Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29
can you email us the full command line and screen output? On Sun, 19 Jan 2020, Devika K wrote: External Email - Use Caution I tried by specicying the subjects name, by following the below command. aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl But still I got the same error. On Sun, Jan 19, 2020, 10:30 PM wrote: Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. RES: Re: freesurfer container - freeview error (marc...@hucff.ufrj.br) 2. registration of dwi images (Sam W) 3. Re: registration of dwi images (Yendiki, Anastasia) 4. Project hippocampus to inflated 3D model? (Mohammad Rashid) 5. Re: aparcstats2table error (Devika K) 6. Re: Project hippocampus to inflated 3D model? (Bruce Fischl) 7. Re: aparcstats2table error (Bruce Fischl) -- Message: 1 Date: Sat, 18 Jan 2020 15:05:15 -0300 From: Subject: [Freesurfer] RES: Re: freesurfer container - freeview error To: Freesurfer support list Message-ID: <5e2383f1.1c69fb81.cfdf5.5...@mx.google.com> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200118/f f64f6b3/attachment-0001.html -- Message: 2 Date: Sun, 19 Jan 2020 00:52:10 +0100 From: Sam W Subject: [Freesurfer] registration of dwi images To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my dataset? After eddy correction I extracted the first b0 image (nodif.nii.gz) and run the bbregister command: bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg /home/samm/nodiffb2orig.dat --dti --init-fsl --o /home/samm/registered_b0.nii.gz Thanks! Sam -- next part -- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/c a86b4c2/attachment-0001.html -- Message: 3 Date: Sun, 19 Jan 2020 00:43:00 + From: "Yendiki, Anastasia" Subject: Re: [Freesurfer] registration of dwi images To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="us-ascii" Hi Sam - You can use mri_vol2vol to apply the transformation that was saved in the registration file nodiffb2orif.dat to any volume that's in the same space as nodif.nii.gz. a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Sam W Sent: Saturday, January 18, 2020 6:52:10 PM To: Freesurfer support list Subject: [Freesurfer] registration of dwi images External Email - Use Caution Hello! I have run eddy on all my dwi images and then run bbregister using the first b0 image as the source image. The b0 image is now well aligned with the anatomical image but how can I apply the same transformation to all other dwi images in my dataset? After eddy correction I extracted the first b0 image (nodif.nii.gz) and run the bbregister command: bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg /home/samm/nodiffb2orig.dat --dti --init-fsl --o /home/samm/registered_b0.nii.gz Thanks! Sam -- next part -- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/6 4bf5201/attachment-0001.html -- Message: 4 Date: Sun, 19 Jan 2020 02:35:22 + From: Mohammad Rashid <
Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29
External Email - Use Caution I tried by specicying the subjects name, by following the below command. aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.tabl But still I got the same error. On Sun, Jan 19, 2020, 10:30 PM wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >1. RES: Re: freesurfer container - freeview error > (marc...@hucff.ufrj.br) >2. registration of dwi images (Sam W) >3. Re: registration of dwi images (Yendiki, Anastasia) >4. Project hippocampus to inflated 3D model? (Mohammad Rashid) >5. Re: aparcstats2table error (Devika K) >6. Re: Project hippocampus to inflated 3D model? (Bruce Fischl) >7. Re: aparcstats2table error (Bruce Fischl) > > > -- > > Message: 1 > Date: Sat, 18 Jan 2020 15:05:15 -0300 > From: > Subject: [Freesurfer] RES: Re: freesurfer container - freeview error > To: Freesurfer support list > Message-ID: <5e2383f1.1c69fb81.cfdf5.5...@mx.google.com> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200118/ff64f6b3/attachment-0001.html > > -- > > Message: 2 > Date: Sun, 19 Jan 2020 00:52:10 +0100 > From: Sam W > Subject: [Freesurfer] registration of dwi images > To: Freesurfer support list > Message-ID: > < > cafyehvvrxw-p0vwvqeia_fmnurmavmsb9wts3zdhlgfvzhc...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello! > I have run eddy on all my dwi images and then run bbregister using the > first b0 image as the source image. > The b0 image is now well aligned with the anatomical image but how can I > apply the same transformation to all other dwi images in my dataset? > > After eddy correction I extracted the first b0 image (nodif.nii.gz) and run > the bbregister command: > bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg > /home/samm/nodiffb2orig.dat --dti --init-fsl --o > /home/samm/registered_b0.nii.gz > > Thanks! > Sam > -- next part -- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/ca86b4c2/attachment-0001.html > > -- > > Message: 3 > Date: Sun, 19 Jan 2020 00:43:00 + > From: "Yendiki, Anastasia" > Subject: Re: [Freesurfer] registration of dwi images > To: Freesurfer support list > Message-ID: > < > bl0pr04mb483326316f9b4242f271210f8a...@bl0pr04mb4833.namprd04.prod.outlook.com > > > > Content-Type: text/plain; charset="us-ascii" > > Hi Sam - You can use mri_vol2vol to apply the transformation that was > saved in the registration file nodiffb2orif.dat to any volume that's in the > same space as nodif.nii.gz. > > a.y > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sam W < > samf...@gmail.com> > Sent: Saturday, January 18, 2020 6:52:10 PM > To: Freesurfer support list > Subject: [Freesurfer] registration of dwi images > > > External Email - Use Caution > > Hello! > I have run eddy on all my dwi images and then run bbregister using the > first b0 image as the source image. > The b0 image is now well aligned with the anatomical image but how can I > apply the same transformation to all other dwi images in my dataset? > > After eddy correction I extracted the first b0 image (nodif.nii.gz) and > run the bbregister command: > bbregister --s sub001 --mov /home/samm/nodif.nii.gz --reg > /home/samm/nodiffb2orig.dat --dti --init-fsl --o > /home/samm/registered_b0.nii.gz > > Thanks! > Sam > -- next part -- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/64bf5201/attachment-0001.html > > -- > > Message: 4 > Date: Sun, 19 Jan 2020 02:35:22 + > From: Mohammad Rashid <17m...@queensu.ca> > Subject: [Freesurfer] Project hippocampus to inflated 3D model? > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > < > ytxpr0101mb0990c9b2c52a93b6dedfae43e7...@ytxpr0101mb0990.canprd01.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > External Email -
