Hi Bruce,
Thanks so much for your response. It`s just when I try to type the "test commands" from this link: https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. The Freeview command does work, but the commands for tkmedit, tksurfer, and qdec do not work. Therefore, my tksurfer command was simply: tksurfer bert rh pial. When I try this, the computer spits out nothing, no error, no window pops up, nada. I have made sure that the bert rh pial file does exist in the surfs and it does (I run this while in my freesurfer/subjects directory. The only thing I can think of is perhaps I installed something wrong, but I followed all of the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall. I wonder however, if in my SetUpFreeSurfer.sh file the script includes the tk tools. Since it`s a third party package, are they automatically installed? As I said before, I did this on another Mac at my other lab where Freesurfer had been previously installed and the command for tksurfer worked perfectly. So I dont think its my command but something with the configuration that`s going wrong. Could also be affecting qdec`s inability to run?

Also I see here:  https://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferGeneralUsage/TkSurferQuickStart that there are two other ways to launch Tksurfer. However the one which suggests lauching it from Freesurfer with the surface button makes it sound like there is a Freesurfer GUI, however I have yet to discover one. Is there a way to launch this as well?

I really appreciate all of your help! I know this will be a lot easier once I get everything up and running.

All the best,
Claire

Here is my full script from my SetUpFreeSurfer.sh file:
#!/bin/bash -p

#
# SetUpFreeSurfer.sh
#

# This is a sample SetUpFreeSurfer.sh file.
# Edit as needed for your specific setup.
# The defaults should work with most installations.

# Set this to the location of the freesurfer installation.
if [ -z $FREESURFER_HOME ]; then
    export FREESURFER_HOME=/usr/local/freesurfer/stable5-pub
fi

# Set this to your subjects/ dir, usually freesurfer/subjects/
if [ -z $SUBJECTS_DIR ]; then
    export SUBJECTS_DIR=$FREESURFER_HOME/subjects
fi

# Set this to your functional sessions dir, usually freesurfer/sessions/
if [ -z $FUNCTIONALS_DIR ]; then
    export FUNCTIONALS_DIR=$FREESURFER_HOME/sessions
fi

# Specify the location of the MINC tools.
# Necessary only if the script $FREESURFER_HOME/FreeSurferEnv.csh
# does not find the tools (and issues warnings pertaining to
# the following two environment variables, which have example
# locations that might need user-specific modification):
#export MINC_BIN_DIR=/usr/pubsw/packages/mni/current/bin
#export MINC_LIB_DIR=/usr/pubsw/packages/mni/current/lib
# ... or just disable the MINC toolkit (although some Freesurfer
# utilities will fail!)
#export NO_MINC=1

# Enable or disable fsfast (enabled by default)
#export NO_FSFAST=1

# Call configuration script:
source $FREESURFER_HOME/FreeSurferEnv.sh


On Wed, Oct 15, 2014 at 6:00 PM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to
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or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: Issues launching tksurfer (Bruce Fischl)
   2. Re: Issues launching tksurfer (dgw)
   3. Re: Transform labels in Diffusion space into MNI space
      (Corinna Bauer)
   4. Re: mri_anatomical_stats for volume (Douglas Greve)
   5. Re: problem with gyrification index extraction (Douglas Greve)
   6. Re: problem with gyrification index extraction (elisa veronese)
   7. Re: Transform labels in Diffusion space into MNI space
      (Douglas Greve)
   8. Re: Transform labels in Diffusion space into MNI space
      (Corinna Bauer)
   9. Re: Transform labels in Diffusion space into MNI space
      (Douglas Greve)
  10. Re: Transform labels in Diffusion space into MNI space
      (Corinna Bauer)
  11. Re: Transform labels in Diffusion space into MNI space
      (Corinna Bauer)
  12. Re: Transform labels in Diffusion space into MNI space
      (Douglas N Greve)


----------------------------------------------------------------------

Message: 1
Date: Wed, 15 Oct 2014 08:30:14 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issues launching tksurfer
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1410150829570.23626@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Claire

can you send us the full output of the command from the time you type
tksurfer

thanks
Bruce
On Wed, 15 Oct 2014, Claire Morley wrote:

