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My bad, I found that the output file from label2vol, vol250-?h.nii.gz, is not
oriented correctly when I view it in fsleyes...
Trying fslorient2std left vol250-?h.nii.gz totally un-impressed with the same
orientation as before.
Fslswapdim also doesn't seem to do the trick.
Would it make more sense to reorient the DTI images to freesurfer space since
I'm using a freesurfer command to extract values anyway?
Or which command would be appropriate to get vol250-?h.nii.gz into fsl space?
This I should probably ask in the fsl mailing list, I guess.
Would you have some advice nonetheless?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner,
Stephanie A
Sent: Friday, December 14, 2018 4:46 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than
vertices {Disarmed} {Disarmed}
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Hi Doug & Bruce,
Thanks again to both of your for your help!
I ended up using label2vol to extend the parcels into the wm and register them
to DTI space.
Using mri_segstats with an FA_skeletonised mask and the dti_FA.nii.gz image, I
get reasonable WM values.
However, for some of the subjects I get more 0 values in the left than the
right hemisphere.
I would have expected to get values for all the parcels or at least zero values
consistently for some parcels as I registered all parcels to the individual
subjects dti_FA.nii.gz image.
Am I missing something?
Thanks,
Steph
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
N.,Ph.D.
Sent: Tuesday, December 11, 2018 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than
vertices {Disarmed}
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It might be that the mri_aparc2aseg route requires two transformations (one to
1mm, then one to your DTI).
On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Doug,
Thanks a lot for getting back to me and your helpful comments!
Good that you mention the mri_aparc2aseg option. I had tried that and
registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister
and mri_vol2vol). Yet, extracting the FA values (mri_segstats) resulted in >70%
of parcels having zero values (with the label2vol approach I get values in
almost all parcels). I checked, aparc.250+2mm.nii.gz and dti_FA.nii.gz seem to
be perfectly coregistered.
Could you think of any reason why that is?
Thanks,
Steph
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas
N.,Ph.D.
Sent: Tuesday, December 11, 2018 10:49 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than
vertices
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That all looks like it would work to me. Another thing you can try is the way
we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in
the recon-all.log file (make sure to set the output name so that you don't
overwrite wmparc.mgz). You can specify the max distance away from cortex that
the label can grow.
On 12/10/18 5:06 PM, Winkelbeiner, Stephanie A wrote:
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Hi Douglas,
I was wondering if I can use an annot file in surf2vol to project those parcels
into the FA image space? Or would label2vol be more appropriate?
Bruce was so kind to give me his advice already and we discussed my challenges
a bit (see below).
Besides surf2vol with lh.white, I tried the following:
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
mri_label2vol \
--annot label/lh.250.aparc.annot \
--temp $dtipath/$subj/dti_FA.nii.gz \
--reg mri/register.dat \
--proj abs -3 -2 .1 \
--subject $subj --hemi lh \
--o mri/vol250-lh.nii.gz
cd ../
fi
done
Then, I used the vol250-lh image with mri_segstats to get the FA values (see
below). This gives reasonable FA values.
Would you consider this a valid approach?
I’d greatly appreciate your input.
Cheers,
Steph
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Winkelbeiner,
Stephanie A
Sent: Sunday, December 09, 2018 8:58 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than
vertices
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Hi Bruce,
you are exactly right. We are interested in projecting the parcellations into
the WM to extract the corresponding FA values.
I had tried
for subj in SPN01*; do
if [ -d "${subj}" ];
then
cd $subj/
# extract FA
mri_segstats \
--seg mri/parc2502dwi.nii.gz \ # parcellation extended &
registered to dti_FA.nii.gz
--ctab colortable.txt \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--sum ../FA/${subj}_fa.stats
cd ../
fi
done
but had so many zero values that I wanted to check first if I get values for
all the parcels if I use the non-extended annot-file.
Thanks a lot for helping me with this problem!
Cheers,
Steph
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>
Sent: Sunday, 9 December 2018 5:24 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than
vertices
External Email. Use Caution.
Hi Steph
I think that mri_segstats would work, but I defer to Doug. The output
should be normal volume, viewable in freeview. I'm not sure why you would
want to do this with FA though. Maybe you could give us more details about
what you are trying to accomplish? Seems like you want to project the annot
into the volume, not the FA maps. Not sure if surf2vol takes annots, again
Doug would know
cheers.
Bruce
On Sun, 9 Dec
2018, Winkelbeiner, Stephanie A wrote:
> External Email - Use Caution
>
> Dear Bruce,
>
> Thanks for your quick and helpful reply!
>
> Using the surface lh.white has worked perfectly.
>
> Do I understand correctly that the output file is the FA volume conform
> with the lh.white surface? Therefore, if I wanted to extract the mean FA
> for each parcel I would use this newly created volume and the annotation
> file? I had previously used mri_segstats, but that wouldn't work here. Is
> that right?
>
> Cheers,
> Steph
>
>
> -----Original Message-----
> From:
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Sunday, December 09, 2018 4:48 PM
> To: Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than
> vertices
>
> External Email. Use Caution.
>
> Hi Stephanie
>
> the -so switch requirees a surface and an overlay. What you have given it is
> an annotation (NOT a surface) and an overlay. Use one of the surfaces instead
> (e.g. lh.white)
>
> cheers
> Bruce
>
>
> On Sun, 9 Dec 2018,
> Winkelbeiner, Stephanie A wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi Freesurfers,
>>
>>
>>
>> I’m trying to project the surface, a fine-grained parcellation
>> (?h.250.aparc.annot), into volume space (dti_FA) with
>>
>>
>>
>> for subj in SPN01*; do
>>
>> if [ -d "${subj}" ];
>>
>> then
>>
>> cd $subj/
>>
>> mri_surf2vol \
>>
>> --o FA/annot2FA.nii.gz \
>>
>> --subject $subj \
>>
>> --so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot
>> $dtipath/$subj/dti_FA.nii.gz
>>
>> cd ../
>>
>> fi
>>
>> done
>>
>>
>>
>> However, I get ERROR: MRISread: file
>> ‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!
>>
>> How can I solve this?
>>
>>
>>
>> Thanks,
>>
>> Stephanie
>>
>>
>>
>> Stephanie Winkelbeiner, MSc
>>
>> Research Coordinator
>>
>> Psychiatry Research
>>
>> Zucker Hillside Hospital
>>
>> 75-59 263 Street
>>
>> Glen Oaks, NY 11004
>>
>> Tel: (718) 470-4588
>>
>> Email: swinkel...@northwell.edu<mailto:swinkel...@northwell.edu>
>>
>>
>>
>> Northwell Health
>>
>> Visit us at Northwell.edu
>>
>>
>>
>>
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