Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
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.harvard.edu_fswiki_FsTutoria l_Tala > ir > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKb 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.harvard.edu_mailman_listinfo_f reesur > fe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPu LToS-_ > 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.edu_mailman_listinfo_fr eesurfe > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF_ c8g2VP7 > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_free surfe >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1S2 TCg3F > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > >
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 CautionHi 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 -inew.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 thevolume 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 entiredicom 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 dorecon-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. Ourfailure rates are usually
> > pretty low (less than a couple of percent). Ifthey 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 transformon 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 creationcan sometimes fail,
> > > particularly in the presence of very largeventricles or lots of
> > > damaged white matter or > > > both. We have a tutorial on checking andcorrecting it here:
> > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
l_Tala > ir > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKb HktL7Q > rJ > > > > >
JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e=
> > > > > > cheers > > > Bruce > > > > > > On > > > Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > Hi,I am a beginner to freesurfer. Neverused it before.
> > > > Currently I am working on some dicomsfrom 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 otherfiles 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...
reesur > fe > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELPu LToS-_ > 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...
eesurfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF_ c8g2VP7 > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
surfer&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1S2 TCg3F > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > >
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.harvard.edu_fswiki_FsTutori a > l_Tala > > ir > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDK 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.harvard.edu_mailman_listinfo_ f > reesur > > fe > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELP u > LToS-_ > > 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.edu_mailman_listinfo_f r > eesurfe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF _ > c8g2VP7 > > > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_fr ee > surfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1 S2 > TCg3F > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > >
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 CautionI 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 ccon my
response)? You only need to give recon-all a single dicom slicethat is
from the correct series. If the rest of the dicoms are in the samedir 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 allthe slices for a
subject without > using the -i flag? I mean I do not want to mention every singleslice'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 otherslices. Is that
correct? > > > > Also some of my slices are noisy, just ears orcompletely 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 seethe volume dimensions
> > as: > > > > Image information > > RunNo 4 > > SeriesNo 5 > > ImageNo 56 > > NImageRows 256 > > NImageCols 240 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 36.2753 164.533599.2486
> > VolRes 1.0000 1.00001.2000
> > VolDim 240 256 1 > > Vc -0.0000 -1.00000.0000
> > Vr -0.0000 -0.0000-1.0000
> > Vs -1.0000 -0.00000.0000
> > 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 theentire dicom series
in > > the same directory so that we can find the otherslices
> > cheers > > Bruce > > > > > > On Mon, 25 Mar 2019, > > Chhavi Yadav wrote: > > > > > > > > External Email - Use Caution > > > > > > attached is a sample on which it fails.I just dorecon-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 ofpercent). If they are all
failing > > > something else is wrong > > > > > > > > > On Mon, 25 Mar 2019, Chhavi Yadav wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > HI Bruce,Thanks for your email. > > > > I actually have 3500 files. So cant dotransform on them
manually. Any > other way? > > Like > > > downloading the > > > > previous version of freesurfer? > > > > Chhavi > > > > > > > > On Mon, Mar 25, 2019 at 10:56 AM BruceFischl
> <fischl@nmr.mgh.harvard.edu> wrote: > > > > Hi Chhavi > > > > > > > > the automated Talairach transformcreation can sometimes
fail, > > > > particularly in the presence ofvery large ventricles or
lots of > > > > damaged white matter or > > > > both. We have a tutorial onchecking and correcting it
here: > > > > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
a > l_Tala > > ir > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDK
b > HktL7Q > > rJ > > > > > > > JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e= > > > > > > > > cheers > > > > Bruce > > > > > > > > On > > > > Mon, 25 Mar 2019, Chhavi Yadavwrote:
> > > > > > > > > > > > > > External Email - UseCaution
> > > > > > > > > > Hi,I am a beginner tofreesurfer. Never used it
before. > > > > > Currently I am working on somedicoms 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 andother 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...