> Good Morning,
> I have a quick question regarding the launch of tksurfer. I have recently
> downloaded Freesurfer onto a Mac OSX after having some experience with it on
> a previous Mac. However, it had been preinstalled on that Mac, and I am
> afraid that I have perhaps installed it wrong on this one as when I test the
> launching of qdec and tksurfer, nothing happens. The terminal doesn`t spit
> out a command error, but it never launches the program. This was also a
> problem on the previous Mac for qdec but not for tksurfer. Therefore, I have
> tried to install everything again from square one and am not sure why now
> neither program is launching. I am simply trying to test the command
> "tksurfer bert lh pial". My environment is setup with Freesurfer and I am
> trying to launch from the surfs directory, as that worked on the previous
> Mac, but it is still giving me nothing. Any tips you could provide me with?
>
> All the best,
> Claire
>
>
> --
>
> We shall not cease from exploration. And the end of all our exploring will
> be to arrive where we started and know the place for the first time- T.S.
> Eliot
>
>
>
>


------------------------------

Message: 2
Date: Wed, 15 Oct 2014 09:00:37 -0400
From: dgw <dgwakeman@gmail.com>
Subject: Re: [Freesurfer] Issues launching tksurfer
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CADM2BTh_RpZUHEOBJgWFDmQta-=qA2nmj+jkiBMrv5Zu38sFsw@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi Claire,

How did you install FreeSurfer? Did you follow the instructions here:
http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall

?
HTH,
D

On Wed, Oct 15, 2014 at 4:02 AM, Claire Morley
<clairemorley2014@u.northwestern.edu> wrote:
> Good Morning,
> I have a quick question regarding the launch of tksurfer. I have recently
> downloaded Freesurfer onto a Mac OSX after having some experience with it on
> a previous Mac. However, it had been preinstalled on that Mac, and I am
> afraid that I have perhaps installed it wrong on this one as when I test the
> launching of qdec and tksurfer, nothing happens. The terminal doesn`t spit
> out a command error, but it never launches the program. This was also a
> problem on the previous Mac for qdec but not for tksurfer. Therefore, I have
> tried to install everything again from square one and am not sure why now
> neither program is launching. I am simply trying to test the command
> "tksurfer bert lh pial". My environment is setup with Freesurfer and I am
> trying to launch from the surfs directory, as that worked on the previous
> Mac, but it is still giving me nothing. Any tips you could provide me with?
>
> All the best,
> Claire
>
>
> --
>
> We shall not cease from exploration. And the end of all our exploring will
> be to arrive where we started and know the place for the first time- T.S.
> Eliot
>
>
>
> _______________________________________________
> 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.
>


------------------------------

Message: 3
Date: Wed, 15 Oct 2014 10:19:01 -0400
From: Corinna Bauer <corinnab83@gmail.com>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJOsP4K_5Vr15qWzj6tN3AUrYVsbuO9j7bYOu4eszBjw3rtweg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Doug,

I'm not sure why, but the registration is off. In tkregister2, the
"coronal" appears as an axial slice and vice versa, while the sagittal is
rotated 90 degrees compared to the target.  I did the following:
1. mni152reg --s MAE_06072013
2. tkregister2 --mov
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
--targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz
--reg MAE_06072013/register.dat --surf

Up until this point, everything looks good and well registered.

4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat


Corinna

On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:

