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 <freesurfer-requ...@nmr.mgh.harvard.edu> 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: <marc...@hucff.ufrj.br> > Subject: [Freesurfer] RES: Re: freesurfer container - freeview error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > 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 <samf...@gmail.com> > Subject: [Freesurfer] registration of dwi images > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > 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 +0000 > From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu> > Subject: Re: [Freesurfer] registration of dwi images > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > 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 <freesurfer@nmr.mgh.harvard.edu> > 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 +0000 > From: Mohammad Rashid <17m...@queensu.ca> > Subject: [Freesurfer] Project hippocampus to inflated 3D model? > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > ytxpr0101mb0990c9b2c52a93b6dedfae43e7...@ytxpr0101mb0990.canprd01.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hello, > > I have had success projecting regions such as the entorhinal region to an > inflated 3D model. But I can't seem to do the same for hippocampi. I > wouldn't need any hippocampal subfields, just projecting the hippocampus as > a whole would be useful. Is there perhaps a particular file used for this > that I am missing? > > Any help is appreciated, > Mohammad Rashid > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/c73c92f1/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Sun, 19 Jan 2020 19:36:43 +0530 > From: Devika K <devikakutt...@gmail.com> > Subject: Re: [Freesurfer] aparcstats2table error > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CA+m7eQEvrwLAmdCt6Oo+X9-78OtP1= > oubwqyxim15mn3drk...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > I tried doing cortical parcellation using Destrieux atlas. I ran the > aparcstats2table command from the SUBJECTS_DIR directory containing all of > the output from recon-all. > But I got an error, PFA. Do I need to run any other commands before running > aparcstats2table command, I would be grateful if anyone could help me to > resolve this issue. > > Many thanks in advance. > Regards > Devika K > Research Scholar, Dept of EEE > e: k_dev...@cb.students.amrita.edu > Amrita Vishwa Vidyapeetham > Coimbatore, India > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/fe6bf01e/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Screenshot from 2020-01-19 16-06-48.png > Type: image/png > Size: 226736 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200119/fe6bf01e/attachment-0001.png > > ------------------------------ > > Message: 6 > Date: Sun, 19 Jan 2020 11:33:22 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Project hippocampus to inflated 3D model? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.21.2001191132410.4...@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mohammad > > you can use mri_tessellate or mri_mc to build a mesh model of the > hippocampus from the aseg if you want, then use mris_inflate on it. You > will lose internal structure though. > > cheers > Bruce > On Sun, 19 Jan 2020, Mohammad Rashid > wrote: > > > > > ????????External Email - Use Caution???????? > > > > Hello, > > > > I have had success projecting regions such as the entorhinal region to an > > inflated 3D model. But I can't seem to do the same for hippocampi. I > > wouldn't need any hippocampal subfields, just projecting the hippocampus > as > > a whole would be useful. Is there perhaps a particular file used for this > > that I am missing? > > > > Any help is appreciated, > > Mohammad Rashid > > > > > > ------------------------------ > > Message: 7 > Date: Sun, 19 Jan 2020 11:38:26 -0500 (EST) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] aparcstats2table error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.21.2001191137270.4...@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Devika > > In the future can you include the text of the command and the output in > your email instead of a screenshot? That will make our job easier. > > Try specifying which subjects you want processed explicitly with > --subjects > > cheers > Bruce > > On Sun, 19 Jan > 2020, Devika K wrote: > > > > > ????????External Email - Use Caution???????? > > > > I tried doing cortical parcellation using Destrieux atlas.? I ran the > > aparcstats2table command from the SUBJECTS_DIR directory containing all > of > > the output from recon-all. > > But I got an error, PFA. Do I need to run any other commands before > running > > aparcstats2table command, I would be grateful if anyone could? help me to > > resolve this issue. > > > > Many thanks in advance.[cleardot.gif] > > Regards > > Devika K > > Research Scholar, Dept of EEE > > e:?k_dev...@cb.students.amrita.edu > > Amrita Vishwa Vidyapeetham > > Coimbatore, India > > > > > > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 191, Issue 29 > ******************************************* >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
