Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only

[Daniel Cole]

Hello again,
Don't mean to be a bother.  I was wondering if anyone had any thoughts on
what possibly be going wrong during my retinotopic analysis that I posted.
 I'm at quite a loss and would appreciate a look.

Thanks and best,
Daniel

On Fri, May 11, 2012 at 11:49 AM, Daniel Cole wrote:

> Hello,
> I have some questions regarding the FsFastIndividual pipeline.  I hope you
> can take a look at the commands I have run and give me some insight into
> what the problem might potentially be.  I have 5 rotating wedge stimuli runs
>
> 1. I set up my subject's directories according to the freesurfer tutorial
> powerpoint and declare my environmental variables using-
> <*export FREESURFER_HOME=/Volumes/RCBI/freesurfer*
> *export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy*
> *source $FREESURFER_HOME/SetUpFreeSurfer.sh*>
>
> Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc)
>
> rtopy.par="
> stimtype polar
> direction neg"
>
> 2. I then reconstruct the strucutural data using-
> <*recon-all -i /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm
> -subjid VG01*>
>
> 3. I create the subjectname file, run preprocessing, and make the analysis
> files.
> <*preproc-sess -surface self lhrh -fwhm 5 -sf sessid -fsd bold*
> *mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2
> -abblocked 38.4 -fsd bold -fwhm 5*
> *mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2
> -abblocked 38.4 -fsd bold -fwhm 5*>
>
> 4. Then I run the analysis using-
> <*selxavg3-sess -analysis rtopy.self.lh -sf sessid*
> *selxavg3-sess -analysis rtopy.self.lh -sf sessid*>
> ~This step was giving me an error until I added "faux" eccentricity run
> folders with runs 1-5 functional data copied and rtopy.par files with
> stimtype eccen.  Rerunning these 2 steps with the faux eccentricity data
> fixed the error message.
>
> 5. Create occipital patch with (http://www.alivelearn.net/?p=65) as
> guideline.  Flatten patch using-
> <*mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat*
> *mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat*>
>
> And create fieldsign map using-
> <*fieldsign-sess -a rtopy.self.lh -occip -sf sessid*
> *fieldsign-sess -a rtopy.self.rh -occip -sf sessid*>
> ~Error that analysis isn't retinotopy (because I used -abblocked),
> retrying step 3 with -retinotopy allowed me to create the fieldsign map.
>
> ---
>
> For the -abblocked and -retinotopy analysis I am able to look at the
> results using <*tksurfer-sess -a rtopy.self.lh -sf sessid*>*.*
> My questions are:
> - Should I be using -abblocked or -retinotopy for a polar only design?
> - Is it ok to create "faux" eccentricity folders and then only look at the
> polar data?
> - Why is it for either of these analyses I can't view the angle map using <
> *tksurfer-sess -a rtopy.self.?h -s sessid -map angle*>? In fact the angle
> file is not created.
>
> Thanks so much for your time and help.
>
> Daniel
> *
> *
>
> --
> Daniel Cole
> University of Rochester
> Brain and Cognitive Sciences
> dcol...@u.rochester.edu
>
>


-- 
Daniel Cole
University of Rochester
Brain and Cognitive Sciences
dcol...@u.rochester.edu
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Re: [Freesurfer] trac-all -path error

[Kiely Donnelly]

Hi Priti - Thanks for your help. The inter-subject registration seems to
have run OK, but there must be something wrong with the intra-subject
registration. When I try to view it using freeview, it's completely dark -
I don't see a brain at all. Is there a way to troubleshoot this?

Thanks,

Kiely

On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan <
rspr...@nmr.mgh.harvard.edu> wrote:

> Hi Kiely,
>
> Have you checked your inter and intra subject registrations? The control
> points going off the dwi is not only for one paths but for all the paths.
> If the registration goes terribly wrong, this can happen. You can take a
> look at
>
> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration diff-anat)
>
> and
>
> /dmri/brain_anat_mni.nii.gz (For inter-subject registration anat-mni)
>
> I would start by checking that first.
>
> Priti
>
> > Hello--
> >
> > I have run Tracula successfully for ~75 healthy subjects. However, the
> > pathway reconstruction seems to fail for a handful of people. I've
> > attached
> > the log file for one of these subjects. It appears that the control
> points
> > are not within the dwi. A similar problem occurred in a subject with
> > substantial signal loss in the dwi, but that doesn't seem to be the case
> > for this particular person. I have been creating the entire set of
> tracts,
> > but at this point, I'm only interested in the SLFt and SLFp.
> >
> > Thanks,
> >
> > Kiely
> > ___
> > 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.
>
>


-- 
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati
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Re: [Freesurfer] trac-all -path error

[Anastasia Yendiki]

Hi Kiely - Looks like you used flirt for the intra-subject registration, 
so you can look in trac-all.log for the flirt command line that registers 
diffusion to anatomical and play around with the parameters.


You can also use bbregister instead of flirt for the intra-subject 
registration - it has the option to initialize with flirt or with SPM.


Hope this helps,
a.y

On Wed, 16 May 2012, Kiely Donnelly wrote:


Hi Priti - Thanks for your help. The inter-subject registration seems to
have run OK, but there must be something wrong with the intra-subject
registration. When I try to view it using freeview, it's completely dark - I
don't see a brain at all. Is there a way to troubleshoot this?
Thanks,

Kiely 

On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
 wrote:
  Hi Kiely,

  Have you checked your inter and intra subject registrations? The
  control
  points going off the dwi is not only for one paths but for all
  the paths.
  If the registration goes terribly wrong, this can happen. You
  can take a
  look at

  /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration
  diff-anat)

  and

  /dmri/brain_anat_mni.nii.gz (For inter-subject registration
  anat-mni)

  I would start by checking that first.

  Priti

  > Hello--
  >
  > I have run Tracula successfully for ~75 healthy subjects.
  However, the
  > pathway reconstruction seems to fail for a handful of people.
  I've
  > attached
  > the log file for one of these subjects. It appears that the
  control points
  > are not within the dwi. A similar problem occurred in a
  subject with
  > substantial signal loss in the dwi, but that doesn't seem to
  be the case
  > for this particular person. I have been creating the entire
  set of tracts,
  > but at this point, I'm only interested in the SLFt and SLFp.
  >
  > Thanks,
  >
  > Kiely
> ___
> 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
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dispose of the e-mail.




--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati

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Re: [Freesurfer] trac-all -path error

[Priti Srinivasan]

Kiely, For flirt, try using corratio, cost function instead of mutualinfo
(which is the default in trac-all) to see if that solves your registration
problem.


> Hi Kiely - Looks like you used flirt for the intra-subject registration,
> so you can look in trac-all.log for the flirt command line that registers
> diffusion to anatomical and play around with the parameters.
>
> You can also use bbregister instead of flirt for the intra-subject
> registration - it has the option to initialize with flirt or with SPM.
>
> Hope this helps,
> a.y
>
> On Wed, 16 May 2012, Kiely Donnelly wrote:
>
>> Hi Priti - Thanks for your help. The inter-subject registration seems to
>> have run OK, but there must be something wrong with the intra-subject
>> registration. When I try to view it using freeview, it's completely dark
>> - I
>> don't see a brain at all. Is there a way to troubleshoot this?
>> Thanks,
>>
>> Kiely 
>>
>> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
>>  wrote:
>>   Hi Kiely,
>>
>>   Have you checked your inter and intra subject registrations? The
>>   control
>>   points going off the dwi is not only for one paths but for all
>>   the paths.
>>   If the registration goes terribly wrong, this can happen. You
>>   can take a
>>   look at
>>
>>   /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration
>>   diff-anat)
>>
>>   and
>>
>>   /dmri/brain_anat_mni.nii.gz (For inter-subject registration
>>   anat-mni)
>>
>>   I would start by checking that first.
>>
>>   Priti
>>
>>   > Hello--
>>   >
>>   > I have run Tracula successfully for ~75 healthy subjects.
>>   However, the
>>   > pathway reconstruction seems to fail for a handful of people.
>>   I've
>>   > attached
>>   > the log file for one of these subjects. It appears that the
>>   control points
>>   > are not within the dwi. A similar problem occurred in a
>>   subject with
>>   > substantial signal loss in the dwi, but that doesn't seem to
>>   be the case
>>   > for this particular person. I have been creating the entire
>>   set of tracts,
>>   > but at this point, I'm only interested in the SLFt and SLFp.
>>   >
>>   > Thanks,
>>   >
>>   > Kiely
>> > ___
>> > 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.
>>
>>
>>
>>
>> --
>> Kiely M. Donnelly, M.A.
>> Doctoral Candidate, Clinical Neuropsychology
>> University of Cincinnati
>>
>>___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] trac-all -path error

[Kiely Donnelly]

Is this something I can change in my dmrirc file or do I need to run flirt
on it's own?