>
> Hi Corinna, once you do #1, you can concatenate the register.dat with the
> mni152.2mm.reg.dat like this
>
> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>
> Check
> tkregister2 --mov dti.nii --targ
> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>
> mri_vol2vol --mov dti.nii --targ
> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
> dti.in.mni.nii
>
> doug
>
>
>
> On 10/14/14 2:57 PM, Corinna Bauer wrote:
>
>    Hello all,
> I am wanting to put labels currently in diffusion space into MNI space.
> Does this make sense or is there a more straight forward way?
>
>  1. mni152reg the subject's structural into MNI space
>  2. inverse transform the MNI in the the subject's T1 space
>  3. Use bbregister to align the DTI to the T1 space
>  4. inverse transform the MNI into DTI space using mri_vol2vol using the
> registration from step 3?
>
>  Cheers,
>
> Corinna
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Message: 4
Date: Wed, 15 Oct 2014 10:24:16 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_anatomical_stats for volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <543E8390.6080603@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Can you send your command line with all variables substituted for actual
arguments?
On 10/15/14 12:26 AM, Vy Dinh wrote:
> Hi Dr. Greve,
>
> I'm encountering a "segmentation fault" for some subjects when I run
> the following command:
>
> mris_anatomical_stats -l $label -t $hemi.volume -b -f $sublabel $sub
> $hemi
>
> *This is the program output for a subject that had the segmentation
> fault.  Strangly, this occurs with the volume labels only (which are
> fairly large). *
>
> label:  lh.volume.15.age.inferiortemporal.label
>
> sublabel:  /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/stats/lh.volume.15.age.inferiortemporal.stats
>
> hemisphere:  lh
>
> limiting computations to label lh.volume.15.age.inferiortemporal.label.
>
> using thickness file lh.volume.
>
> reading volume
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/mri/wm.mgz...
>
> reading input surface
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/surf/lh.white...
>
> reading input pial surface
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/surf/lh.pial...
>
> reading input white surface
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/surf/lh.white...
>
> batch_mris_anatomical_stats.sh: line 75: 31130 *Segmentation fault *
>   (core dumped) mris_anatomical_stats -l $label -t $j.volume -b -f
> $sublabel $m $j
>
>
>
> *This is the program output for a subject that worked. If I wanted to
> extract other values (e.g. pial surface area, surface area, curvature,
> sulci), do I need to specify the measurement's corresponding
> "thickness" file in the mri_anatomical_stats command?*
>
> label: rh.volume.15.age.superiorfrontal.label
>
> sublabel:
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/stats/rh.volume.15.age.superiorfrontal.stats
>
> hemisphere: rh
>
> limiting computations to label rh.volume.15.age.superiorfrontal.label.
>
> using *thickness file rh.volume*.
>
> reading volume
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/mri/wm.mgz...
>
> reading input surface
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/surf/rh.white...
>
> reading input pial surface
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/surf/rh.pial...
>
> reading input white surface
> /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/surf/rh.white...
>
>
> table columns are:
>
>   number of vertices
>
>   total surface area (mm^2)
>
>   total gray matter volume (mm^3)
>
>   average cortical thickness +- standard deviation (mm)
>
>   integrated rectified mean curvature
>
>   integrated rectified Gaussian curvature
>
>   folding index
>
>   intrinsic curvature index
>
>   structure name
>
>
> 7244   4701  14611  1.912 1.468     0.166     0.166      577 36.7
> rh.volume.15.age.superiorfrontal.label
>
> subject dir: /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029
>
> ---------------------------------
>
>
> Thank you,
>
> Vy
>
>
> On Tue, Oct 14, 2014 at 9:53 PM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>     Use -t hemi.volume (and change the name of the output file:-)
>     doug
>
>
>     On 10/14/14 2:30 PM, Vy Dinh wrote:
>>     Dear experts,
>>
>>     Can one use mri_anatomical_stats to extract volume information? I
>>     have a set of labels that has been mapped to each subject's
>>     native space (using mri_label2label; the original labels were
>>     extracted from group comparisons using mri_glmfit).
>>
>>     I have successfully extracted the thickness measures using
>>     mri_anatomical_stats and am curious if this can be done with the
>>     labels from my volume group comparisons as well.
>>
>>     This is the command I used for the extracting the thickness measures:
>>     mris_anatomical_stats -l $label -t $hemi.thickness -b -f
>>     $sublabel $sub $hemi
>>
>>     Thanks in advance,
>>
>>     --
>>     Vy Dinh
>>     MD Candidate, Class of 2017
>>     University of Wisconsin School of Medicine and Public Health
>>
>>
>>     _______________________________________________
>>     Freesurfer mailing list
>>     Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto: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.
>
>
>
>
> --
> Vy Dinh
> MD Candidate, Class of 2017
> University of Wisconsin School of Medicine and Public Health
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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------------------------------

Message: 5
Date: Wed, 15 Oct 2014 10:26:20 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] problem with gyrification index extraction
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <543E840C.7030701@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


It is a little confusing, but when you pass a map with -t  lh.map, then
the values in the map go into the column labeled "thickness" regardless
of what the map is. When you then run aparcstats2table and specify
"thickness" you get whatever is in the thickness column regardless of
whether it is thickness or not.


