[WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
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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
Hi Chhavi
the automated Talairach transform creation can sometimes fail, particularly in the presence of very large ventriles or lots of damaged white matter or both. We have a tutorial on checking and correcting it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
cheers Bruce
On Mon, 25 Mar 2019, Chhavi Yadav wrote:
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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
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 ventriles 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.harvard....
cheers Bruce
On Mon, 25 Mar 2019, Chhavi Yadav wrote:
External Email - Use CautionHi,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.harvard.ed...
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.harvard.... ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJ 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.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPuLToS-_5l kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e=
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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 CautionHI 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.harvard....
ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJ
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 topreprocess.
> 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.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPuLToS-_5l
kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e=
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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:
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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.harvard.edu_fswiki_FsTutorial_Talair >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJ > 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.harvard.edu_mailman_listinfo_freesurfe >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPuLToS-_5l > kY&s=bKPWvTI6mhmqTDXPcjuZiBrd9LczeJVcqb47rKN8Lvg&e= > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF_c8g2VP7 LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e=
freesurfer@nmr.mgh.harvard.edu
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Chhavi Yadav