[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 Fernánd

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 li

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 im

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 mispar

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

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 cor

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 li

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

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

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,W