f > reesur > > fe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJELP
u > LToS-_ > > 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...
r > eesurfe > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20WsF _ > c8g2VP7 > > > > >
LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e=
> > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
ee > surfe >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv1 S2 > TCg3F > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > >
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.harvard.edu_fswiki_FsTut ori > a > > l_Tala > > > ir > > > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVT 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.harvard.edu_mailman_listin fo_ > f > > reesur > > > fe > > > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJ ELP > u > > LToS-_ > > > 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.edu_mailman_listinfo_ f > r > > eesurfe > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20Ws F > _ > > c8g2VP7 > > > > > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_f r > ee > > surfe > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv 1 > S2 > > TCg3F > > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > > > > > > > > > > >
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 CautionOkay 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 amtrying 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 therest 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 (whichI'll cc on my
> response)? You only need to give recon-all a single dicomslice that is
> from the correct series. If the rest of the dicoms are inthe 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 -autorecon1for all the slices for
a > subject without > > using the -i flag? I mean I do not want to mention everysingle 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 withthe other slices. Is
that > correct? > > > > > > Also some of my slices are noisy, just ears orcompletely 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 youwill see the volume
dimensions > > > as: > > > > > > Image information > > > RunNo 4 > > > SeriesNo 5 > > > ImageNo 56 > > > NImageRows 256 > > > NImageCols 240 > > > NFrames 1 > > > SliceArraylSize 1 > > > IsMosaic 0 > > > ImgPos 36.2753164.5335 99.2486
> > > VolRes 1.00001.0000 1.2000
> > > VolDim 240 2561> > > Vc -0.0000-1.0000 0.0000
> > > Vr -0.0000-0.0000 -1.0000
> > > Vs -1.0000-0.0000 0.0000
> > > VolCenter 35.675344.5335 -28.7514
> > > TransferSyntaxUID1.2.840.10008.1.2.1
> > > > > > > > > so it is only a single slice. You need tohave the entire dicom
series > in > > > the same directory so that we can find theother slices
> > > cheers > > > Bruce > > > > > > > > > On Mon, 25 Mar 2019, > > > Chhavi Yadav wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > attached is a sample on which it fails.Ijust 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 BruceFischl
> <fischl@nmr.mgh.harvard.edu> > > wrote: > > > > did all of them fail? That seemsunlikely. Our failure
rates are > usually > > > > pretty low (less than a couple ofpercent). If they are
all > failing > > > > something else is wrong > > > > > > > > > > > > On Mon, 25 Mar 2019, Chhavi Yadavwrote:
> > > > > > > > > > > > > > External Email - UseCaution
> > > > > > > > > > HI Bruce,Thanks for your email. > > > > > I actually have 3500 files. Socant do transform on
them > manually. Any > > other way? > > > Like > > > > downloading the > > > > > previous version of freesurfer? > > > > > Chhavi > > > > > > > > > > On Mon, Mar 25, 2019 at 10:56 AMBruce Fischl
> > <fischl@nmr.mgh.harvard.edu> wrote: > > > > > Hi Chhavi > > > > > > > > > > the automated Talairachtransform creation can
sometimes > fail, > > > > > particularly in thepresence of very large
ventricles or > lots of > > > > > damaged white matter or > > > > > both. We have a tutorialon checking and
correcting it > here: > > > > > > > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard....
ori > a > > l_Tala > > > ir > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVT
tDK > b > > HktL7Q > > > rJ > > > > > > > > > >JELPuLToS-_5lkY&s=LpBDOkEFGzHx0owj2xszaOGP5m2RG6gsMN9vq30fOBU&e=
> > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > On > > > > > Mon, 25 Mar 2019, ChhaviYadav wrote:
> > > > > > > > > > > > > > > > > External Email -Use Caution
> > > > > > > > > > > > Hi,I am a beginner tofreesurfer. Never used
it > before. > > > > > > Currently I am workingon 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 errorlog 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...
