On the vcAtlas website, it says "The cytoarchitectonic atlas is
available on the FreeSurfer average surface (fsaverage). Thus your data
need to be aligned to the fsaverage brain." so I assumed the input label
is in fsaverage space. Only labels and annot files are available from
the vcAtlas -- so I guess this is not quite a whole brain in VPNL?
Sorry, I'm a bit lost....
Gina
> Message: 2
> Date: Thu, 29 Mar 2018 10:17:17 -0400
> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu>
> Subject: Re: [Freesurfer] convert labels to volume in MNI?
> To: <freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <918c2e1e-f860-5892-16fe-8257f2936...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> 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
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.
