Hi all,

So after recon-all -autorecon1 -i slicename, I got a volume brainmask.mgz.

When I open brainmask.mgz in freeview, I can only see one output slice corresponding to the input slice. How do I see all the other slices or the volume?

On Mon, Mar 25, 2019 at 7:33 PM Glasser, Matthew <glasserm@wustl.edu> wrote:

He¹s probably got some clinical software that only accepts DICOMs. While
converting volume files back to DICOMs is possible, I don¹t know if that
is something FreeSurfer supports. You might need to find another tool to
do that conversion.

Matt.

On 3/25/19, 6:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
fischl@nmr.mgh.harvard.edu> wrote:

>I'm not sure what you mean by "what my system will further deal with".
>You
>could extract slices I suppose, but typical MRI acquisitions that are
>highres are volumes. The brainmask.mgz will be volume as will everthing
>else in the mri dir
>
>
>On
>Mon, 25 Mar 2019, Chhavi Yadav wrote:
>
>>
>> External Email - Use Caution
>>
>> ok so after the recon-all command runs, in the output directory's mri
>>folder, a file called
>> brainmask.mgz is formed. I have been doing a freeview -v of this file
>>which corresponds to the final
>> skull stripped output for my input slice that I wanted. Now as per the
>>information that you gave me,
>> I should have a volume. This leads me to two questions. How do I
>>access the volume, where is it in
>> the folder ? And how to I get slices again from this volume because
>>originally I had slices and
>> slices is what my system will further deal with.
>>
>> On Mon, Mar 25, 2019 at 7:20 PM Bruce Fischl
>><fischl@nmr.mgh.harvard.edu> wrote:
>> there are no outputs for single slices, only for volumes. After we
>> convert the dicom series everything is a volume from then on, no
>>more
>> single slices
>> On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Okay but then how do I access the mgzs of the rest of the
>>slices? since only one
>> folder was formed
>> > which I suppose has the output for a single slice which was
>>mentioned in the recon-all
>> command with
>> > -i flag.
>> >
>> > On Mon, Mar 25, 2019 at 7:15 PM Bruce Fischl
>><fischl@nmr.mgh.harvard.edu> wrote:
>> > yes, you don't need to process them separately. We don't
>>in general
>> > process slices - we process entire volumes
>> >
>> > cheers
>> > Bruce
>> > On Mon, 25 Mar 2019, Chhavi Yadav
>> > wrote:
>> >
>> > >
>> > > External Email - Use Caution
>> > >
>> > > I meant I want to run autorecon1 over all the slices. I
>>am trying to
>> preprocess all
>> > the slices." If
>> > > the rest of the dicoms are in the same dir we
>> > > will find them and properly assemble the volume from
>>them." means I dont have
>> to
>> > preprocess all the
>> > > slices separately? How do I get the preprocessed mgzs
>>of all the rest of the
>> slices?
>> > >
>> > > On Mon, Mar 25, 2019 at 7:08 PM Bruce Fischl
>><fischl@nmr.mgh.harvard.edu>
>> wrote:
>> > > Hi Chhavi
>> > >
>> > > can you post this type of question to the FS list
>>(which I'll cc on my
>> > > response)? You only need to give recon-all a
>>single dicom slice that is
>> > > from the correct series. If the rest of the
>>dicoms are in the same dir
>> we
>> > > will find them and properly assemble the volume
>>from them.
>> > >
>> > > cheers
>> > > Bruce
>> > >
>> > >
>> > > On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>> > >
>> > > >
>> > > > External Email - Use Caution
>> > > >