fo_ > f > > reesur > > > fe > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJJ
ELP > u > > LToS-_ > > > 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...
f > r > > eesurfe > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU20Ws
F > _ > > c8g2VP7 > > > > > > >LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e=
> > > > > > > > > > >
> > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
r > ee > > surfe > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8kv 1 > S2 > > TCg3F > > >
G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e=
> > > > > > > > > > > > > > > > > >
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.harvard.edu_fswiki_FsTu t > ori > > a > > > l_Tala > > > > ir > > > > > > > > > > >ach-5Ffreeview&d=DwIDaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&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.harvard.edu_mailman_listi n > fo_ > > f > > > reesur > > > > fe > > > > > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=jmk4B1izuOm3OQVTtDKbHktL7QrJ J > ELP > > u > > > LToS-_ > > > > 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.edu_mailman_listin fo_ > f > > r > > > eesurfe > > > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQWvKqc6fZyhUQKNa911LU2 0Ws > F > > _ > > > c8g2VP7 > > > > > > > > > LM&s=DgN0IsA48XVzgAFsDxvg5H2euo0dyxsaX8Y4v0koRB0&e= > > > > > > > > > > > > > > >_______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_ f > r > > ee > > > surfe > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-HDM_3l0J3ZVznuaBX1sw-F8k v > 1 > > S2 > > > TCg3F > > > > G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
External Email - Use Caution
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 Cautionok 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 theslices? 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 stillwriterecon-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 Om3OQVTtDKbHktL7QrJ
J > ELP > > u > > > LToS-_ > > > > 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.harvar d.edu_mailman_listin
fo_ > f > > r > > > eesurfe > > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQW vKqc6fZyhUQKNa911LU2
0Ws > F > > _ > > > c8g2VP7 > > > > > > > > > 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 DM_3l0J3ZVznuaBX1sw-F8k
v > 1 > > S2 > > > TCg3F > > > >G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
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External Email - Use Caution
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 Cautionok 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 theslices? 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 stillwriterecon-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 Om3OQVTtDKbHktL7QrJ
J > ELP > > u > > > LToS-_ > > > > 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.harvar
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fo_ > f > > r > > > eesurfe > > > > > > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQW vKqc6fZyhUQKNa911LU2
0Ws > F > > _ > > > c8g2VP7 > > > > > > > > > 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
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f > r > > ee > > > surfe > > >r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=0en6N_H-H DM_3l0J3ZVznuaBX1sw-F8k
v > 1 > > S2 > > > TCg3F > > > >G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >
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page-up/page-down or the arrow keys should scroll through slices. Or alt-[xyz] to change the viewing orientation
On Thu, 28 Mar 2019, Chhavi Yadav wrote:
External Email - Use Caution
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 >>>Om3OQVTtDKbHktL7QrJ >> J >> > ELP >> > > u >> > > > LToS-_ >> > > > > 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.harvar >>>d.edu_mailman_listin >> fo_ >> > f >> > > r >> > > > eesurfe >> > > > > >> > > > > >>>r&d=DwICAg&c=slrrB7dE8n7gBJbeO0g-IQ&r=N9tx5lNt4OZx_Y6zKcYlyQ&m=rJfQ3hIQW >>>vKqc6fZyhUQKNa911LU2 >> 0Ws >> > F >> > > _ >> > > > c8g2VP7 >> > > > > >> > > > > > >> 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 >>>DM_3l0J3ZVznuaBX1sw-F8k >> v >> > 1 >> > > S2 >> > > > TCg3F >> > > > > >>G0&s=9Qp6YLWJpuHPgkqfW-Sv0N-cNqEect_0FX7_G-R_V10&e= >> > > > > >> > > > > >> > > > > >> > > > >> > > > >> > > > >> > > >> > > >> > > >> > >> > >> > >> >> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chhavi Yadav -
Glasser, Matthew