25 Mar
2019
25 Mar
'19
7:15 p.m.
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= > > > > > > > > >