[Freesurfer] Change image orientation
External Email - Use Caution Dear Freesurfer devs, Is possible to change the image orientation of the t1.nii images? In that case, what command should be used?. I would like to change them from a LPI orientation to a RAI orientation. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Change image orientation
External Email - Use Caution Hi Miguel, this should work with mri_convert --in_orientation RAI t1.nii t1_RAI.nii. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu Im Auftrag von Miguel Ángel Rivas Fernández Gesendet: Freitag, 5. Juli 2019 11:00 An: Freesurfer support list Betreff: [Freesurfer] Change image orientation External Email - Use Caution Dear Freesurfer devs, Is possible to change the image orientation of the t1.nii images? In that case, what command should be used?. I would like to change them from a LPI orientation to a RAI orientation. Best regards, -- Miguel Ángel Rivas Fernández ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Change image orientation
Hi Miguel yes, check out the help text in mri_convert. It should give you the info you need. cheers Bruce On Fri, 5 Jul 2019, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Dear Freesurfer devs, Is possible to change the image orientation of the t1.nii images? In that case, what command should be used?. I would like to change them from a LPI orientation to a RAI orientation. Best regards, -- Miguel Ángel Rivas Fernández ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] rostral anterior cingulate fix?
Hi Victor can you render the parcellation in that area on the surface (in freeview) and show it to us? cheers Bruce On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: Hi Freesurfer group - I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm seeing a misparcellation of the right rostral anterior cingulate using tkmedit (I know tkmedit is sorta deprecated), and it doesn't seem inappropriate to use control point fixes. How would you best fix this (I'm open to using freeview), without just editing the aparc+aseg.mgz? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in mris_convert thickness file from ascii format
External Email - Use Caution Hi Bruce, I obtained the curv vector and used read_surf.m to get the face lists in lh.inflated for fsaverage. If the faces list was generated as a 327680x3 double, would it be correct to say that the number of faces is 327680 as the input argument for write_curv.m? Thanks so much for your help, JeeSu -- Date: Thu, 4 Jul 2019 12:56:57 -0400 (EDT) From: Bruce Fischl Subject: Re: [Freesurfer] Error in mris_convert thickness file from ascii format To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8" Hi JeeSu which surface you use is irrelevant (we only need one with the right topology). As for converting from ascii back to curv, matlab is probably the easist using read_ascii_curv.m and write_curv.m. You will need to also read in a surface to get the number of faces. Again, any one of the same topology ones should be fine (e.g. lh.inflated for lh.thickness.asc) cheers Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in mris_convert thickness file from ascii format
yes, I believe so cheers Bruce On Fri, 5 Jul 2019, Jee Su Suh wrote: External Email - Use Caution Hi Bruce, I obtained the curv vector and used read_surf.m to get the face lists in lh.inflated for fsaverage. If the faces list was generated as a 327680x3 double, would it be correct to say that the number of faces is 327680 as the input argument for write_curv.m? Thanks so much for your help, JeeSu -- Date: Thu, 4 Jul 2019 12:56:57 -0400 (EDT) From: Bruce Fischl Subject: Re: [Freesurfer] Error in mris_convert thickness file from ascii format To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8" Hi JeeSu which surface you use is irrelevant (we only need one with the right topology). As for converting from ascii back to curv, matlab is probably the easist using read_ascii_curv.m and write_curv.m. You will need to also read in a surface to get the number of faces. Again, any one of the same topology ones should be fine (e.g. lh.inflated for lh.thickness.asc) cheers Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [External] Re: rostral anterior cingulate fix?
Sorry, I thought I attached something Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Friday, July 5, 2019 10:24 AM To: Freesurfer support list Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix? Hi Victor can you render the parcellation in that area on the surface (in freeview) and show it to us? cheers Bruce On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > > Hi Freesurfer group - > > > I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm > seeing a misparcellation of > the right rostral anterior cingulate using tkmedit (I know tkmedit is sorta > deprecated), and it > doesn't seem inappropriate to use control point fixes. How would you best fix > this (I'm open to > using freeview), without just editing the aparc+aseg.mgz? > > > Victor Zeng > Beth Israel Deaconess Medical Center > Keshavan Lab > ph: 617 754 1237 > -- > > > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain > information that is privileged, confidential, or otherwise protected from > disclosure under > applicable law. If you are not the intended recipient, any dissemination, > distribution, copying, or > use of this information is prohibited. If you have received this message in > error, please > permanently delete it and immediately notify the sender. Thank you. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] [External] Re: rostral anterior cingulate fix?
you did, but not a surface rendering. Load it with freeview and show it as a surface (maybe inflated and white) On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > > Sorry, I thought I attached something > Victor Zeng > Beth Israel Deaconess Medical Center > Keshavan Lab > ph: 617 754 1237 > -- > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Friday, July 5, 2019 10:24 AM > To: Freesurfer support list > Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix? > > Hi Victor > > can you render the parcellation in that area on the surface (in freeview) > and show it to us? > > cheers > Bruce > > > On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > >> >> Hi Freesurfer group - >> >> >> I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm >> seeing a misparcellation of >> the right rostral anterior cingulate using tkmedit (I know tkmedit is sorta >> deprecated), and it >> doesn't seem inappropriate to use control point fixes. How would you best >> fix this (I'm open to >> using freeview), without just editing the aparc+aseg.mgz? >> >> >> Victor Zeng >> Beth Israel Deaconess Medical Center >> Keshavan Lab >> ph: 617 754 1237 >> -- >> >> >> >> This message is intended for the use of the person(s) to whom it may be >> addressed. It may contain >> information that is privileged, confidential, or otherwise protected from >> disclosure under >> applicable law. If you are not the intended recipient, any dissemination, >> distribution, copying, or >> use of this information is prohibited. If you have received this message in >> error, please >> permanently delete it and immediately notify the sender. Thank you. >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all Error : inputs cannot have multiple frames.
External Email - Use Caution My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple? My inputs' format is dicom,when it is about 200kB,the software can run and has no such error.but when the dicom is more than 500kB,the next error will happen: Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames My English is so bad that you know.. Forgive me,please! WISH TO YOUR TEACHING AND REPLY. From a graduate student of China Liaoning University .___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all Error : inputs cannot have multiple frames.
I think the dicom series that 1.DCM is part of is not a 3D T1-weighted structural. Can you run mri_info on it, or dcmdump (or both)? On Sat, 6 Jul 2019, Yueming wrote: External Email - Use Caution My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple? My inputs' format is dicom,when it is about 200kB,the software can run and has no such error.but when the dicom is more than 500kB,the next error will happen: [IMAGE] Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames My English is so bad that you know.. Forgive me,please! WISH TO YOUR TEACHING AND REPLY. From a graduate student of China Liaoning University . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