Thanks,

Kiely

On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan <
rspr...@nmr.mgh.harvard.edu> wrote:

> Kiely, For flirt, try using corratio, cost function instead of mutualinfo
> (which is the default in trac-all) to see if that solves your registration
> problem.
>
>
> > Hi Kiely - Looks like you used flirt for the intra-subject registration,
> > so you can look in trac-all.log for the flirt command line that registers
> > diffusion to anatomical and play around with the parameters.
> >
> > You can also use bbregister instead of flirt for the intra-subject
> > registration - it has the option to initialize with flirt or with SPM.
> >
> > Hope this helps,
> > a.y
> >
> > On Wed, 16 May 2012, Kiely Donnelly wrote:
> >
> >> Hi Priti - Thanks for your help. The inter-subject registration seems to
> >> have run OK, but there must be something wrong with the intra-subject
> >> registration. When I try to view it using freeview, it's completely dark
> >> - I
> >> don't see a brain at all. Is there a way to troubleshoot this?
> >> Thanks,
> >>
> >> Kiely
> >>
> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
> >>  wrote:
> >>   Hi Kiely,
> >>
> >>   Have you checked your inter and intra subject registrations? The
> >>   control
> >>   points going off the dwi is not only for one paths but for all
> >>   the paths.
> >>   If the registration goes terribly wrong, this can happen. You
> >>   can take a
> >>   look at
> >>
> >>   /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration
> >>   diff-anat)
> >>
> >>   and
> >>
> >>   /dmri/brain_anat_mni.nii.gz (For inter-subject registration
> >>   anat-mni)
> >>
> >>   I would start by checking that first.
> >>
> >>   Priti
> >>
> >>   > Hello--
> >>   >
> >>   > I have run Tracula successfully for ~75 healthy subjects.
> >>   However, the
> >>   > pathway reconstruction seems to fail for a handful of people.
> >>   I've
> >>   > attached
> >>   > the log file for one of these subjects. It appears that the
> >>   control points
> >>   > are not within the dwi. A similar problem occurred in a
> >>   subject with
> >>   > substantial signal loss in the dwi, but that doesn't seem to
> >>   be the case
> >>   > for this particular person. I have been creating the entire
> >>   set of tracts,
> >>   > but at this point, I'm only interested in the SLFt and SLFp.
> >>   >
> >>   > Thanks,
> >>   >
> >>   > Kiely
> >> > ___
> >> > 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.
> >>
> >>
> >>
> >>
> >> --
> >> Kiely M. Donnelly, M.A.
> >> Doctoral Candidate, Clinical Neuropsychology
> >> University of Cincinnati
> >>
> >>___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>


-- 
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati
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Re: [Freesurfer] trac-all -path error

[Anastasia Yendiki]

No, this is something you have to try yourself on the command line. If you 
want to make the change permanent, you can edit the relevant line in 
$FREESURFER_HOME/bin/trac-preproc.


On Wed, 16 May 2012, Kiely Donnelly wrote:


Is this something I can change in my dmrirc file or do I need to run flirt
on it's own?
Thanks,

Kiely

On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan
 wrote:
  Kiely, For flirt, try using corratio, cost function instead of
  mutualinfo
  (which is the default in trac-all) to see if that solves your
  registration
  problem.


  > Hi Kiely - Looks like you used flirt for the intra-subject
  registration,
  > so you can look in trac-all.log for the flirt command line
  that registers
  > diffusion to anatomical and play around with the parameters.
  >
  > You can also use bbregister instead of flirt for the
  intra-subject
  > registration - it has the option to initialize with flirt or
  with SPM.
  >
  > Hope this helps,
  > a.y
  >
  > On Wed, 16 May 2012, Kiely Donnelly wrote:
  >
  >> Hi Priti - Thanks for your help. The inter-subject
  registration seems to
  >> have run OK, but there must be something wrong with the
  intra-subject
  >> registration. When I try to view it using freeview, it's
  completely dark
  >> - I
  >> don't see a brain at all. Is there a way to troubleshoot
  this?
  >> Thanks,
  >>
  >> Kiely 
  >>
  >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
  >>  wrote:
  >>       Hi Kiely,
  >>
  >>       Have you checked your inter and intra subject
  registrations? The
  >>       control
  >>       points going off the dwi is not only for one paths but
  for all
  >>       the paths.
  >>       If the registration goes terribly wrong, this can
  happen. You
  >>       can take a
  >>       look at
  >>
  >>       /dmri/lowb_brain_anat.flt.nii.gz (For intra subject
  registration
  >>       diff-anat)
  >>
  >>       and
  >>
  >>       /dmri/brain_anat_mni.nii.gz (For inter-subject
  registration
  >>       anat-mni)
  >>
  >>       I would start by checking that first.
  >>
  >>       Priti
  >>
  >>       > Hello--
  >>       >
  >>       > I have run Tracula successfully for ~75 healthy
  subjects.
  >>       However, the
  >>       > pathway reconstruction seems to fail for a handful of
  people.
  >>       I've
  >>       > attached
  >>       > the log file for one of these subjects. It appears
  that the
  >>       control points
  >>       > are not within the dwi. A similar problem occurred in
  a
  >>       subject with
  >>       > substantial signal loss in the dwi, but that doesn't
  seem to
  >>       be the case
  >>       > for this particular person. I have been creating the
  entire
  >>       set of tracts,
  >>       > but at this point, I'm only interested in the SLFt
  and SLFp.
  >>       >
  >>       > Thanks,
  >>       >
  >>       > Kiely
  >> > ___
  >> > 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.
  >>
  >>
  >>
  >>
  >> --
  >> Kiely M. Donnelly, M.A.
  >> Doctoral Candidate, Clinical Neuropsychology
  >> University of Cincinnati
  >>
  >>___
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati

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but does not contai

Re: [Freesurfer] trac-all -path error

[Priti Srinivasan]

you have to run flirt commandline separately to check if it solves your
problem.


> Is this something I can change in my dmrirc file or do I need to run flirt
> on it's own?
>
> Thanks,
>
> Kiely
>
> On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan <
> rspr...@nmr.mgh.harvard.edu> wrote:
>
>> Kiely, For flirt, try using corratio, cost function instead of
>> mutualinfo
>> (which is the default in trac-all) to see if that solves your
>> registration
>> problem.
>>
>>
>> > Hi Kiely - Looks like you used flirt for the intra-subject
>> registration,
>> > so you can look in trac-all.log for the flirt command line that
>> registers
>> > diffusion to anatomical and play around with the parameters.
>> >
>> > You can also use bbregister instead of flirt for the intra-subject
>> > registration - it has the option to initialize with flirt or with SPM.
>> >
>> > Hope this helps,
>> > a.y
>> >
>> > On Wed, 16 May 2012, Kiely Donnelly wrote:
>> >
>> >> Hi Priti - Thanks for your help. The inter-subject registration seems
>> to
>> >> have run OK, but there must be something wrong with the intra-subject
>> >> registration. When I try to view it using freeview, it's completely
>> dark
>> >> - I
>> >> don't see a brain at all. Is there a way to troubleshoot this?
>> >> Thanks,
>> >>
>> >> Kiely
>> >>
>> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
>> >>  wrote:
>> >>   Hi Kiely,
>> >>
>> >>   Have you checked your inter and intra subject registrations?
>> The
>> >>   control
>> >>   points going off the dwi is not only for one paths but for all
>> >>   the paths.
>> >>   If the registration goes terribly wrong, this can happen. You
>> >>   can take a
>> >>   look at
>> >>
>> >>   /dmri/lowb_brain_anat.flt.nii.gz (For intra subject
>> registration
>> >>   diff-anat)
>> >>
>> >>   and
>> >>
>> >>   /dmri/brain_anat_mni.nii.gz (For inter-subject registration
>> >>   anat-mni)
>> >>
>> >>   I would start by checking that first.
>> >>
>> >>   Priti
>> >>
>> >>   > Hello--
>> >>   >
>> >>   > I have run Tracula successfully for ~75 healthy subjects.
>> >>   However, the
>> >>   > pathway reconstruction seems to fail for a handful of people.
>> >>   I've
>> >>   > attached
>> >>   > the log file for one of these subjects. It appears that the
>> >>   control points
>> >>   > are not within the dwi. A similar problem occurred in a
>> >>   subject with
>> >>   > substantial signal loss in the dwi, but that doesn't seem to
>> >>   be the case
>> >>   > for this particular person. I have been creating the entire
>> >>   set of tracts,
>> >>   > but at this point, I'm only interested in the SLFt and SLFp.
>> >>   >
>> >>   > Thanks,
>> >>   >
>> >>   > Kiely
>> >> > ___
>> >> > 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.
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Kiely M. Donnelly, M.A.
>> >> Doctoral Candidate, Clinical Neuropsychology
>> >> University of Cincinnati
>> >>
>> >>___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
> --
> Kiely M. Donnelly, M.A.
> Doctoral Candidate, Clinical Neuropsychology
> University of Cincinnati
>

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Re: [Freesurfer] Inter-hemispheric registration issue

[Douglas N Greve]

Irene, this is a problem with the script. The work-around is to run 
xhemireg before running surfreg with the --xhemi option.