>> > > > Hi Bruce, is there a way I can do recon-all
>>-autorecon1 for all the
>> slices for
>> > a
>> > > subject without
>> > > > using the -i flag? I mean I do not want to
>>mention every single
>> slice's name
>> > in the
>> > > command.
>> > > >
>> > > > On Mon, Mar 25, 2019 at 12:59 PM Bruce Fischl
>> <fischl@nmr.mgh.harvard.edu>
>> > wrote:
>> > > >
>> > > > On Mon, 25 Mar 2019, Chhavi Yadav wrote:
>> > > >
>> > > > >
>> > > > > External Email - Use Caution
>>
>> > > > >
>> > > > > Okay got it. So I will still
>>writerecon-all -autorecon1 -i
>> new.dcm -s
>> > outnew
>> > > > > Just that new.dcm should be in the
>>folder with the other
>> slices. Is
>> > that
>> > > correct?
>> > > > >
>> > > > > Also some of my slices are noisy, just
>>ears or completely
>> black.
>> > > > > Sorry for sending to the list.
>> > > > >
>> > > > > Thanks for your help..
>> > > > > Chhavi
>> > > > >
>> > > > >
>> > > > > On Mon, Mar 25, 2019 at 12:44 PM Bruce
>>Fischl
>> > <fischl@nmr.mgh.harvard.edu>
>> > > wrote:
>> > > > > Hi Chhavi
>> > > > >
>> > > > > if you look in the recon-all.log
>>file you will see the
>> volume
>> > dimensions
>> > > > > as:
>> > > > >
>> > > > > Image information
>> > > > > RunNo 4
>> > > > > SeriesNo 5
>> > > > > ImageNo 56
>> > > > > NImageRows 256
>> > > > > NImageCols 240
>> > > > > NFrames 1
>> > > > > SliceArraylSize 1
>> > > > > IsMosaic 0
>> > > > > ImgPos
>>36.2753 164.5335 99.2486
>> > > > > VolRes
>>1.0000 1.0000 1.2000
>> > > > > VolDim 240
>> 256 1
>> > > > > Vc
>>-0.0000 -1.0000 0.0000
>> > > > > Vr
>>-0.0000 -0.0000 -1.0000
>> > > > > Vs
>>-1.0000 -0.0000 0.0000
>> > > > > VolCenter
>>35.6753 44.5335 -28.7514
>> > > > > TransferSyntaxUID
>>1.2.840.10008.1.2.1
>> > > > >
>> > > > >
>> > > > > so it is only a single slice. You
>>need to have the
>> entire dicom
>> > series
>> > > in
>> > > > > the same directory so that we can
>>find the other slices
>> > > > > cheers
>> > > > > Bruce
>> > > > >
>> > > > >
>> > > > > On Mon, 25 Mar 2019,
>> > > > > Chhavi Yadav wrote:
>> > > > >
>> > > > > >
>> > > > > > External Email - Use
>>Caution
>> > > > > >
>> > > > > > attached is a sample on which
>>it fails.I just do
>> recon-all
>> > -autorecon1
>> > > -i
>> > > > new.dcm -s outnew
>> > > > > >
>> > > > > > Is this okay? Also attached is
>>the log.
>> > > > > > I haven't tried all.
>> > > > > >
>> > > > > > On Mon, Mar 25, 2019 at 12:26
>>PM Bruce Fischl
>> > > <fischl@nmr.mgh.harvard.edu>
>> > > > wrote:
>> > > > > > did all of them fail?
>>That seems unlikely. Our
>> failure
>> > rates are
>> > > usually
>> > > > > > pretty low (less than a
>>couple of percent). If
>> they are
>> > all
>> > > failing
>> > > > > > something else is wrong
>> > > > > >
>> > > > > >
>> > > > > > On Mon, 25 Mar 2019,
>>Chhavi Yadav wrote:
>> > > > > >
>> > > > > > >
>> > > > > > > External Email
>>- Use Caution
>> > > > > > >
>> > > > > > > HI Bruce,Thanks for
>>your email.
>> > > > > > > I actually have 3500
>>files. So cant do
>> transform on
>> > them
>> > > manually. Any
>> > > > other way?
>> > > > > Like
>> > > > > > downloading the
>> > > > > > > previous version of
>>freesurfer?
>> > > > > > > Chhavi
>> > > > > > >
>> > > > > > > On Mon, Mar 25, 2019 at
>>10:56 AM Bruce Fischl
>> > > > <fischl@nmr.mgh.harvard.edu> wrote:
>> > > > > > > Hi Chhavi
>> > > > > > >
>> > > > > > > the automated
>>Talairach transform
>> creation can
>> > sometimes
>> > > fail,
>> > > > > > > particularly in
