25 Mar
2019
25 Mar
'19
7:30 p.m.
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= > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >