024 
Nicotine_HSF.txt 
Gathering results from subjects in: 
/Users/afrancis/Desktop/Connectome/HSF/ 
Using the suffix name: 
Smoke_e024 
And writing them to: 
Nicotine_HSF.txt 

However, when I opened the Nicotine_HSF.txt, there was nothing there. The 
Subjects directory is the same folder. 

Please advice - thanks so much, 

Alan 

On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias < e.igles...@bcbl.eu > 
wrote: 

BQ_BEGIN

Hi Alan, 

Re: [Freesurfer] HSF in 5.3

[Alan Francis]

Hi Eugenio:

Here is the list of files in the 'mri' directory of a given subject:

afrancis-mac:HSF afrancis$ cd Smoke_d004/
afrancis-mac:Smoke_d004 afrancis$ cd mri
afrancis-mac:mri afrancis$ ls -la
total 93464
drwxrwxr-x  47 afrancis  staff  1598 Dec 23 01:05 .
drwxr-xr-x  13 afrancis  staff   442 Dec 22 13:14 ..
-rw-r--r--@  1 afrancis  staff  6148 Dec 18 15:11 .DS_Store
-rwxrw-rw-   1 afrancis  staff 0 Dec  8 16:52 .xdebug_mris_calc
-rw-rw-r--   1 afrancis  staff   5497095 Dec 22 13:25 T1.mgz
-rw-rw-r--   1 afrancis  staff387540 Dec 22 23:27 aparc+aseg.mgz
-rw-rw-r--   1 afrancis  staff418008 Dec 22 23:29 aparc.a2009s+aseg.mgz
-rw-rw-r--   1 afrancis  staff223392 Dec 22 17:35 aseg.auto.mgz
-rw-rw-r--   1 afrancis  staff  1545 Dec 22 17:06
aseg.auto_noCCseg.label_intensities.txt
-rw-rw-r--   1 afrancis  staff222988 Dec 22 17:34 aseg.auto_noCCseg.mgz
-rw-rw-r--   1 afrancis  staff328176 Dec 22 23:29 aseg.mgz
-rw-rw-r--   1 afrancis  staff223419 Dec 22 23:25 aseg.presurf.hypos.mgz
-rw-rw-r--   1 afrancis  staff223392 Dec 22 17:35 aseg.presurf.mgz
-rw-rw-r--   1 afrancis  staff   1245108 Dec 22 17:39 brain.finalsurfs.mgz
-rw-rw-r--   1 afrancis  staff   1245108 Dec 22 17:39 brain.mgz
-rw-rw-r--   1 afrancis  staff   1248043 Dec 22 13:43 brainmask.auto.mgz
-rw-rw-r--   1 afrancis  staff   1248043 Dec 22 13:43 brainmask.mgz
-rw-rw-r--   1 afrancis  staff482728 Dec 22 14:08 ctrl_pts.mgz
-rw-rw-r--   1 afrancis  staff129128 Dec 22 17:43 filled.mgz
-rw-rw-r--   1 afrancis  staff 69210 Dec 23 00:36
lh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  staff 66085 Dec 23 00:36
lh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  staff   286 Dec 23 00:36
lh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  staff107428 Dec 22 23:13 lh.ribbon.mgz
-rw-rw-r--   1 afrancis  staff 20564 Dec 22 13:51 mri_nu_correct.mni.log
-rw-rw-r--   1 afrancis  staff 17647 Dec 22 13:22
mri_nu_correct.mni.log.bak
-rw-rw-r--   1 afrancis  staff   1314015 Dec 22 14:08 norm.mgz
-rw-rw-r--   1 afrancis  staff   3901730 Dec 22 13:51 nu.mgz
-rw-rw-r--   1 afrancis  staff   2735369 Dec 22 16:29 nu_noneck.mgz
drwxrwxr-x   3 afrancis  staff   102 Dec  8 15:38 orig
-rw-rw-r--   1 afrancis  staff   6690110 Dec 22 13:14 orig.mgz
-rw-rw-r--   1 afrancis  staff   6922353 Dec 22 13:22 orig_nu.mgz
-rwxrw-r--   1 afrancis  staff  10717567 Dec 22 13:14 rawavg.mgz
-rw-rw-r--   1 afrancis  staff 69132 Dec 23 01:05
rh.hippoSfLabels-T1.v10.T1space.mgz
-rw-rw-r--   1 afrancis  staff 62976 Dec 23 01:05
rh.hippoSfLabels-T1.v10.mgz
-rw-rw-r--   1 afrancis  staff   286 Dec 23 01:05
rh.hippoSfVolumes-T1.v10.txt
-rw-rw-r--   1 afrancis  staff109623 Dec 22 23:13 rh.ribbon.mgz
-rw-rw-r--   1 afrancis  staff203963 Dec 22 23:13 ribbon.mgz
-rw-rw-r--   1 afrancis  staff   119 Dec 22 17:40 segment.dat
-rw-rw-r--   1 afrancis  staff  1545 Dec 22 15:02
talairach.label_intensities.txt
-rw-rw-r--   1 afrancis  staff   214 Dec 22 14:05 talairach.log
-rw-rw-r--   1 afrancis  staff   214 Dec 22 13:42
talairach_with_skull.log
-rw-rw-r--   1 afrancis  staff   214 Dec 22 16:51
talairach_with_skull_2.log
drwxrwxr-x  13 afrancis  staff   442 Dec 22 17:35 transforms
-rw-rw-r--   1 afrancis  staff382039 Dec 22 17:42 wm.asegedit.mgz
-rw-rw-r--   1 afrancis  staff382750 Dec 22 17:42 wm.mgz
-rw-rw-r--   1 afrancis  staff415355 Dec 22 17:41 wm.seg.mgz
-rw-rw-r--   1 afrancis  staff435034 Dec 22 23:39 wmparc.mgz