>>the presence of very
>> large
>> > ventricles or
>> > > lots of
>> > > > > > > damaged white
>>matter or
>> > > > > > > both. We have a
>>tutorial on checking and
>> > correcting it
>> > > here:
>> > > > > > >
>> > > > > >
>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harv
>>>ard.edu_fswiki_FsTu
>> t
>> > ori
>> > > a
>> > > > l_Tala
>> > > > > ir
>> > > > > >
>> > > > > >
>>>ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYly
>>>Q&m=jmk4B1izuOm3OQV
>> T
>> > tDK
>> > > b
>> > > > HktL7Q
>> > > > > rJ
>> > > > > >
>> > > > > > >
>> > >
>>JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e=
>> > > > > > >
>> > > > > > > cheers
>> > > > > > > Bruce
>> > > > > > >
>> > > > > > > On
>> > > > > > > Mon, 25 Mar 2019,
>>Chhavi Yadav wrote:
>> > > > > > >
>> > > > > > > >
>> > > > > > > >
>>External Email - Use
>> Caution
>> > > > > > > >
>> > > > > > > > Hi,I am a
>>beginner to freesurfer.
>> Never used
>> > it
>> > > before.
>> > > > > > > > Currently I am
>>working on some dicoms
>> from
>> > ADNI that I
>> > > want to
>> > > > preprocess.
>> > > > > > > > But I am
>>getting this 'talairach_afd:
>> > Talairach
>> > > Transform:
>> > > > > transforms/talairach.xfm
>> > > > > > > ***FAILED*** '
>>error.
>> > > > > > > > I am attaching
>>the error log and other
>> files
>> > for your
>> > > > reference. Please
>> > > > > help me
>> > > > > > out.
>> > > > > > > >
>> > > > > > > > Regards,
>> > > > > > > > Chhavi
>> > > > > > > >
>> > > > > > >
>> >_______________________________________________
>> > > > > > > Freesurfer
>>mailing list
>> > > > > > >
>>Freesurfer@nmr.mgh.harvard.edu
>> > > > > >
>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvar
>>>d.edu_mailman_listi
>> n
>> > fo_
>> > > f
>> > > > reesur
>> > > > > fe
>> > > > > >
>> > > > > >
>>>r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izu
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>> > > > LToS-_
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>> > > > > >
>> > > > > > >
>> > kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e=
>> > > > > > >
>> > > > > > >
>> > > > > >
>>>_______________________________________________
>> > > > > > Freesurfer mailing list
>> > > > > >
>>Freesurfer@nmr.mgh.harvard.edu
>> > > > >
>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvar
>>>d.edu_mailman_listin
>> fo_
>> > f
>> > > r
>> > > > eesurfe
>> > > > >
>> > > > >
>>>r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQW
>>>vKqc6fZyhUQKNa911LU2
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>> > > _
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>> > > > >
>> > > > > >
>> LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e=
>> > > > > >
>> > > > > >
>> > > > >
>>>_______________________________________________
>> > > > > Freesurfer mailing list
>> > > > > Freesurfer@nmr.mgh.harvard.edu
>> > > >
>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvar
>>>d.edu_mailman_listinfo_
>> f
>> > r
>> > > ee
>> > > > surfe
>> > > >
>>>r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-H
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>> > 1
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>> > > > >
>>G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e=
>> > > > >
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>> > > >
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>> >
>> >
>> >
>>
>>

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