19 May
2022
19 May
'22
2:10 p.m.
something went wrong with that process, don't know what
On 5/13/2022 10:35 AM, Zhang, Fan wrote:
External Email - Use Caution
Hi Dr. Greve,
I created the mgh file with “save_mgh” in MATLAB. I am not sure if it showed empty here because the program failed to read it. I was able to run the script with the same mgh files two months ago. I also just verified the mgh file with the “load_mgh” in MATLAB and it showed the dimension is [10242, 1, 1, 78].
Thanks,
Fan
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Thursday, May 12, 2022 10:42 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mri_surf2surf error
That mgh file has nothing in it (all dimensions 0). How did you create it?
On 5/12/2022 5:20 PM, Zhang, Fan wrote:
* External Email - Use Caution * Hi Dr. Greve, I got this when I ran the line you sent. Thanks, Fan Hans-iMac-Pro:CCn_band fanzhang$ mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh Volume information for lh.CCn_band.Seed1_20220314.V1.13subjs.mgh type: MGH dimensions: 0 x 0 x 0 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 0.000 dof: 0 xstart: 0.0, xend: 0.0 ystart: 0.0, yend: 0.0 zstart: 0.0, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 0 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform not present xform info: x_r =-1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s =-1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -1.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 0.0000 0.0000-1.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000-0.0000-0.0000-0.0000 -0.0000-0.0000-1.0000-0.0000 -0.0000 1.0000-0.0000-0.0000 -0.0000-0.0000-0.0000 1.0000 ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Sent:* Thursday, May 5, 2022 3:33 PM *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] mri_surf2surf error what happens if you run mri_info lh.CCn_band.Seed1_20220314.V1.13subjs.mgh On 5/3/2022 11:54 AM, Zhang, Fan wrote: * External Email - Use Caution * Hello Everyone, I am trying to run mri_surf2surf. But I got some errors saying "no such file or directory" while in fact there are files in the pathway. I was able to run this previously, so I am not sure if this is relevant to the recent upgrade of the Mac operation system (12.2.1). My FreeSurfer version is (Darwin-OSX-stable-pub-v6.0.0-2beb96c). Does anyone know how to resolve this? Thank you so much for the help! Fan mri_surf2surf --hemi lh --s fsaverage5 --sval lh.CCn_band.Seed1_20220314.V1.13subjs.mgh --fwhm 13 --tval lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh sysnameDarwin hostname Hans-iMac-Pro.local machinex86_64 userfanzhang srcsubject = fsaverage5 srcval= lh.CCn_band.Seed1_20220314.V1.13subjs.mgh srctype= trgsubject = fsaverage5 trgval= lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame= 0 fwhm-in= 0 fwhm-out= 13 label-src= (null) label-trg= (null) OKToRevFaceOrder= 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere.reg Loading source data MRIallocSequence(0, 0, 0, 0): bad parm No such file or directory Segmentation fault: 11 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1dwqCP0MXI3_CaY2cniBYo29kx3qedM8keYOLSqzupLvxZNJEJ-mAeDt1TyrklMTgSj7jnSEkqKr0kwxYeE-qPOcle0jf8wgfNLnFN2kOFMJ8sOayr9uiBMFqUip_ABQoSAinNIU8hb6I8w4XtCwb3UjWMuvIpJtG4NANE_eQaunDRVJ67OQeGLYi5AWebQsOfmeslk0gPMAJ6qp_Ysq6HLr0oeeVzXSgABbDg4cPZMTjSwLy8VsVXXzdyS4nmGe-rjiw4hYSjGNdTOwuxRAskJBIGIhtjyAGFHTbuJc2sojPs-WBMSncOVs0XDg6XnCXh_QiW1i6nW-1J8hNt3A-bw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1tHRemZ_gTR3c_QCNb4Ux-6Mg4r2Y6qIIX5xkTfD2f-2vvSmVVnJdvoJxXolnSjysiLrCrBf3rl5X-XmvwkGOnjk1UqGOrma26Iq7JEJe_WRmxcDtpgPMqhNcV0aJ1SXPWHFfHzJAPTSK2iqUd_ehj2CSoHKY00gCgy4-S0cQW7GpyMt6hKypvU5uK3rQ-_bY-RhxkJR-pFrcH3a9FYtJoJE_CPqbmi8mrNd49OlHEoY_dLuy5vKCC1IPBvf-6TmJw-UGyQTZy-gEBXBTydzv6BeEf80KAoVZ1Z-3pP971-0JLmqOY3NsRxmTRrFIqhKg%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2F%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21GNU8KkXDZlD12Q%2A217nh2wJ_qnB1qlhoBnzo_piSFvSQm3tqdVng0Ux7-C0VmV6R2U0n_ERXbjgFNzRU8h7HZ8c3QGR-eTl5v8MPbp41xJg%2A24__%3BJSUlJSUlJSUlJSUlJSUlJQ%21%21GNU8KkXDZlD12Q%2189skkf_Lm13yv7_QFBwFmWXhPZlHjpkRJHmrPbBKqs4PjGH-twbVaAm-SlGU0hOdduIgWNglpGU2tBqcyqEUUcAqEQ%24> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/11f-jaQKboNVs15wr5wDs_ccBiOvvvDCgGLVR9t1oAHYvnMFuugo6TeH1lysDc5sXFjOVjGoaCkg6-VawHCevC4nGJim-NVD2bO5vhSIQzy0hpX8oXbM7Hgt5u5EJGr7DoWNgkdAt13LDzvV5pQ1lK-f3qPuXMqs-U07IRxPLDviCWddkmrsn-SjAPncxt9nVmB18uU9cExx3DXMtSW82i_RAJrQVEWK22TiseDMQR7iBgoicjtg7l2AA2IGt_dqeEYg0oDWDVJsRmgBCRE3maCakD-XkvFCxTeyT_P5KFd_HAKLoVaIyFwwRMjoe7NvWxhQxxK1UHBcSL0Z3BIQiwQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__%3B%21%21GNU8KkXDZlD12Q%2189skkf_Lm13yv7_QFBwFmWXhPZlHjpkRJHmrPbBKqs4PjGH-twbVaAm-SlGU0hOdduIgWNglpGU2tBqcyqF0CZg52g%24>
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