On 10/15/14 7:44 AM, elisa veronese wrote:
> Thank you Douglas, but I'm afraid I'm still missing the point.
> The -m option allows me measuring area (default), volume,
> thickness,thicknessstd, meancurv, gauscurv, foldind, curvind. Anyway
> my problem regards gyrification index, so I cannot understand why you
> suggested me to use -m thickness.
>
> Thank you.
> Best,
>
> elisa
>
>
>
> 2014-10-14 17:50 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>:
>
>
>     That call to aparcstats2table will give you the surface area. Use "-m
>     thickness". With this, it will report whatever you passed as the -t
>     option to mris_anatomical_stats (rh.pial_lgi in this case).
>
>     doug
>
>
>     On 10/13/2014 07:49 AM, elisa veronese wrote:
>     > Dear FreeSurfers,
>     >
>     > I'm facing a problem with the estimation of local gyrification
>     index.
>     > I've already performed the analysis with QDEC and the insertion
>     of the
>     > MEASURE1 = pial_lgi line in the .Qdecrc file, but I'd like to see if
>     > it is possible to use the /aparcstats2table /command in order to
>     have
>     > more concise and easy-to-read results.
>     >
>     > From the QDEC GUI I've drawn a label in the temporal pole, and
>     applied
>     > it to all my subjects (/mris_anatomical_stats -l rh.MR_TmpPole.label
>     > -t rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh/)
>     >
>     > The problem is that when I call the
>     > /aparcstats2table --hemi rh --subjects s1 s2 ... --parc
>     MR_TmpPole -t
>     > GI_MR_TmpPole.txt/
>     > /
>     > /
>     > I get a .txt file like this:
>     >
>     > rh.MR_TmpPole.arearh_rh.MR_TmpPole.label_arearh_WhiteSurfArea_area
>     > s1                  6623.096171.8
>     > s2                  6257.085247.3
>     > ...
>     >
>     > but I'm not sure what those numbers stand for. I'm afraid they have
>     > nothing to do with the gyrification index.
>     >
>     > Thank you,
>     >
>     > best
>     >
>     > elisa
>     >
>     >
>     > --
>     > Elisa Veronese - PhD
>     >
>     > /
>     > Research Unit on Brain Imaging and Neuropsychology (RUBIN)
>     > /
>     > /
>     > Inter-University Center for Behavioral Neurosciences (ICBN)
>     > University of Udine and University of Verona, Italy
>     > /
>     > ICBN Website: http://icbn.uniud.it/tiki-index.php
>     > /
>     >
>     > /
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358 <tel:617-724-2358>
>     Fax: 617-726-7422 <tel:617-726-7422>
>
>     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>     www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     Outgoing:
>     ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto: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.
>
>
>
>
> --
> Elisa Veronese - PhD
>
> /
> Research Unit on Brain Imaging and Neuropsychology (RUBIN)
> /
> /
> Inter-University Center for Behavioral Neurosciences (ICBN)
> University of Udine and University of Verona, Italy
> /
> ICBN Website: http://icbn.uniud.it/tiki-index.php
> /
>
> /
>
>
> _______________________________________________
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 6
Date: Wed, 15 Oct 2014 16:28:04 +0200
From: elisa veronese <dovreipensarci@gmail.com>
Subject: Re: [Freesurfer] problem with gyrification index extraction
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJdvW4c-Fcd4Az7eA+3qeWe5hu4LwxAJ4Q4KKv+d_mRFmxH+5w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Great, thank you Douglas, now it's not confusing :)

Best,
elisa

2014-10-15 16:26 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu>:

>
> It is a little confusing, but when you pass a map with -t  lh.map,  then
> the values in the map go into the column labeled "thickness" regardless of
> what the map is. When you then run aparcstats2table and specify "thickness"
> you get whatever is in the thickness column regardless of whether it is
> thickness or not.
>
>
>
> On 10/15/14 7:44 AM, elisa veronese wrote:
>
> Thank you Douglas, but I'm afraid I'm still missing the point.
> The -m option allows me measuring area (default), volume, thickness, thicknessstd,
> meancurv, gauscurv, foldind, curvind. Anyway my problem regards
> gyrification index, so I cannot understand why you suggested me to use -m
> thickness.
>
>  Thank you.
> Best,
>
>  elisa
>
>
>
> 2014-10-14 17:50 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>:
>
>>
>> That call to aparcstats2table will give you the surface area. Use "-m
>> thickness". With this, it will report whatever you passed as the -t
>> option to mris_anatomical_stats (rh.pial_lgi in this case).
>>
>> doug
>>
>>
>> On 10/13/2014 07:49 AM, elisa veronese wrote:
>> > Dear FreeSurfers,
>> >
>> > I'm facing a problem with the estimation of local gyrification index.
>> > I've already performed the analysis with QDEC and the insertion of the
>> > MEASURE1 = pial_lgi line in the .Qdecrc file, but I'd like to see if
>> > it is possible to use the /aparcstats2table /command in order to have
>> > more concise and easy-to-read results.
>> >
>> > From the QDEC GUI I've drawn a label in the temporal pole, and applied
>> > it to all my subjects (/mris_anatomical_stats -l rh.MR_TmpPole.label
>> > -t rh.pial_lgi -b -f s1/stats/rh.MR_TmpPole.stats s1 rh/)
>> >
>> > The problem is that when I call the
>> > /aparcstats2table --hemi rh --subjects s1 s2 ... --parc MR_TmpPole -t
>> > GI_MR_TmpPole.txt/
>> > /
>> > /
>> > I get a .txt file like this:
>> >
>> > rh.MR_TmpPole.arearh_rh.MR_TmpPole.label_arearh_WhiteSurfArea_area
>> > s1                  6623.096171.8
>> > s2                  6257.085247.3
>> > ...
>> >
>> > but I'm not sure what those numbers stand for. I'm afraid they have
>> > nothing to do with the gyrification index.
>> >
>> > Thank you,
>> >
>> > best
>> >
>> > elisa
>> >
>> >
>> > --
>> > Elisa Veronese - PhD
>> >
>> > /
>> > Research Unit on Brain Imaging and Neuropsychology (RUBIN)
>> > /
>> > /
>> > Inter-University Center for Behavioral Neurosciences (ICBN)
>> > University of Udine and University of Verona, Italy
>> > /
>> > ICBN Website: http://icbn.uniud.it/tiki-index.php
>> > /
>> >
>> > /
>> >
>> >
>> > _______________________________________________
>> > 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
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
>  --
> Elisa Veronese - PhD
>
>   * Research Unit on Brain Imaging and Neuropsychology (RUBIN) *
>
>
> * Inter-University Center for Behavioral Neurosciences (ICBN) University
> of Udine and University of Verona, Italy ICBN
> Website: http://icbn.uniud.it/tiki-index.php
> <http://icbn.uniud.it/tiki-index.php> *
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