doug

On 05/16/2012 01:56 AM, Irene Altarelli wrote:
> Dear Doug,
>
> here is what I get.
>
> First, I ran surfreg --s aa_tris --t fsaverage_sym --lh and got the
> attached log file. Here is the terminal output:
>
> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/
> cd /home/ialtarelli
> /home/ialtarelli/freesurfer/bin/surfreg --s aa_tris --t fsaverage_sym
> --lh
>
> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012
> x86_64 GNU/Linux
> #@# lh mardi 15 mai 2012, 19:23:56 (UTC+0200)
> #CMD# mris_register -curv -annot
> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere 
> /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif 
> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg
> using smoothwm curvature for final alignment
> zeroing medial wall in aparc.annot
> $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $
>$Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $
> reading surface
> from /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.sphere...
> reading colortable from annotation file...
> colortable with 36 entries read
> (originally 
> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> reading template parameterization
> from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif...
> ripping medial wall...
> writing registered surface
> to 
> /home/ialtarelli/DATABASE/Karla5//aa_tris/surf/lh.fsaverage_sym.sphere.reg...
> curvature mean = 0.007, std = 0.603
> curvature mean = 0.030, std = 0.806
> curvature mean = 0.024, std = 0.853
> curvature mean = 0.009, std = 0.826
> curvature mean = 0.011, std = 0.936
> curvature mean = 0.003, std = 0.836
> curvature mean = 0.005, std = 0.972
> curvature mean = 0.001, std = 0.837
> curvature mean = 0.001, std = 0.988
> curvature mean = -0.032, std = 0.312
> curvature mean = 0.032, std = 0.124
> curvature mean = 0.079, std = 0.315
> curvature mean = 0.031, std = 0.151
> curvature mean = 0.049, std = 0.489
> curvature mean = 0.031, std = 0.165
> curvature mean = 0.028, std = 0.631
> curvature mean = 0.031, std = 0.171
> curvature mean = 0.011, std = 0.749
> 159: 0 negative triangles
> surfreg-Run-Time-Hours aa_tris lh 0 0,90
> mardi 15 mai 2012, 20:17:58 (UTC+0200)
> surfreg done
>
> Then, I ran surfreg --s aa_tris --t fsaverage_sym --lh --xhemi and the
> terminal output is just:
>
> ERROR: cannot
> find /home/ialtarelli/DATABASE/Karla5//aa_tris/xhemi/surf/lh.sphere
>
> without any log file, at least I can't find any modified file in the
> subject's folder.
>
>
> Hope this helps make things clearer.
> Many thanks in advance!
> Irene
>
>
> Le mardi 15 mai 2012 à 15:19 -0400, Douglas N Greve a écrit :
>> Can you send me the command line and terminal output? Did you run
>> xhemireg first? Should not have had to ...
>>
>> On 05/15/2012 03:02 PM, irene.altare...@ens.fr wrote:
>>> Dear Doug,
>>>
>>> where would that log file be? As the /subject/xhemi fails to be created the 
>>> log
>>> normally appearing in there cannot be found.. Sorry if I misunderstood
>>> something.
>>>
>>> Thanks,
>>> Irene
>>>
>>>
>>> Selon Douglas N Greve:
>>>
 Hi Irene, can you send the log file for the command that is failing?
 doug

 On 05/15/2012 01:28 PM, Irene Altarelli wrote:
> Dear all,
>
> I'm trying to use the new script for the inter-hemisphere analysis, in
> Fs version 5.0. I have downloaded the files as suggested
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html).
>
> Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym
> --lh), but I have problems then with the --xhemi option. Some files
> appear to be missing, I get the following error messages:
>
> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere
> ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm
> ERROR: cannot find /path/subject/xhemi/surf/lh.sphere
> ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot
>
> lh.fsaverage_sym.sphere.reg is created in $subject as it should (please
> find the surfreg log below).
>
> Thank you in advance,
> Irene
>
>
> Log file for surfreg
> samedi 12 mai 2012, 17:36:31 (UTC+0200)
>
> setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/
> cd /home/ialtarelli
> /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym
> --lh
>
> Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012
> x86_64 GNU/Linux
> #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200)
> #CMD# mris_register -curv -annot
> aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere
 /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif
 /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsavera

[Freesurfer] Fwd: Re: FsFastIndividual Retinotopy - Polar Only

[Douglas N Greve]

Hi Daniel, did you miss my responses from last week?
doug

 Original Message 
Subject:Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only
Date:   Fri, 11 May 2012 12:49:32 -0400
From:   Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu



Hi Daniel, answers below
doug

On 05/11/2012 11:49 AM, Daniel Cole wrote:
>  Hello,
>  I have some questions regarding the FsFastIndividual pipeline.  I hope
>  you can take a look at the commands I have run and give me some
>  insight into what the problem might potentially be.  I have 5 rotating
>  wedge stimuli runs
>
>  1. I set up my subject's directories according to the freesurfer
>  tutorial powerpoint and declare my environmental variables using-
>/export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy/
>  /source $FREESURFER_HOME/SetUpFreeSurfer.sh/>
>
>  Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc)
>
>  rtopy.par="
>  stimtype polar
>  direction neg"
>
>  2. I then reconstruct the strucutural data using-
>/Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01/>
>
>  3. I create the subjectname file, run preprocessing, and make the
>  analysis files.
>/mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2
>  -abblocked 38.4 -fsd bold -fwhm 5/
>  /mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2
>  -abblocked 38.4 -fsd bold -fwhm 5/>
>
>  4. Then I run the analysis using-
>/selxavg3-sess -analysis rtopy.self.lh -sf sessid/>
>  ~This step was giving me an error until I added "faux" eccentricity
>  run folders with runs 1-5 functional data copied and rtopy.par files
>  with stimtype eccen.  Rerunning these 2 steps with the faux
>  eccentricity data fixed the error message.
>
>  5. Create occipital patch with (http://www.alivelearn.net/?p=65) as
>  guideline.  Flatten patch using-
>/mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat/>
>
>  And create fieldsign map using-
>/fieldsign-sess -a rtopy.self.rh -occip -sf sessid/>
>  ~Error that analysis isn't retinotopy (because I used -abblocked),
>  retrying step 3 with -retinotopy allowed me to create the fieldsign map.
Field sign is meaningless because you need polar and eccen
>
>  ---
>
>  For the -abblocked and -retinotopy analysis I am able to look at the
>  results using/./
>  My questions are:
>  - Should I be using -abblocked or -retinotopy for a polar only design?
retinotopy is fine as long as you have the faux eccen
>  - Is it ok to create "faux" eccentricity folders and then only look at
>  the polar data?
yes
>  - Why is it for either of these analyses I can't view the angle map
>  using? In fact
>  the angle file is not created.

It won't be created for the abblocked, but it should be for the
retinotopy. Can you double check? Note that the fieldsign is meaningless.
doug

>
>  Thanks so much for your time and help.
>
>  Daniel
>  /
>  /
>
>  -- 
>  Daniel Cole
>  University of Rochester
>  Brain and Cognitive Sciences
>  dcol...@u.rochester.edu
>
>
>
>  ___
>  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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html


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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] gzipRe: Fwd: Load Brodmann surface area into inflated surface

[_andreia_]

Thanks Bruce! Those are the main questions now (not only to V1, but  
also to the rest of the Brodmann areas). I really want to be sure  
where the measures come from. I want that the different measures (i.e.  
cortical thickness and area are really from the same region in the  
cortex), to know what should be exported to run the statistical  
analysis.

At some point the list email was not in Cc anymore... Here it goes to  
the list too.

Thank you so much for your help!

Andreia


Citando Bruce Fischl :

> where do the V1 stats in the stats dir come from? What binary and  
> what surface?
>
> On Wed, 16 May 2012, Douglas N Greve wrote:
>
>> sorry, what is the question?
>>
>> On 05/16/2012 11:23 AM, Bruce Fischl wrote:
>>> I'm not sure where the stats dir output comes from, Doug would  
>>> know. The others seem reasonable, and certainly the pial should be  
>>> bigger than the white. We also generate a couple of V1 labels, one  
>>> from the Hinds atlas and one from the Zilles labels I think,  
>>> although maybe the Hinds one isn't generated by default anymore.  
>>> Nick can answer that question.
>>>
>>> Also, please cc the list on these emails! You will get a faster  
>>> response time and the right people will be able to help you
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 May 2012, _andre...@sapo.pt wrote:
>>>
 Hi Bruce!

 Ok!

 In fact I've already tried to use 0 as threshold, here's what happens:

 surface area from
 - stats directory output: 2081
 - label_area -t 0 -s white rh S11 rh.V1: 2840.946
 - label_area -t 0 -s pial rh S11 rh.V1: 3509.024

 That's way too different. Using label_area  is given higher  
 values. Why? Could this have something to do with the  
 substitution of the label_area file? This would mean that at some  
 poit recon-all used the previous one to generate the output of  
 the stats directory?

 Since pial and white surfaces usually do not follow exactly the  
 same shape and, thus the same area (since there are different  
 thickness in between) , I'm antecipating reviwers questions of  
 things like "from what surface are you reporting the values?"



 Cheers,
 Andreia


 Citando Bruce Fischl :

> Hi Andreia
>
> did I say use 1.1? If I did, I'm sorry and take it back. 0 would  
> give you all the vertices in the label (this is the default).  
> 1.1 would give you an empty label since nothing would pass that  
> threshold.
>
> I wouldn't worry about thresholding the aparc boundaries, as  
> there we want a complete parcellation of the cortex, so if you  
> took it out of one parcel you would have to give it to another  
> (less likely) one.
>
> cheers
> Bruce
>
>
> On Wed, 16 May 2012, _andre...@sapo.pt wrote:
>
>> Sorry now I'm confused. I understood you said that I should try  
>> 1.1 as threshold. Anyway, this means that the values in the  
>> outputs from the stats directory do not take into account any  
>> threshold. Thus, the surface area given is from the bigger  
>> probable area no matter how unlikely all the points belong to  
>> it, correct? Could this be a problem when interpreting results  
>> using cortical thickness, surface area and/or volume of the  
>> studied regions?
>>
>> And concerning the aparc areas, is the ideia the same?
>>
>> I'm sorry to be insisting on this but I need to know what is  
>> the meaning of the values I'm using, principally because when  
>> discussing measures like these one must be carefull, as you  
>> know :)
>>
>> Thanks!!
>> Andreia
>>
>>
>> Citando Bruce Fischl :
>>
>>> Hi Andreia
>>>
>>> the threshold should be in [0 1], as the label->stat is a  
>>> fraction not a pct. You should be able to run it for multiple  
>>> subjects. Nick or Doug might have some suggestions about how  
>>> to create a table of values. You can probably get something  
>>> similar out of other binaries.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 16 May 2012, _andre...@sapo.pt wrote:
>>>
 Hi Bruce,

 So if label_area is not used by recon-all when I run it I'll  
 just use it to obtain the area from the surface I specify,  
 that's ok. Is it possible to use it to get these measures  
 from multiple subjects and areas (areas from the aparc file  
 also) at once (and maybe to create an output where they all  
 come together?). However it would be good if one could be  
 sure of the surface that is being used to stats output in  
 fact. In fact, I was trying to know that by using the  
 label_area, but I cannot find a coincident value because I  
 can't use a threshold higher than 1.

 The rh.V1.label file

Re: [Freesurfer] trac-all -path error

[Kiely Donnelly]

I tried using corratio and it seems to have fixed the registration issue.
I'm very new to this so just want to make sure I did it correctly before I
move forward. Should the command line look something like this if I am
running it in this individuals dmri directory:


flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out
lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio


Thanks so much for your help.

Kiely

On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan <
rspr...@nmr.mgh.harvard.edu> wrote:

> you have to run flirt commandline separately to check if it solves your
> problem.
>
>
> > Is this something I can change in my dmrirc file or do I need to run
> flirt
> > on it's own?
> >
> > Thanks,
> >
> > Kiely
> >
> > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan <
> > rspr...@nmr.mgh.harvard.edu> wrote:
> >
> >> Kiely, For flirt, try using corratio, cost function instead of
> >> mutualinfo
> >> (which is the default in trac-all) to see if that solves your
> >> registration
> >> problem.
> >>
> >>
> >> > Hi Kiely - Looks like you used flirt for the intra-subject
> >> registration,
> >> > so you can look in trac-all.log for the flirt command line that
> >> registers
> >> > diffusion to anatomical and play around with the parameters.
> >> >
> >> > You can also use bbregister instead of flirt for the intra-subject
> >> > registration - it has the option to initialize with flirt or with SPM.
> >> >
> >> > Hope this helps,
> >> > a.y
> >> >
> >> > On Wed, 16 May 2012, Kiely Donnelly wrote:
> >> >
> >> >> Hi Priti - Thanks for your help. The inter-subject registration seems
> >> to
> >> >> have run OK, but there must be something wrong with the intra-subject
> >> >> registration. When I try to view it using freeview, it's completely
> >> dark
> >> >> - I
> >> >> don't see a brain at all. Is there a way to troubleshoot this?
> >> >> Thanks,
> >> >>
> >> >> Kiely
> >> >>
> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
> >> >>  wrote:
> >> >>   Hi Kiely,
> >> >>
> >> >>   Have you checked your inter and intra subject registrations?
> >> The
> >> >>   control
> >> >>   points going off the dwi is not only for one paths but for all
> >> >>   the paths.
> >> >>   If the registration goes terribly wrong, this can happen. You
> >> >>   can take a
> >> >>   look at
> >> >>
> >> >>   /dmri/lowb_brain_anat.flt.nii.gz (For intra subject
> >> registration
> >> >>   diff-anat)
> >> >>
> >> >>   and
> >> >>
> >> >>   /dmri/brain_anat_mni.nii.gz (For inter-subject registration
> >> >>   anat-mni)
> >> >>
> >> >>   I would start by checking that first.
> >> >>
> >> >>   Priti
> >> >>
> >> >>   > Hello--
> >> >>   >
> >> >>   > I have run Tracula successfully for ~75 healthy subjects.
> >> >>   However, the
> >> >>   > pathway reconstruction seems to fail for a handful of people.
> >> >>   I've
> >> >>   > attached
> >> >>   > the log file for one of these subjects. It appears that the
> >> >>   control points
> >> >>   > are not within the dwi. A similar problem occurred in a
> >> >>   subject with
> >> >>   > substantial signal loss in the dwi, but that doesn't seem to
> >> >>   be the case
> >> >>   > for this particular person. I have been creating the entire
> >> >>   set of tracts,
> >> >>   > but at this point, I'm only interested in the SLFt and SLFp.
> >> >>   >
> >> >>   > Thanks,
> >> >>   >
> >> >>   > Kiely
> >> >> > ___
> >> >> > 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.
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Kiely M. Donnelly, M.A.
> >> >> Doctoral Candidate, Clinical Neuropsychology
> >> >> University of Cincinnati
> >> >>
> >> >>___
> >> > Freesurfer mailing list
> >> > Freesurfer@nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >
> >
> > --
> > Kiely M. Donnelly, M.A.
> > Doctoral Candidate, Clinical Neuropsychology
> > University of Cincinnati
> >
>
>


-- 
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati
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Re: [Freesurfer] trac-all -path error

[Anastasia Yendiki]

The .mat registration matrix should be saved under dmri/xfms/.


On Wed, 16 May 2012, Kiely Donnelly wrote:


I tried using corratio and it seems to have fixed the registration issue.
I'm very new to this so just want to make sure I did it correctly before I
move forward. Should the command line look something like this if I am
running it in this individuals dmri directory: 

flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out
lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio


Thanks so much for your help.

Kiely

On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
 wrote:
  you have to run flirt commandline separately to check if it
  solves your
  problem.


  > Is this something I can change in my dmrirc file or do I need
  to run flirt
  > on it's own?
  >
  > Thanks,
  >
  > Kiely
  >
  > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan <
  > rspr...@nmr.mgh.harvard.edu> wrote:
  >
  >> Kiely, For flirt, try using corratio, cost function instead
  of
  >> mutualinfo
  >> (which is the default in trac-all) to see if that solves your
  >> registration
  >> problem.
  >>
  >>
  >> > Hi Kiely - Looks like you used flirt for the intra-subject
  >> registration,
  >> > so you can look in trac-all.log for the flirt command line
  that
  >> registers
  >> > diffusion to anatomical and play around with the
  parameters.
  >> >
  >> > You can also use bbregister instead of flirt for the
  intra-subject
  >> > registration - it has the option to initialize with flirt
  or with SPM.
  >> >
  >> > Hope this helps,
  >> > a.y
  >> >
  >> > On Wed, 16 May 2012, Kiely Donnelly wrote:
  >> >
  >> >> Hi Priti - Thanks for your help. The inter-subject
  registration seems
  >> to
  >> >> have run OK, but there must be something wrong with the
  intra-subject
  >> >> registration. When I try to view it using freeview, it's
  completely
  >> dark
  >> >> - I
  >> >> don't see a brain at all. Is there a way to troubleshoot
  this?
  >> >> Thanks,
  >> >>
  >> >> Kiely
  >> >>
  >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
  >> >>  wrote:
  >> >>       Hi Kiely,
  >> >>
  >> >>       Have you checked your inter and intra subject
  registrations?
  >> The
  >> >>       control
  >> >>       points going off the dwi is not only for one paths
  but for all
  >> >>       the paths.
  >> >>       If the registration goes terribly wrong, this can
  happen. You
  >> >>       can take a
  >> >>       look at
  >> >>
  >> >>       /dmri/lowb_brain_anat.flt.nii.gz (For intra subject
  >> registration
  >> >>       diff-anat)
  >> >>
  >> >>       and
  >> >>
  >> >>       /dmri/brain_anat_mni.nii.gz (For inter-subject
  registration
  >> >>       anat-mni)
  >> >>
  >> >>       I would start by checking that first.
  >> >>
  >> >>       Priti
  >> >>
  >> >>       > Hello--
  >> >>       >
  >> >>       > I have run Tracula successfully for ~75 healthy
  subjects.
  >> >>       However, the
  >> >>       > pathway reconstruction seems to fail for a handful
  of people.
  >> >>       I've
  >> >>       > attached
  >> >>       > the log file for one of these subjects. It appears
  that the
  >> >>       control points
  >> >>       > are not within the dwi. A similar problem occurred
  in a
  >> >>       subject with
  >> >>       > substantial signal loss in the dwi, but that
  doesn't seem to
  >> >>       be the case
  >> >>       > for this particular person. I have been creating
  the entire
  >> >>       set of tracts,
  >> >>       > but at this point, I'm only interested in the SLFt
  and SLFp.
  >> >>       >
  >> >>       > Thanks,
  >> >>       >
  >> >>       > Kiely
  >> >> > ___
  >> >> > 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] Asegstat2 table error

[Douglas N Greve]

Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats?
Also, please remember to copy the list so that others can see the answer 
and so that others can help with the answer.
thanks!
doug