thank you,

Alan


On Thu, Jan 28, 2016 at 5:14 PM, Eugenio Iglesias 
wrote:

> Hi Alan,
> can you please list the files in the mri directory of any of the subjects
> and send me the output?
> Cheers,
> Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Alan Francis" 
> *To: *"Eugenio Iglesias" 
> *Cc: *"Freesurfer support list" 
> *Sent: *Thursday, January 28, 2016 9:18:46 PM
> *Subject: *Re: HSF in 5.3
>
> Hi Eugenio:
>
> As you advised, I ran the following command:
>
> afrancis-mac:HSF afrancis$ quantifyHippocampalSubfields.sh Smoke_e024
> Nicotine_HSF.txt
> Gathering results from subjects in:
>/Users/afrancis/Desktop/Connectome/HSF/
> Using the suffix name:
>Smoke_e024
> And writing them to:
>Nicotine_HSF.txt
>
> However, when I opened the Nicotine_HSF.txt, there was nothing there. The
> Subjects directory is the same folder.
>
> Please advice - thanks so much,
>
> Alan
>
> On Fri, Dec 11, 2015 at 12:51 PM, Eugenio Iglesias 
> wrote:
>
>> Hi Alan,
>> the subfield module is not present in 5.3; you'll need to download the
>> development version (or wait until 6.0 is released, which should be pretty
>> soon=.
>> Cheers,
>> Eugenio
>>
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal discla

Re: [Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Just to note for people who are interested:

It does seem that when voxel-to-ras determinant > 0, then the file is
neurological.

-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 1/26/16, 10:09 PM, "Yang, Daniel"  wrote:

>Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so
>it’s most likely to be radiological.
>
>Just curious, so determinant > 0 means neurological then?
>
>Daniel
>
>
>-- 
>Daniel Yang, Ph.D.
>Yale Child Study Center
>
>E-mail: daniel.yj.y...@yale.edu
>
>
>
>
>On 1/26/16, 4:26 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>Douglas N Greve" gr...@nmr.mgh.harvard.edu> wrote:
>
>>If the determinant is less than 0, then it is radiological (probably it
>>will be radiological).
>>
>>On 01/26/2016 04:20 PM, Yang, Daniel wrote:
>>> Dear Doug,
>>>
>>> Thanks for your reply. Is it possible to upload the raw DICOM to a
>>>server
>>> so that you can see if mri_convert is making the orientation in the
>>>output
>>> NII file neurological? I just want to make sure what my image
>>>orientation
>>> is and how mri_convert interacts with it.
>>>
>>> Many thanks!
>>> Daniel
>>>
>>>
>>
>>-- 
>>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/
>>
>>___
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>>
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>>z
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Re: [Freesurfer] Wm correction

[Bruce Fischl]

sure, let us know after you have uploaded it.

Bruce
On Fri, 29 Jan 2016, maryam 
koochaki wrote:



Thanks, I also have another major problem with the subjects I am working on.
Two of the subjects intend to freeze at #@# Fix Topology rh step while
running reconstruction process.
CORRECTING DEFECT 12 (vertices=29993, convex hull=7603)

I will upload one of the subjects to your ftp site, if you could take a look
to see what is the defect.
Really appreciate your help in advance,

Maryam
 






Regards,
Maryam Kouchakidivkolaei




On Thursday, January 28, 2016 5:51 PM, Bruce Fischl
 wrote:


Hi Maryam
We are working hard to get it out, but it's not quite ready yet. We will
make an announcement when we have a beta version
Bruce

On Jan 28, 2016, at 8:25 PM, maryam koochaki 
wrote:

  Hi Bruce,
How can I download version 6?


Best,
Maryam
 






Regards,
Maryam Kouchakidivkolaei


On Thursday, January 28, 2016 5:55 AM, Bruce Fischl
 wrote:


Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle
the
very large ventricles in this subject. Try manually editing it. V6
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in
Lateral
> Ventricle. As you can see in the image attached, the big part is
excluded in
> both hemisphere. I tried to fill it by editing wm volume but the
problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
>
>
>
>
>
>
>
>
>

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The information in this e-mail is intended only for the person to whom
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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