--
Elisa Veronese - PhD

*Research Unit on Brain Imaging and Neuropsychology (RUBIN)*


*Inter-University Center for Behavioral Neurosciences (ICBN)University of
Udine and University of Verona, ItalyICBN
Website: http://icbn.uniud.it/tiki-index.php
<http://icbn.uniud.it/tiki-index.php>*
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Message: 7
Date: Wed, 15 Oct 2014 10:28:46 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <543E849E.103@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg ...
doug

On 10/15/14 10:19 AM, Corinna Bauer wrote:
> Hi Doug,
>
> I'm not sure why, but the registration is off. In tkregister2, the
> "coronal" appears as an axial slice and vice versa, while the sagittal
> is rotated 90 degrees compared to the target.  I did the following:
> 1. mni152reg --s MAE_06072013
> 2. tkregister2 --mov
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
> --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
> --reg
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
> 3. tkregister2 --mov
> MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
> MAE_06072013/register.dat --surf
>
> Up until this point, everything looks good and well registered.
>
> 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>
>
> Corinna
>
> On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>     Hi Corinna, once you do #1, you can concatenate the register.dat
>     with the mni152.2mm.reg.dat like this
>
>     mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>
>     Check
>     tkregister2 --mov dti.nii --targ
>     $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>
>     mri_vol2vol --mov dti.nii --targ
>     $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
>     dti.in.mni.nii
>
>     doug
>
>
>
>     On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>     Hello all,
>>     I am wanting to put labels currently in diffusion space into MNI
>>     space. Does this make sense or is there a more straight forward way?
>>
>>     1. mni152reg the subject's structural into MNI space
>>     2. inverse transform the MNI in the the subject's T1 space
>>     3. Use bbregister to align the DTI to the T1 space
>>     4. inverse transform the MNI into DTI space using mri_vol2vol
>>     using the registration from step 3?
>>
>>     Cheers,
>>
>>     Corinna
>>
>>
>>     _______________________________________________
>>     Freesurfer mailing list
>>     Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto: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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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 8
Date: Wed, 15 Oct 2014 10:29:12 -0400
From: Corinna Bauer <corinnab83@gmail.com>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJOsP4+W-rh7tnK4oJdjt93TnD41yyVTd78QYnyuaC6eyGGodg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Doug, instead of using the register.dat (which was generated from
bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg
register.dat), I had to use the registration file generated from the
mri_vol2vol step where the orig T1 is put into dti space:
    mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg
register.dat --inv --o ${mri_indtispace}.

mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat

Corinna

On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com>
wrote:

> Hi Doug,
>
> I'm not sure why, but the registration is off. In tkregister2, the
> "coronal" appears as an axial slice and vice versa, while the sagittal is
> rotated 90 degrees compared to the target.  I did the following:
> 1. mni152reg --s MAE_06072013
> 2. tkregister2 --mov
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
> --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
> 3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz
> --reg MAE_06072013/register.dat --surf
>
> Up until this point, everything looks good and well registered.
>
> 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>
>
> Corinna
>
> On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
> > wrote:
>
>>
>> Hi Corinna, once you do #1, you can concatenate the register.dat with the
>> mni152.2mm.reg.dat like this
>>
>> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>>
>> Check
>> tkregister2 --mov dti.nii --targ
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>>
>> mri_vol2vol --mov dti.nii --targ
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
>> dti.in.mni.nii
>>
>> doug
>>
>>
>>
>> On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>
>>    Hello all,
>> I am wanting to put labels currently in diffusion space into MNI space.
>> Does this make sense or is there a more straight forward way?
>>
>>  1. mni152reg the subject's structural into MNI space
>>  2. inverse transform the MNI in the the subject's T1 space
>>  3. Use bbregister to align the DTI to the T1 space
>>  4. inverse transform the MNI into DTI space using mri_vol2vol using the
>> registration from step 3?
>>
>>  Cheers,
>>
>> Corinna
>>
>>
>> _______________________________________________
>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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Message: 9
Date: Wed, 15 Oct 2014 10:31:18 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <543E8536.3060009@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


I'm not sure what is in that file.  Try doing it the way that I
suggested and see if it works.
doug


On 10/15/14 10:29 AM, Corinna Bauer wrote:
> Doug, instead of using the register.dat (which was generated from
> bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg
> register.dat), I had to use the registration file generated from the
> mri_vol2vol step where the orig T1 is put into dti space:
>     mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz
> --reg register.dat --inv --o ${mri_indtispace}.
>
> mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
>
> Corinna
>
> On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com
> <mailto:corinnab83@gmail.com>> wrote:
>
>     Hi Doug,
>
>     I'm not sure why, but the registration is off. In tkregister2, the
>     "coronal" appears as an axial slice and vice versa, while the
>     sagittal is rotated 90 degrees compared to the target.  I did the
>     following:
>     1. mni152reg --s MAE_06072013
>     2. tkregister2 --mov
>     /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
>     --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
>     --reg
>     /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
>     3. tkregister2 --mov
>     MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
>     MAE_06072013/register.dat --surf
>
>     Up until this point, everything looks good and well registered.
>
>     4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg
>     -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>
>
>     Corinna
>
>     On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve
>     <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>         Hi Corinna, once you do #1, you can concatenate the
>         register.dat with the mni152.2mm.reg.dat like this
>
>         mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>
>         Check
>         tkregister2 --mov dti.nii --targ
>         $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>
>         mri_vol2vol --mov dti.nii --targ
>         $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>         --o dti.in.mni.nii
>
>         doug
>
>
>
>         On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>         Hello all,
>>         I am wanting to put labels currently in diffusion space into
>>         MNI space. Does this make sense or is there a more straight
>>         forward way?
>>
>>         1. mni152reg the subject's structural into MNI space
>>         2. inverse transform the MNI in the the subject's T1 space
>>         3. Use bbregister to align the DTI to the T1 space
>>         4. inverse transform the MNI into DTI space using mri_vol2vol
>>         using the registration from step 3?
>>
>>         Cheers,
>>
>>         Corinna
>>
>>
>>         _______________________________________________
>>         Freesurfer mailing list
>>         Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>         _______________________________________________
>         Freesurfer mailing list
>         Freesurfer@nmr.mgh.harvard.edu
>         <mailto:Freesurfer@nmr.mgh.harvard.edu>
>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>         The information in this e-mail is intended only for the person
>         to whom it is
>         addressed. If you believe this e-mail was sent to you in error
>         and the e-mail
>         contains patient information, please contact the Partners
>         Compliance HelpLine at
>         http://www.partners.org/complianceline . If the e-mail was
>         sent to you in error
>         but does not contain patient information, please contact the
>         sender and properly
>         dispose of the e-mail.
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 10
Date: Wed, 15 Oct 2014 10:32:05 -0400
From: Corinna Bauer <corinnab83@gmail.com>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJOsP4KfqWQO00gemK04-2zsS9GKTyiyAbcZ3Q7Pfni2N0zcwA@mail.gmail.com>
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I'm pretty sure it came from mni152reg. Here are the last few lines of the
mni152 reg output:

Final tkRAS-to-tkRAS Matrix is:
 1.013   0.045   0.047  -1.659;
 0.062  -0.209  -1.043  -15.101;
-0.025   0.933  -0.227   33.122;
 0.000   0.000   0.000   1.000;


Vox2Vox Matrix is:
 2.025   0.094  -0.090   36.461;
-0.049  -0.455  -1.865   206.757;
-0.124   2.086  -0.418   23.848;
 0.000   0.000   0.000   1.000;

Resampling
Output registration matrix is identity
INFO: writing registration to
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.lta
transformed matrix:
 1.000   0.000  -0.000  -1.566;
-0.000  -0.000  -1.000  -23.577;
 0.000   1.000  -0.000   9.029;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.500   0.000   0.000  -18.500;
 0.000   0.500   0.000  -9.500;
 0.000   0.000   0.500  -18.500;
 0.000   0.000   0.000   1.000;
INFO: writing registration matrix to
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
To check registration, run:

  tkregister2 --mov
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
--targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
/drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg


mri_vol2vol done

On Wed, Oct 15, 2014 at 10:28 AM, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:

>
> Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg
> ...
> doug
>
>
> On 10/15/14 10:19 AM, Corinna Bauer wrote:
>
>   Hi Doug,
>
>  I'm not sure why, but the registration is off. In tkregister2, the
> "coronal" appears as an axial slice and vice versa, while the sagittal is
> rotated 90 degrees compared to the target.  I did the following:
> 1. mni152reg --s MAE_06072013
> 2. tkregister2 --mov
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
> --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
>  3. tkregister2 --mov
> MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
> MAE_06072013/register.dat --surf
>
> Up until this point, everything looks good and well registered.
>
> 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>
>
>  Corinna
>
> On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
> > wrote:
>
>>
>> Hi Corinna, once you do #1, you can concatenate the register.dat with the
>> mni152.2mm.reg.dat like this
>>
>> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>>
>> Check
>> tkregister2 --mov dti.nii --targ
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>>
>> mri_vol2vol --mov dti.nii --targ
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
>> dti.in.mni.nii
>>
>> doug
>>
>>
>>
>> On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>
>>     Hello all,
>> I am wanting to put labels currently in diffusion space into MNI space.
>> Does this make sense or is there a more straight forward way?
>>
>>  1. mni152reg the subject's structural into MNI space
>>  2. inverse transform the MNI in the the subject's T1 space
>>  3. Use bbregister to align the DTI to the T1 space
>>  4. inverse transform the MNI into DTI space using mri_vol2vol using the
>> registration from step 3?
>>
>>  Cheers,
>>
>> Corinna
>>
>>
>>  _______________________________________________
>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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Message: 11
Date: Wed, 15 Oct 2014 10:33:37 -0400
From: Corinna Bauer <corinnab83@gmail.com>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAJOsP4LvhgfrHBo3u21wGpFFcPdZeOGMpW+Mi8JAhE7Z18NbdA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

I tried your suggestion first and the registration was off, whereby the
axial and coronal were switched and sagittal was rotated 90 degrees.

Corinna

On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve <greve@nmr.mgh.harvard.edu>
wrote:

>
> I'm not sure what is in that file.  Try doing it the way that I suggested
> and see if it works.
> doug
>
>
>
> On 10/15/14 10:29 AM, Corinna Bauer wrote:
>
>  Doug, instead of using the register.dat (which was generated from
> bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg
> register.dat), I had to use the registration file generated from the
> mri_vol2vol step where the orig T1 is put into dti space:
>     mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg
> register.dat --inv --o ${mri_indtispace}.
>
> mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
> MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
>
>  Corinna
>
> On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com>
> wrote:
>
>>   Hi Doug,
>>
>>  I'm not sure why, but the registration is off. In tkregister2, the
>> "coronal" appears as an axial slice and vice versa, while the sagittal is
>> rotated 90 degrees compared to the target.  I did the following:
>> 1. mni152reg --s MAE_06072013
>> 2. tkregister2 --mov
>> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
>> --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
>> /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
>>  3. tkregister2 --mov
>> MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
>> MAE_06072013/register.dat --surf
>>
>> Up until this point, everything looks good and well registered.
>>
>> 4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
>> MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>>
>>
>>  Corinna
>>
>>  On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <
>> greve@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Corinna, once you do #1, you can concatenate the register.dat with
>>> the mni152.2mm.reg.dat like this
>>>
>>> mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat
>>>
>>> Check
>>> tkregister2 --mov dti.nii --targ
>>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>>>
>>> mri_vol2vol --mov dti.nii --targ
>>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o
>>> dti.in.mni.nii
>>>
>>> doug
>>>
>>>
>>>
>>> On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>>
>>>     Hello all,
>>> I am wanting to put labels currently in diffusion space into MNI space.
>>> Does this make sense or is there a more straight forward way?
>>>
>>>  1. mni152reg the subject's structural into MNI space
>>>  2. inverse transform the MNI in the the subject's T1 space
>>>  3. Use bbregister to align the DTI to the T1 space
>>>  4. inverse transform the MNI into DTI space using mri_vol2vol using the
>>> registration from step 3?
>>>
>>>  Cheers,
>>>
>>> Corinna
>>>
>>>
>>>  _______________________________________________
>>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>  The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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> 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
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Message: 12
Date: Wed, 15 Oct 2014 11:17:40 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Transform labels in Diffusion space into MNI
        space
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <543E9014.1060904@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Sorry, I gave you a bad command line. Try this

