By using -reg $FREESURFER_HOME/average/mni152.register.dat you are
indicating that the input label is in fsaverage space. You need to have
a registration from your source space (VPNL) to the MNI152. If you have
a whole brain in VPNL, then you can run recon-all on it to generate
surfaces. Do the same thing with the MNI152, then use mri_label2label
with surface registration to map between the two.
On 03/29/2018 07:08 AM, gj wrote:
> The labels are from Stanford VPNL's vcAtlas (cytorchitectonic atlas of
> the human ventral visual system).
>
> Does this mean that my mri_label2vol command which I posted earlier
> looks okay?
>
> To doublecheck my files in freeview, I did a simple
>
> freeview -v $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
> $wd/MPM_rh.FG2.label.nii \
> -l $VC/MPM_rh.FG2.label &
>
> where *.label.nii is the output from the mri_label2vol command I ran.
> I couldn't figure out how you load the ROI NIFTI mask as an ROI so that
> you can see it on top of the structural template -- the -l switch seems
> to only take label formats?
>
> In the attached screenshot freesurfer_prob_1.png, you see the yellow ROI
> corresponding to one label (fusiform gyrus) from the vcAtlas, which
> appears to be incorrectly rotated by 90deg.
>
> The second attached screenshot freesurfer_prob_1.png shows the output
> from mri_label2vol as a white cluster, which if all were right, I would
> assume would overlap with the yellow cluster corresponding to the
> original atlas label...but I guess the volumetric ROI looks roughly in
> the right place, but still not quite right? Why does it look so
> different in mricron?
>
> Sorry for flood of newbie Qs....
> Thank you!
> Gina
>
>
>
> ------------------------------ FWD'd msg ------------------
> Douglas N. Greve Wed, 28 Mar 2018 10:18:40 -0700
>
> what is your freeview command line? In the mri_label2vol command below,
> where does the label come from?
>
>
>
> On 2018-03-28 19:11, gj wrote:
>> Hi,
>>
>> I loaded the 2mm MNI152 template and the mri_label2vol outputs in
>> mricron, and I saw that the labels are completely outside the template.
>> So, I know now to use freeview rather than the deprecated tkmedit so I
>> can also load the original atlas labels to check against (using the 2mm
>> MNI152 template as background) -- in any case, I don't even see the
>> labels, I guess because the ROIs/masks lie outside the display. I'm also
>> not sure what the equivalent of tkmedit's overlay-reg is for freeview? I
>> assume my not loading one is why I get the error, "Label coordinate out
>> of bound" when I try and load the original atlas labels (in fsaverage
>> space) on the MNI152 template?
>>
>> Thank you!
>> Gina
>>
>> P.S. Can't find a straightforward way to reply with the entire thread
>> when receiving only a digest from the listserv -- reply to the digest
>> takes the freesurfer-request address rather than the list address and
>> the button on the website for archives only gives the option of replying
>> directly to the person who posted)...what am I missing?
>>
>>
>> ------------------------------
>>
>> Douglas Greve dgreve at mgh.harvard.edu
>> Tue Mar 27 14:01:16 EDT 2018
>>
>> how are you verifying that it is not in the right place? You should view
>> it on the 2mm MNI152 using freeview. Also, your label should be a label
>> in fsaverage space.
>>
>>
>> On 3/27/18 9:52 AM, gj wrote:
>>> Hi,
>>>
>>> Newbie question....I want to take FreeSurfer labels (from an atlas in
>>> fsaverage space) and convert it into a volumetric NIFTI mask. I ran the
>>> following command, but I must be missing something because the output is
>>> not in the right space (far too posterior):
>>>
>>> $FREESURFER_HOME/bin/mri_label2vol \
>>> --label $ll \
>>> --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
>>> --reg $FREESURFER_HOME/average/mni152.register.dat \
>>> --fillthresh .5 \
>>> --o $wd/${ll}.nii
>>>
>>> Am I perhaps supposed to first create the volumetric file without
>>> mapping into MNI space and then use tkregister2?
>>>
>>> Thanks in advance for any help or advice!
>>> Gina
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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