On 05/16/2012 11:56 AM, Rashmi Singh wrote:
>
> Dough,
>
> Yes, the stat files exist with all its content. I can individually 
> import the text aseg files into  xcell sheet, but I have 44 data 
> files, so I was trying asegstat2table option.
> What do you think may be going wrong. The output file says that recon 
> all completed without error for all my subject files.
>
> Thanks,
> Rashmi.
>
>
>
>
> Do those files exist? Do they have content in them?
> doug
>
> On 05/15/2012 05:51 PM, Rashmi Singh wrote:
>
> Hello,
>   I am trying to get the asegmentation information after the recon-all
> run in the table form, but I am continuously getting the following
> error
>
> asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume
> --tablefile asegstats.txt
> SUBJECTS_DIR : /opt/freesurfer/subjects
> Parsing the .stats files
> ERROR: The stats file
> /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is
> too small to be a valid statsfile
> Use --skip flag to automatically skip bad stats files
>
> I did try to use the skip option , but then , it skips all the files
> giving the same error.
> When I individually open the aseg files from the stats folder, those
> look fine to me.
>
> Please advise.
>
> Rashmi.
>
>
> 
>
> This document may contain information covered under the Privacy Act, 5 
> USC 552(a), and/or the Health Insurance Portability and Accountability 
> Act (PL 104-191) and its various implementing regulations and must be 
> protected in accordance with those provisions. Healthcare information 
> is personal and sensitive and must be treated accordingly. If this 
> correspondence contains healthcare information it is being provided to 
> you after appropriate authorization from the patient or under 
> circumstances that don't require patient authorization. You, the 
> recipient, are obligated to maintain it in a safe, secure and 
> confidential manner. Redisclosure without additional patient consent 
> or as permitted by law is prohibited. Unauthorized redisclosure or 
> failure to maintain confidentiality subjects you to application of 
> appropriate sanction. If you have received this correspondence in 
> error, please notify the sender at once and destroy any copies you 
> have made.

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Asegstat2 table error

[Rashmi Singh]

Doug,
Attached are the aseg.stat files of the two different runs (AA262.G1 and
AB054.G1) where I got the error message.
Thanks
Rashmi.


On 5/16/12 11:41 AM, "Douglas N Greve"  wrote:

>Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats?
>Also, please remember to copy the list so that others can see the answer
>and so that others can help with the answer.
>thanks!
>doug
>
>On 05/16/2012 11:56 AM, Rashmi Singh wrote:
>>
>> Dough,
>>
>> Yes, the stat files exist with all its content. I can individually
>> import the text aseg files into  xcell sheet, but I have 44 data
>> files, so I was trying asegstat2table option.
>> What do you think may be going wrong. The output file says that recon
>> all completed without error for all my subject files.
>>
>> Thanks,
>> Rashmi.
>>
>>
>>
>>
>> Do those files exist? Do they have content in them?
>> doug
>>
>> On 05/15/2012 05:51 PM, Rashmi Singh wrote:
>>
>> Hello,
>>   I am trying to get the asegmentation information after the
>>recon-all
>> run in the table form, but I am continuously getting the following
>> error
>>
>> asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume
>> --tablefile asegstats.txt
>> SUBJECTS_DIR : /opt/freesurfer/subjects
>> Parsing the .stats files
>> ERROR: The stats file
>> /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or
>>is
>> too small to be a valid statsfile
>> Use --skip flag to automatically skip bad stats files
>>
>> I did try to use the skip option , but then , it skips all the files
>> giving the same error.
>> When I individually open the aseg files from the stats folder, those
>> look fine to me.
>>
>> Please advise.
>>
>> Rashmi.
>>
>>
>> 
>>
>> This document may contain information covered under the Privacy Act, 5
>> USC 552(a), and/or the Health Insurance Portability and Accountability
>> Act (PL 104-191) and its various implementing regulations and must be
>> protected in accordance with those provisions. Healthcare information
>> is personal and sensitive and must be treated accordingly. If this
>> correspondence contains healthcare information it is being provided to
>> you after appropriate authorization from the patient or under
>> circumstances that don't require patient authorization. You, the
>> recipient, are obligated to maintain it in a safe, secure and
>> confidential manner. Redisclosure without additional patient consent
>> or as permitted by law is prohibited. Unauthorized redisclosure or
>> failure to maintain confidentiality subjects you to application of
>> appropriate sanction. If you have received this correspondence in
>> error, please notify the sender at once and destroy any copies you
>> have made.
>
>--
>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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
>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.
>




This document may contain information covered under the Privacy Act, 5 USC 
552(a), and/or the Health Insurance Portability and Accountability Act (PL 
104-191) and its various implementing regulations and must be protected in 
accordance with those provisions. Healthcare information is personal and 
sensitive and must be treated accordingly. If this correspondence contains 
healthcare information it is being provided to you after appropriate 
authorization from the patient or under circumstances that don't require 
patient authorization. You, the recipient, are obligated to maintain it in a 
safe, secure and confidential manner. Redisclosure without additional patient 
consent or as permitted by law is prohibited. Unauthorized redisclosure or 
failure to maintain confidentiality subjects you to application of appropriate 
sanction. If you have received this correspondence in error, please notify the 
sender at once and destroy any copies you have made.


aseg.stats
Description: aseg.stats


aseg.stats
Description: aseg.stats
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[Freesurfer] Different values for cortical thickness

[Nooshin Zadeh]

Dear Freesurfer Friends

I have a question about cortical thickness. I do not understand why these
commands give us DIFFERENT values for "average cortical thickness".
Can you please let me know if you have any idea.
Thanks a lot

mris_anatomical_stats N2207 lh
number of vertices  = 157417
total surface area  = 102378 mm^2
total gray matter volume= 234251 mm^3
average cortical thickness  = 2.080 mm +- 0.889 mm
average integrated rectified mean curvature = 0.198
average integrated rectified Gaussian curvature = 0.223
folding index   = 13893
intrinsic curvature index   = 1137.3


mris_anatomical_stats -t N2207/label/lh.cortex.label -b N2207 lh
same as
mris_anatomical_stats -t -b N2207 lh
number of vertices  = 157417
total surface area  = 102378 mm^2
total gray matter volume=  0 mm^3
average cortical thickness  = 0.000 mm +- 0.000 mm
average integrated rectified mean curvature = 0.198
average integrated rectified Gaussian curvature = 0.223
folding index   = 13893
intrinsic curvature index   = 1137.3
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Re: [Freesurfer] Asegstat2 table error

[Douglas N Greve]

I was able to load both of those. Try this:

cd /opt/freesurfer/subjects/AA262.G1/stats
asegstats2table -i aseg.stats -t test.dat

doug




On 05/16/2012 01:25 PM, Rashmi Singh wrote:
> Doug,
> Attached are the aseg.stat files of the two different runs (AA262.G1 and
> AB054.G1) where I got the error message.
> Thanks
> Rashmi.
>
>
> On 5/16/12 11:41 AM, "Douglas N Greve"  wrote:
>
>> Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats?
>> Also, please remember to copy the list so that others can see the answer
>> and so that others can help with the answer.
>> thanks!
>> doug
>>
>> On 05/16/2012 11:56 AM, Rashmi Singh wrote:
>>> Dough,
>>>
>>> Yes, the stat files exist with all its content. I can individually
>>> import the text aseg files into  xcell sheet, but I have 44 data
>>> files, so I was trying asegstat2table option.
>>> What do you think may be going wrong. The output file says that recon
>>> all completed without error for all my subject files.
>>>
>>> Thanks,
>>> Rashmi.
>>>
>>>
>>>
>>>
>>> Do those files exist? Do they have content in them?
>>> doug
>>>
>>> On 05/15/2012 05:51 PM, Rashmi Singh wrote:
>>>
>>>  Hello,
>>>I am trying to get the asegmentation information after the
>>> recon-all
>>>  run in the table form, but I am continuously getting the following
>>>  error
>>>
>>>  asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume
>>>  --tablefile asegstats.txt
>>>  SUBJECTS_DIR : /opt/freesurfer/subjects
>>>  Parsing the .stats files
>>>  ERROR: The stats file
>>>  /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or
>>> is
>>>  too small to be a valid statsfile
>>>  Use --skip flag to automatically skip bad stats files
>>>
>>>  I did try to use the skip option , but then , it skips all the files
>>>  giving the same error.
>>>  When I individually open the aseg files from the stats folder, those
>>>  look fine to me.
>>>
>>>  Please advise.
>>>
>>>  Rashmi.
>>>
>>>
>>> 
>>>
>>> This document may contain information covered under the Privacy Act, 5
>>> USC 552(a), and/or the Health Insurance Portability and Accountability
>>> Act (PL 104-191) and its various implementing regulations and must be
>>> protected in accordance with those provisions. Healthcare information
>>> is personal and sensitive and must be treated accordingly. If this
>>> correspondence contains healthcare information it is being provided to
>>> you after appropriate authorization from the patient or under
>>> circumstances that don't require patient authorization. You, the
>>> recipient, are obligated to maintain it in a safe, secure and
>>> confidential manner. Redisclosure without additional patient consent
>>> or as permitted by law is prohibited. Unauthorized redisclosure or
>>> failure to maintain confidentiality subjects you to application of
>>> appropriate sanction. If you have received this correspondence in
>>> error, please notify the sender at once and destroy any copies you
>>> have made.
>> --
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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.
>>
>
> 
>
> This document may contain information covered under the Privacy Act, 5 USC 
> 552(a), and/or the Health Insurance Portability and Accountability Act (PL 
> 104-191) and its various implementing regulations and must be protected in 
> accordance with those provisions. Healthcare information is personal and 
> sensitive and must be treated accordingly. If this correspondence contains 
> healthcare information it is being provided to you after appropriate 
> authorization from the patient or under circumstances that don't require 
> patient authorization. You, the recipient, are obligated to maintain it in a 
> safe, secure and confidential manner. Redisclosure without additional patient 
> consent or as permitted by law is prohibited. Unauthorized redisclosure or 
> failure to maintain confidentiality subjects you to application of 
> appropriate sanction. If you have received this correspondence in error, 
> please notify the sender at once and destroy any copies you have made.