mri_matrix_multiply -im MAE_06072013/register.dat  -iim
MAE_06072013/mri/mni152.orig.mgz.reg  -om MAE_06072013/newmnireg.dat

doug


On 10/15/2014 10:33 AM, Corinna Bauer wrote:
> I tried your suggestion first and the registration was off, whereby
> the axial and coronal were switched and sagittal was rotated 90 degrees.
>
> Corinna
>
> On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>
>     I'm not sure what is in that file.  Try doing it the way that I
>     suggested and see if it works.
>     doug
>
>
>
>     On 10/15/14 10:29 AM, Corinna Bauer wrote:
>>     Doug, instead of using the register.dat (which was generated from
>>     bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl
>>     --reg register.dat), I had to use the registration file generated
>>     from the mri_vol2vol step where the orig T1 is put into dti space:
>>         mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz
>>     --reg register.dat --inv --o ${mri_indtispace}.
>>
>>     mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim
>>     MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat
>>
>>     Corinna
>>
>>     On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer
>>     <corinnab83@gmail.com <mailto:corinnab83@gmail.com>> wrote:
>>
>>         Hi Doug,
>>
>>         I'm not sure why, but the registration is off. In
>>         tkregister2, the "coronal" appears as an axial slice and vice
>>         versa, while the sagittal is rotated 90 degrees compared to
>>         the target.  I did the following:
>>         1. mni152reg --s MAE_06072013
>>         2. tkregister2 --mov
>>         /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz
>>         --targ
>>         /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz
>>         --reg
>>         /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
>>         3. tkregister2 --mov
>>         MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg
>>         MAE_06072013/register.dat --surf
>>
>>         Up until this point, everything looks good and well registered.
>>
>>         4. mri_matrix_multiply -im
>>         MAE_06072013/mri/mni152.orig.mgz.reg -iim
>>         MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat
>>
>>
>>         Corinna
>>
>>         On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve
>>         <greve@nmr.mgh.harvard.edu
>>         <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>>
>>
>>             Hi Corinna, once you do #1, you can concatenate the
>>             register.dat with the mni152.2mm.reg.dat like this
>>
>>             mri_matrix_multipy -im mnireg.dat -iim register.dat -o
>>             newreg.dat
>>
>>             Check
>>             tkregister2 --mov dti.nii --targ
>>             $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat
>>
>>             mri_vol2vol --mov dti.nii --targ
>>             $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg
>>             newreg.dat --o dti.in.mni.nii
>>
>>             doug
>>
>>
>>
>>             On 10/14/14 2:57 PM, Corinna Bauer wrote:
>>>             Hello all,
>>>             I am wanting to put labels currently in diffusion space
>>>             into MNI space. Does this make sense or is there a more
>>>             straight forward way?
>>>
>>>             1. mni152reg the subject's structural into MNI space
>>>             2. inverse transform the MNI in the the subject's T1 space
>>>             3. Use bbregister to align the DTI to the T1 space
>>>             4. inverse transform the MNI into DTI space using
>>>             mri_vol2vol using the registration from step 3?
>>>
>>>             Cheers,
>>>
>>>             Corinna
>>>
>>>
>>>             _______________________________________________
>>>             Freesurfer mailing list
>>>             Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>             https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>             _______________________________________________
>>             Freesurfer mailing list
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>>             <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>             https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>             The information in this e-mail is intended only for the
>>             person to whom it is
>>             addressed. If you believe this e-mail was sent to you in
>>             error and the e-mail
>>             contains patient information, please contact the Partners
>>             Compliance HelpLine at
>>             http://www.partners.org/complianceline . If the e-mail
>>             was sent to you in error
>>             but does not contain patient information, please contact
>>             the sender and properly
>>             dispose of the e-mail.
>>
>>
>>
>>
>>
>>     _______________________________________________
>>     Freesurfer mailing list
>>     Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     _______________________________________________
>     Freesurfer mailing list
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>
>
>     The information in this e-mail is intended only for the person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in error and
>     the e-mail
>     contains patient information, please contact the Partners
>     Compliance HelpLine at
>     http://www.partners.org/complianceline . If the e-mail was sent to
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--

We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot