I'm getting the same error, despite doing just that.  :-/

[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz
mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to mni305.nii.gz...
niiWrite(): error opening file mni305.nii.gz
ERROR: failure writing mni305.nii.gz



On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo <ythomas@csail.mit.edu> wrote:
Hi Paul,

You have to give it the full path:

mri_convert  /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz

--Thomas


On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach <pabeach1@gmail.com> wrote:
The mri_convert command did not work...

[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz
mri_convert mni305.cor.mgz mni305.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from mni305.cor.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to mni305.nii.gz...
niiWrite(): error opening file mni305.nii.gz
ERROR: failure writing mni305.nii.gz



On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo <ythomas@csail.mit.edu> wrote:
Hi Paul,

Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?

--Thomas


On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach <pabeach1@gmail.com> wrote:
Thomas,

1) this cannot be loaded into AFNI or fslview - in freeview it looks fine
2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine 

I'm not sure if that clarifies anything, though.


On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo <ythomas@csail.mit.edu> wrote:
Hi Paul,

Just to clarify, 

1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your other software?

2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does it look mis-oriented in your other software?

--Thomas


On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach <pabeach1@gmail.com> wrote:
Hi Thomas,

Thank you for the advice.

I ran: 
tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz

and tkmedit opened the transformed subject.

This is what I see:
Inline image 1

So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.


On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo <ythomas@csail.mit.edu> wrote:
That's strange. FSL_MNI152_FreeSurferConformed_1mm.nii.gz should correspond exactly to norm.mgz obtained from running $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz through recon-all (FS4.5).

So Doug's command should work as well. Just to confirm, can you run

>> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

The two templates should be exactly overlapping. 

--Thomas


On Tue, Oct 1, 2013 at 9:40 PM, Paul Beach <pabeach1@gmail.com> wrote:
Doug,

Unfortunately I cannot load this volume into tkmedit as this is not a subject that has been ran through Freesurfer - it's the downloadable FSL-based T1 volume from the "Yeo_JNeurophysiol11_MNI152" package available on the Freesurfer website. I'm trying to convert this and subsequent functional networks to MNI305 for connectivity analysis.

However, I did open up the results in FSLview and Freeview. I have attached screen shots of each, respectively.
FSLview
Inline image 1
Freeview
Inline image 2

Again, these images are resultant from the following script:
mri_vol2vol --mov /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz \
--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \
--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \
--inv --o FSL_MNI305_2mm.nii.gz


Thanks,
Paul



On Mon, Sep 30, 2013 at 7:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

View it in tkmedit to see if it is really a problem with your vol2vol command.
doug







On 09/30/2013 07:33 PM, Paul Beach wrote:
No. That was just a general example of how the image looks - from a stock google image of an FSL brain (I'm not in the lab and so cannot put up actual images). I've been using AFNI to view them.


On Mon, Sep 30, 2013 at 7:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Is this in tkmedit?


    On 09/30/2013 06:59 PM, Paul Beach wrote:

        Hi Doug,

        Sorry, I should have been more specific. I meant for when one
        looks at the resulting transformation in a sagittal view.

        More specifically...
        Instead of this:
        Inline image 1

        It looks more like this (though more like a 70degree shift
        than 90):
        Inline image 2
        The other views are obviously affected as well. Performing a
        dataset "nudge" using afni generally "corrects" this problem,
        but I'd like to prevent it from happening in the first place.

        I'm suspicious that this is occurring because I'm using
        '/mni305.cor.mgz/' instead of '/mni305.2mm.nii.gz/' for the
        'mov' command. However, I don't have the latter file anywhere
        in my Freesurfer directory. The former file is the closest
        thing I could find.


        Thoughts?
        Paul



        On Mon, Sep 30, 2013 at 5:52 PM, Douglas N Greve
        <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
        <mailto:greve@nmr.mgh.harvard.edu

        <mailto:greve@nmr.mgh.harvard.edu>>> wrote:

            what do you mean the frontal lobe is pointing straight up?




            On 09/30/2013 02:32 PM, Paul Beach wrote:
            > Freesurfer experts,
            >
            > I'm attempting to utilize an archived e-mail's contents
        to resample
            > data in MNI152 to 305.
            >
            > The script I'm using is as follows:
            > /mri_vol2vol \/
            > /--mov
            >
                   /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz
            > \/
            > /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/
            > /--reg
                   $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/
            > /--inv --o FSL_MNI305_2mm.nii.gz/
            > /
            > /
            > /
            > /
            > This series of commands is based on the following suggestion
            from Doug
            > in a previously archived e-mail exchange from someone
        attempting
            to do
            > something similar:
            > />> To go from mni152 to the MNI305 2mm space, use/
            > />>/
            > />> mri_vol2vol --mov mni305.2mm.nii.gz \/
            > />>  --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \/
            > />>  --reg
            >
        $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/
            > />>  --inv --o output.mni305.2mm.nii.gz/
            > />>/
            > />> This will resample MNI152_T1_2mm.nii.gz (or anything
        in that
            > space) to the/
            > />> mni305 2mm space./
            >
            >
            > However, this changing the orientation of my data -
        essentially all
            > images are being rotated 90degrees so the frontal lobe
        is pointed
            > straight up.
            >
            > Are there any suggestions to ameliorate this problem?
            >
            > Thanks!
            > --
            > Paul Beach
            > DO/PhD candidate - Year VI
            > Michigan State University
            > - College of Osteopathic Medicine
            > - Neuroscience Program
            >    - Bozoki Lab: Neurology/Radiology
            >
            >
            > _______________________________________________
            > Freesurfer mailing list
            > Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
            <mailto: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>
        <mailto:greve@nmr.mgh.harvard.edu

        <mailto:greve@nmr.mgh.harvard.edu>>
            Phone Number: 617-724-2358 <tel:617-724-2358>
        <tel:617-724-2358 <tel:617-724-2358>>
            Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422

        <tel:617-726-7422>>

            Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
        <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
            <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
            FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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        <http://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/

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            The information in this e-mail is intended only for the
        person to
            whom it is
            addressed. If you believe this e-mail was sent to you in
        error and
            the e-mail
            contains patient information, please contact the Partners
            Compliance HelpLine at
        http://www.partners.org/complianceline . If the e-mail was sent to
            you in error
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            sender and properly
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        --         Paul Beach
        DO/PhD candidate - Year VI
        Michigan State University
        - College of Osteopathic Medicine
        - Neuroscience Program
           - Bozoki Lab: Neurology/Radiology


    --     Douglas N. Greve, Ph.D.
    MGH-NMR Center
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology



--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology

_______________________________________________
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.





--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology




--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology




--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology




--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
   - Bozoki Lab: Neurology/Radiology