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-742

Re: [Freesurfer] Asegstat2 table error

[Douglas N Greve]

It just loads in a single file and creates a "table" with one row.

On 05/16/2012 02:02 PM, Rashmi Singh wrote:
> Can you also let me know what does the following command do.
> Thanks,
> Rashmi.
>
> On 5/16/12 12:58 PM, "Douglas N Greve"  wrote:
>
>> I was able to load both of those. Try this:
>>
>> cd /opt/freesurfer/subjects/AA262.G1/stats
>> asegstats2table -i aseg.stats -t test.dat
>>
>> doug
>>
>>
>>
>>
>> On 05/16/2012 01:25 PM, Rashmi Singh wrote:
>>> Doug,
>>> Attached are the aseg.stat files of the two different runs (AA262.G1 and
>>> AB054.G1) where I got the error message.
>>> Thanks
>>> Rashmi.
>>>
>>>
>>> On 5/16/12 11:41 AM, "Douglas N Greve"
>>> wrote:
>>>
 Can you send me /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats?
 Also, please remember to copy the list so that others can see the
 answer
 and so that others can help with the answer.
 thanks!
 doug

 On 05/16/2012 11:56 AM, Rashmi Singh wrote:
> Dough,
>
> Yes, the stat files exist with all its content. I can individually
> import the text aseg files into  xcell sheet, but I have 44 data
> files, so I was trying asegstat2table option.
> What do you think may be going wrong. The output file says that recon
> all completed without error for all my subject files.
>
> Thanks,
> Rashmi.
>
>
>
>
> Do those files exist? Do they have content in them?
> doug
>
> On 05/15/2012 05:51 PM, Rashmi Singh wrote:
>
>   Hello,
> I am trying to get the asegmentation information after the
> recon-all
>   run in the table form, but I am continuously getting the
> following
>   error
>
>   asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas
> volume
>   --tablefile asegstats.txt
>   SUBJECTS_DIR : /opt/freesurfer/subjects
>   Parsing the .stats files
>   ERROR: The stats file
>   /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found
> or
> is
>   too small to be a valid statsfile
>   Use --skip flag to automatically skip bad stats files
>
>   I did try to use the skip option , but then , it skips all the
> files
>   giving the same error.
>   When I individually open the aseg files from the stats folder,
> those
>   look fine to me.
>
>   Please advise.
>
>   Rashmi.
>
>
>
> ---
> -
>
> This document may contain information covered under the Privacy Act, 5
> USC 552(a), and/or the Health Insurance Portability and Accountability
> Act (PL 104-191) and its various implementing regulations and must be
> protected in accordance with those provisions. Healthcare information
> is personal and sensitive and must be treated accordingly. If this
> correspondence contains healthcare information it is being provided to
> you after appropriate authorization from the patient or under
> circumstances that don't require patient authorization. You, the
> recipient, are obligated to maintain it in a safe, secure and
> confidential manner. Redisclosure without additional patient consent
> or as permitted by law is prohibited. Unauthorized redisclosure or
> failure to maintain confidentiality subjects you to application of
> appropriate sanction. If you have received this correspondence in
> error, please notify the sender at once and destroy any copies you
> have made.
 --
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



 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.

>>> 
>>>
>>> This document may contain information covered under the Privacy Act, 5
>>> USC 552(a), and/or the Health Insurance Portability and Accountability
>>> Act (PL 104-191) and its various implementing regulations and must be
>>> protected in accordance with those provisions. Healthcare information is
>>> personal and sensitive and must be treated accordingly. If this
>>> correspondence contains healthcare information it is being provided to
>>> you after appropriate authorization from the patient or under
>>> circumstances that don't require 

[Freesurfer] Dependent measures qdec

[Mahinda Yogarajah]

Dear All,

Could someone explain (or point me in the right direction) as to the
meaning of the dependent measures (which can be used in qdec)

- intensity_deep/intensity_superficial
- intensity_deep.mgz/intensity_superficial.mgz
- white K/H

What do they represent ?

Thanks.

Mahinda
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Flip brain

[Tadeu Kubo]

Dear FS experts,

How can I flip hemispheres? I read the mail list and Doug said that (2010):

The problem with this is that you will get different results when you
use the left hemi and the right-flipped-to-left hemi as compared to the
right hemi and the left-flipped-to-right hemi. You'll actually get
different areas that appear to be significant. This is because the
right-flipped-to-left is registered to the left template target and it
does not register as well as the left registered to the left template
target (and the same in the other direction). I'm sure it means
something, but I don't know how to interpret it.

doug

I'm specially interesting because we're studying MTS. The status of this
procedure remains the same or it is possible to do it ?

Thank you,
Tadeu
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Re: [Freesurfer] Flip brain

[Douglas N Greve]

Hi Tadeu, It will be available in 5.2. If you can't wait until then, 
then follow the instructions here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html
doug

On 05/16/2012 03:51 PM, Tadeu Kubo wrote:
> Dear FS experts,
>
> How can I flip hemispheres? I read the mail list and Doug said that 
> (2010):
> The problem with this is that you will get different results when you
> use the left hemi and the right-flipped-to-left hemi as compared to the
> right hemi and the left-flipped-to-right hemi. You'll actually get
> different areas that appear to be significant. This is because the
> right-flipped-to-left is registered to the left template target and it
> does not register as well as the left registered to the left template
> target (and the same in the other direction). I'm sure it means
> something, but I don't know how to interpret it.
>
> doug
>
> I'm specially interesting because we're studying MTS. The status of 
> this procedure remains the same or it is possible to do it ?
>
> Thank you,
> Tadeu
>
>
>
>
>
> ___
> Freesurfer mailing list
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> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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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
dispose of the e-mail.

Re: [Freesurfer] Flip brain

[Tadeu Kubo]

Hi Doug

Thank you!

Tadeu




On Wed, May 16, 2012 at 5:02 PM, Douglas N Greve
wrote:

> Hi Tadeu, It will be available in 5.2. If you can't wait until then,
> then follow the instructions here:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html
> doug
>
> On 05/16/2012 03:51 PM, Tadeu Kubo wrote:
> > Dear FS experts,
> >
> > How can I flip hemispheres? I read the mail list and Doug said that
> > (2010):
> > The problem with this is that you will get different results when you
> > use the left hemi and the right-flipped-to-left hemi as compared to the
> > right hemi and the left-flipped-to-right hemi. You'll actually get
> > different areas that appear to be significant. This is because the
> > right-flipped-to-left is registered to the left template target and it
> > does not register as well as the left registered to the left template
> > target (and the same in the other direction). I'm sure it means
> > something, but I don't know how to interpret it.
> >
> > doug
> >
> > I'm specially interesting because we're studying MTS. The status of
> > this procedure remains the same or it is possible to do it ?
> >
> > Thank you,
> > Tadeu
> >
> >
> >
> >
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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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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[Freesurfer] aseg.stats not matching up

[Joshua Lee]

Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill
tool to relabel the *entire* left hippocampus segmentation to
'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left
hippocampus volume from the original aseg.stats be identical to the volume
of MyImaginaryLabel in the newly generated aseg.stats?

 Every voxel from the prior label is now assigned to the new label; yet, I
am getting different results (by about 100 voxels in the ones I've tried).

The command Im using to recalculate:
mri_segstats --seg
/usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz --sum
/usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats --pv
/usr/local/freesurfer/subjects/s02/mri/norm.mgz --excludeid 0
--brain-vol-from-seg --brainmask
/usr/local/freesurfer/subjects/s02/mri/brainmask.mgz --in
/usr/local/freesurfer/subjects/s02/mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --ctab
/usr/local/freesurfer/8regions.txt --subject s02;

Now if I were to relabel 'MyNewImaginaryLabel' to 'AthirdLabel', and again
changing every voxel in 'MyNewImaginaryLabel' to the new label, the
computed volumes do not change. This led me to suspect that aseg.mgz
contains probability estimates at each voxel that are then subsequently
overwritten by my tkmedits. However, per a previous conversation from a
year ago or so with Bruce and also the relevant Freesurfer documentation
this does not seem to be the case. Partial volume information is not
contained within the aseg.mgz (right!?), but is computed by mri_segstats by
comparing border voxels with intensities in the norm.mgz. So I am at a loss
on why these should be different.

This has been replicated in version 4.5 and 5.1
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
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Re: [Freesurfer] aseg.stats not matching up

[Bruce Fischl]

Hi Joshua

probabilities are computed internally, but not stored nor used in volume 
calcualtions. Are you actually doing a 3D fill? I don't think the 
hippocampus label is guaranteed to be connected. Can you try instead 
replacing every voxel in matlab with the hippocampus index to your new one? 
That I think should give you the same results.


cheers
Bruce


On Wed, 16 May 2012, Joshua Lee wrote:


Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill
tool to relabel the entire left hippocampus segmentation to
'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left
hippocampus volume from the original aseg.stats be identical to the volume
of MyImaginaryLabel in the newly generated aseg.stats?

 Every voxel from the prior label is now assigned to the new label; yet, I
am getting different results (by about 100 voxels in the ones I've tried).

The command Im using to recalculate:
mri_segstats --seg
/usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz --sum
/usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats --pv
/usr/local/freesurfer/subjects/s02/mri/norm.mgz --excludeid 0
--brain-vol-from-seg --brainmask
/usr/local/freesurfer/subjects/s02/mri/brainmask.mgz --in
/usr/local/freesurfer/subjects/s02/mri/norm.mgz --in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --ctab
/usr/local/freesurfer/8regions.txt --subject s02;

Now if I were to relabel 'MyNewImaginaryLabel' to 'AthirdLabel', and again
changing every voxel in 'MyNewImaginaryLabel' to the new label, the computed
volumes do not change. This led me to suspect that aseg.mgz contains
probability estimates at each voxel that are then subsequently overwritten
by my tkmedits. However, per a previous conversation from a year ago or so
with Bruce and also the relevant Freesurfer documentation this does not seem
to be the case. Partial volume information is not contained within the
aseg.mgz (right!?), but is computed by mri_segstats by comparing border
voxels with intensities in the norm.mgz. So I am at a loss on why these
should be different.

This has been replicated in version 4.5 and 5.1
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805

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Re: [Freesurfer] FsFastIndividual Retinotopy - Polar Only

[Daniel Cole]

Hey Doug,
Sorry I did miss your response last time, thank you for the advice.

I tried running the analysis again and this time it did create the angle
file.  However, now I'm running into a different problem.

I can get the angle map to show up on the surface of my subject's brain but
I can't get the color wheel overlay to work.  When I select it the surface
of the brain goes black and the segmentation lines are the only things
remaining.  Is the color wheel display not working a known issue by any
chance?

Thanks so much,
Daniel

On Wed, May 16, 2012 at 9:21 AM, Daniel Cole wrote:

> Hello again,
> Don't mean to be a bother.  I was wondering if anyone had any thoughts on
> what possibly be going wrong during my retinotopic analysis that I posted.
>  I'm at quite a loss and would appreciate a look.
>
> Thanks and best,
> Daniel
>
>
> On Fri, May 11, 2012 at 11:49 AM, Daniel Cole wrote:
>
>> Hello,
>> I have some questions regarding the FsFastIndividual pipeline.  I hope
>> you can take a look at the commands I have run and give me some insight
>> into what the problem might potentially be.  I have 5 rotating wedge
>> stimuli runs
>>
>> 1. I set up my subject's directories according to the freesurfer tutorial
>> powerpoint and declare my environmental variables using-
>> <*export FREESURFER_HOME=/Volumes/RCBI/freesurfer*
>> *export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy*
>> *source $FREESURFER_HOME/SetUpFreeSurfer.sh*>
>>
>> Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc)
>>
>> rtopy.par="
>> stimtype polar
>> direction neg"
>>
>> 2. I then reconstruct the strucutural data using-
>> <*recon-all -i
>> /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01*>
>>
>> 3. I create the subjectname file, run preprocessing, and make the
>> analysis files.
>> <*preproc-sess -surface self lhrh -fwhm 5 -sf sessid -fsd bold*
>> *mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2
>> -abblocked 38.4 -fsd bold -fwhm 5*
>> *mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2
>> -abblocked 38.4 -fsd bold -fwhm 5*>
>>
>> 4. Then I run the analysis using-
>> <*selxavg3-sess -analysis rtopy.self.lh -sf sessid*
>> *selxavg3-sess -analysis rtopy.self.lh -sf sessid*>
>> ~This step was giving me an error until I added "faux" eccentricity run
>> folders with runs 1-5 functional data copied and rtopy.par files with
>> stimtype eccen.  Rerunning these 2 steps with the faux eccentricity data
>> fixed the error message.
>>
>> 5. Create occipital patch with (http://www.alivelearn.net/?p=65) as
>> guideline.  Flatten patch using-
>> <*mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat
>> *
>> *mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat*
>> >
>>
>> And create fieldsign map using-
>> <*fieldsign-sess -a rtopy.self.lh -occip -sf sessid*
>> *fieldsign-sess -a rtopy.self.rh -occip -sf sessid*>
>> ~Error that analysis isn't retinotopy (because I used -abblocked),
>> retrying step 3 with -retinotopy allowed me to create the fieldsign map.
>>
>> ---
>>
>> For the -abblocked and -retinotopy analysis I am able to look at the
>> results using <*tksurfer-sess -a rtopy.self.lh -sf sessid*>*.*
>> My questions are:
>> - Should I be using -abblocked or -retinotopy for a polar only design?
>> - Is it ok to create "faux" eccentricity folders and then only look at
>> the polar data?
>> - Why is it for either of these analyses I can't view the angle map using
>> <*tksurfer-sess -a rtopy.self.?h -s sessid -map angle*>? In fact the
>> angle file is not created.
>>
>> Thanks so much for your time and help.
>>
>> Daniel
>> *
>> *
>>
>> --
>> Daniel Cole
>> University of Rochester
>> Brain and Cognitive Sciences
>> dcol...@u.rochester.edu
>>
>>
>
>
> --
> Daniel Cole
> University of Rochester
> Brain and Cognitive Sciences
> dcol...@u.rochester.edu
>
>


-- 
Daniel Cole
University of Rochester
Brain and Cognitive Sciences
dcol...@u.rochester.edu
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Re: [Freesurfer] aseg.stats not matching up

[Joshua Lee]

Hi Bruce,

First, let me add that if I run the mri_segstats without the --pv flag, the
two will have identical volumes. This indicates to me that we captured all
the voxels into the new label.

Joshua

-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl wrote:

> Hi Joshua
>
> probabilities are computed internally, but not stored nor used in volume
> calcualtions. Are you actually doing a 3D fill? I don't think the
> hippocampus label is guaranteed to be connected. Can you try instead
> replacing every voxel in matlab with the hippocampus index to your new one?
> That I think should give you the same results.
>
> cheers
> Bruce
>
>
>
> On Wed, 16 May 2012, Joshua Lee wrote:
>
>  Suppose I were to open a subject aseg.mgz in tkmedit, and use the 3D fill
>> tool to relabel the entire left hippocampus segmentation to
>> 'MyNewImaginaryLabel'. If I then re-run the aseg stats, should the left
>> hippocampus volume from the original aseg.stats be identical to the volume
>> of MyImaginaryLabel in the newly generated aseg.stats?
>>
>>  Every voxel from the prior label is now assigned to the new label; yet, I
>> am getting different results (by about 100 voxels in the ones I've tried).
>>
>> The command Im using to recalculate:
>> mri_segstats --seg
>> /usr/local/freesurfer/**subjects/s02/new_MRI/new/aseg.**auto.mgz --sum
>> /usr/local/freesurfer/**subjects/s02/stats/**NEWmethod1aseg_Hipp.stats
>> --pv
>> /usr/local/freesurfer/**subjects/s02/mri/norm.mgz --excludeid 0
>> --brain-vol-from-seg --brainmask
>> /usr/local/freesurfer/**subjects/s02/mri/brainmask.mgz --in
>> /usr/local/freesurfer/**subjects/s02/mri/norm.mgz --in-intensity-name
>> norm
>> --in-intensity-units MR --etiv --surf-wm-vol --ctab
>> /usr/local/freesurfer/**8regions.txt --subject s02;
>>
>> Now if I were to relabel 'MyNewImaginaryLabel' to 'AthirdLabel', and again
>> changing every voxel in 'MyNewImaginaryLabel' to the new label, the
>> computed
>> volumes do not change. This led me to suspect that aseg.mgz contains
>> probability estimates at each voxel that are then subsequently overwritten
>> by my tkmedits. However, per a previous conversation from a year ago or so
>> with Bruce and also the relevant Freesurfer documentation this does not
>> seem
>> to be the case. Partial volume information is not contained within the
>> aseg.mgz (right!?), but is computed by mri_segstats by comparing border
>> voxels with intensities in the norm.mgz. So I am at a loss on why these
>> should be different.
>>
>> This has been replicated in version 4.5 and 5.1
>> -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain &
>> Department of Psychology
>> University of California, Davis
>> 530.747.3805
>>
>>
>>
>
> 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] aseg.stats not matching up

[Bruce Fischl]

hmmm, that is convincing. I don't think there's anything in mri_segstats 
that knows about the meaning of any of the indices, but maybe Doug can 
correct me?


On Wed, 16 May 2012, Joshua Lee wrote:


Hi Bruce,

First, let me add that if I run the mri_segstats without the --pv flag, the
two will have identical volumes. This indicates to me that we captured all
the voxels into the new label.

Joshua

-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805


On Wed, May 16, 2012 at 1:38 PM, Bruce Fischl 
wrote:
  Hi Joshua

  probabilities are computed internally, but not stored nor used
  in volume calcualtions. Are you actually doing a 3D fill? I
  don't think the hippocampus label is guaranteed to be connected.
  Can you try instead replacing every voxel in matlab with the
  hippocampus index to your new one? That I think should give you
  the same results.

  cheers
  Bruce


  On Wed, 16 May 2012, Joshua Lee wrote:

Suppose I were to open a subject aseg.mgz in
tkmedit, and use the 3D fill
tool to relabel the entire left hippocampus
segmentation to
'MyNewImaginaryLabel'. If I then re-run the aseg
stats, should the left
hippocampus volume from the original aseg.stats be
identical to the volume
of MyImaginaryLabel in the newly generated
aseg.stats?

 Every voxel from the prior label is now assigned to
the new label; yet, I
am getting different results (by about 100 voxels in
the ones I've tried).

The command Im using to recalculate:
mri_segstats --seg
/usr/local/freesurfer/subjects/s02/new_MRI/new/aseg.auto.mgz
--sum
/usr/local/freesurfer/subjects/s02/stats/NEWmethod1aseg_Hipp.stats
--pv
/usr/local/freesurfer/subjects/s02/mri/norm.mgz
--excludeid 0
--brain-vol-from-seg --brainmask
/usr/local/freesurfer/subjects/s02/mri/brainmask.mgz
--in
/usr/local/freesurfer/subjects/s02/mri/norm.mgz
--in-intensity-name norm
--in-intensity-units MR --etiv --surf-wm-vol --ctab
/usr/local/freesurfer/8regions.txt --subject s02;

Now if I were to relabel 'MyNewImaginaryLabel' to
'AthirdLabel', and again
changing every voxel in 'MyNewImaginaryLabel' to the
new label, the computed
volumes do not change. This led me to suspect that
aseg.mgz contains
probability estimates at each voxel that are then
subsequently overwritten
by my tkmedits. However, per a previous conversation
from a year ago or so
with Bruce and also the relevant Freesurfer
documentation this does not seem
to be the case. Partial volume information is not
contained within the
aseg.mgz (right!?), but is computed by mri_segstats
by comparing border
voxels with intensities in the norm.mgz. So I am at
a loss on why these
should be different.

This has been replicated in version 4.5 and 5.1
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805




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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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[Freesurfer] Question about DODS model and DOSS model

[ZhiLiangLong]

Hi all:
 I'm a little confused about the DODS model and DOSS model. I have two 
groups (patient and control) and one covariate (age), and I want to compare the 
diffirence of thickness between the groups with age as the covariate. In DODS 
model, is the process the analysis of variance substantially (group is a factor 
and age is another factor)?
   Generally, if there is no interaction between age and group, then i can 
re-run with the DOSS model to increase the statistical power.But i don't know 
how to determine whether  there is no interaction . I hope someone give me some 
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[Freesurfer] Problem in building FreeSurfer from source

[Akio Yamamoto]

I'm having a problem in building FreeSurfer from the source codes (both
'stable5' and 'release_5_1_0') downloaded from the CVS repository.

When I run 'make', it stopped with the following error message:

mri_convert.c:39:40: error: unwarpGradientNonlinearity.h: No such file
or directory
mri_convert.c: In function 'main':
mri_convert.c:1158: error: 'unwarp_flag' undeclared (first use in this
function)
mri_convert.c:1158: error: (Each undeclared identifier is reported only once
mri_convert.c:1158: error: for each function it appears in.)
..

I actually could not find the file "unwarpGradientNonlinearity.h" in the
distribution, and am wondering if the open source distribution is
confirmed to be successfully built without any modification.

Are there additional things that I need to do before running 'make'?
Or, is a newer version of the source code available?

Thanks,
Akio
--
Akio Yamamoto
Research Associate, The University of Tokyo


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Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

[Michael Waskom]

Oops i just realized I only sent this to Bruce:

Thanks!  It looks like this involves some manual intervention.  Matt., I
assume you're not manually making control points on 1000s of subjects (I
imagine this is for the human connectcome project).  Is your code public
somewhere?

Cheers,
Michael

On Tue, May 15, 2012 at 7:36 PM, Michael Waskom wrote:

> Thanks!  It looks like this involves some manual intervention.  Matt., I
> assume you're not manually making control points on 1000s of subjects (I
> imagine this is for the human connectcome project).  Is your code public
> somewhere?
>
> Cheers,
> Michael
>
>
> On Tue, May 15, 2012 at 9:14 AM, Bruce Fischl 
> wrote:
>
>> sure, here's mine. Matt's is probably a lot more polished as they intend
>> to run it on hundreds or thousands of subjects
>>
>> On Tue, 15 May 2012, Michael Waskom wrote:
>>
>>  Hi Bruce,
>>> Sounds cool, I'd be very interested in checking out the script.
>>>
>>> Cheers,
>>> Michael
>>>
>>> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>  you need to call mris_make_surfaces directly. It's a bit
>>>  complicated as you need to intensity normalize and register the
>>>  hires volume to the surfaces first. I have an example script if
>>>  anyone is interested, but no one has used it yet but me I don't
>>>  think (unless Matt Glasser has gotten his version working, which
>>>  on second thought he probably has)
>>>
>>>  On Mon, 14 May 2012, Michael Waskom wrote:
>>>
>>>Hi Bruce,
>>>Is there a flag for this on recon-all?  Or do you
>>>need to use
>>>mri_make_surfaces directly?
>>>
>>>Best,
>>>Michael
>>>
>>>On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl
>>>
>>>wrote:
>>> Hi Joshua
>>>
>>> yes, we already have upgraded
>>>mris_make_surfaces to take higher
>>> res data
>>> and refine the surfaces with it. Haven't tried
>>>it on the aseg
>>> yet, but if
>>> you upload a sample dataset I could see how
>>>hard it is.
>>>
>>> cheers
>>> Bruce
>>> On Mon, 14 May 2012,
>>> Joshua Lee wrote:
>>>
>>> > Dear Freesurfers,
>>> >
>>> > Over the last years, MR imaging technology
>>>hasimproved such
>>> that sub 1-mm
>>> > isotropic scans can be obtained with good
>>>signal to noise
>>> characteristics.
>>> > For example, our lab uses 0.7mm isotropic
>>>structural MR
>>> images. I understand
>>> > that the Freesurfer pipeline will up-sample
>>>these to 1mm
>>> isotropic, but it
>>> > seems a shame that so much information is
>>>left unused which
>>> could be used to
>>> > improve the accuracy of sub-cortical and
>>>cortical
>>> segmentation. My question
>>> > is whether there are any plans at Freesurfer
>>>to change the
>>> reference
>>> > standard resolution from 1mm isotropic, or
>>>provide another
>>> solution that can
>>> > help researchers make the most of your
>>>technology.
>>> >
>>> > Sincerely,
>>> >
>>> >
>>> > Joshua
>>> > -
>>> > Joshua
>>> >
>>> >
>>> >
>>>__**_
>>>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] Freesurfer 1mm Isotropic standard and the Future

[Bruce Fischl]

Only because I was lazy! You can use surfaces for normalization too. I think 
the script I gave Matt probably had that in it



On May 16, 2012, at 9:21 PM, Michael Waskom  wrote:

> Oops i just realized I only sent this to Bruce:
> 
> Thanks!  It looks like this involves some manual intervention.  Matt., I 
> assume you're not manually making control points on 1000s of subjects (I 
> imagine this is for the human connectcome project).  Is your code public 
> somewhere?
> 
> Cheers,
> Michael
> 
> On Tue, May 15, 2012 at 7:36 PM, Michael Waskom  wrote:
> Thanks!  It looks like this involves some manual intervention.  Matt., I 
> assume you're not manually making control points on 1000s of subjects (I 
> imagine this is for the human connectcome project).  Is your code public 
> somewhere?
> 
> Cheers,
> Michael
> 
> 
> On Tue, May 15, 2012 at 9:14 AM, Bruce Fischl  
> wrote:
> sure, here's mine. Matt's is probably a lot more polished as they intend to 
> run it on hundreds or thousands of subjects
> 
> On Tue, 15 May 2012, Michael Waskom wrote:
> 
> Hi Bruce,
> Sounds cool, I'd be very interested in checking out the script.
> 
> Cheers,
> Michael
> 
> On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl 
> wrote:
>  you need to call mris_make_surfaces directly. It's a bit
>  complicated as you need to intensity normalize and register the
>  hires volume to the surfaces first. I have an example script if
>  anyone is interested, but no one has used it yet but me I don't
>  think (unless Matt Glasser has gotten his version working, which
>  on second thought he probably has)
> 
>  On Mon, 14 May 2012, Michael Waskom wrote:
> 
>Hi Bruce,
>Is there a flag for this on recon-all?  Or do you
>need to use
>mri_make_surfaces directly?
> 
>Best,
>Michael
> 
>On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl
>
>wrote:
> Hi Joshua
> 
> yes, we already have upgraded
>mris_make_surfaces to take higher
> res data
> and refine the surfaces with it. Haven't tried
>it on the aseg
> yet, but if
> you upload a sample dataset I could see how
>hard it is.
> 
> cheers
> Bruce
> On Mon, 14 May 2012,
> Joshua Lee wrote:
> 
> > Dear Freesurfers,
> >
> > Over the last years, MR imaging technology
>hasimproved such
> that sub 1-mm
> > isotropic scans can be obtained with good
>signal to noise
> characteristics.
> > For example, our lab uses 0.7mm isotropic
>structural MR
> images. I understand
> > that the Freesurfer pipeline will up-sample
>these to 1mm
> isotropic, but it
> > seems a shame that so much information is
>left unused which
> could be used to
> > improve the accuracy of sub-cortical and
>cortical
> segmentation. My question
> > is whether there are any plans at Freesurfer
>to change the
> reference
> > standard resolution from 1mm isotropic, or
>provide another
> solution that can
> > help researchers make the most of your
>technology.
> >
> > Sincerely,
> >
> >
> > Joshua
> > -
> > Joshua
> >
> >
> >
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>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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