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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, May 5, 2022 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto: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
sysname Darwin
hostname Hans-iMac-Pro.local
machine x86_64
user fanzhang
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://secure-web.cisco.com/1bFSuAhsJv5-aLIQsXSEJ8ef431QrtxVoVvaxCKWweTwMTWGjMvitxLcoezfFFs-t_D-sZspY9AAeD_qunzj3cUhtpWNeKswGO1jq003s9k_iz-EExOxlsXU_Hg5A3pce_xfBuBom02GkyH3IGzUbb3wOKvUriyElRtgrgRDcDnhKTKefRVWG8RXiB7p3XpEIJTggVyJH2gR7VMExCIYSsNAV8HUi5OsvypVBiYGjkcbw1O0ms-gosdC_Phfr2uSId3ip4SazSzUDk44oiBUNTB5_wdqmyu7S29M2Y65jZgHr0ga3vwBUIzOCN8IzGrSh_9L5uBAF6lNt_myDHGFpyA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1rqAaeD9sQvTm5M2IEQ7kxRmq0VE5-R4IyqqilwuMHt19eCfu-XfHGPGhm_TTF_ilfeBhXlIbE9XR0Dyju7ikxV1KSTlGv4QKKdYrCGyLAm9NRIhzhPZihBahU4uvvH_jR-FCNWMpbwAZ_VkKmpuzASopi2bpqTTMio4ML0DIXoHhs1lPbjKRZnvVba0-ivq89usEKEMdVSfFQZ53zeDZQkAaWFRUOSsNE9R1QVSPZPdQWklEBjDwTXkQTP4r979WJ0httqWkAwmU61A3iujW5bJDyyt7E2788uhiRR7tR7OCF1B75511oqZImC96Nx4FYUZy2u5oTfrRiM6jwCVeFg/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*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21GNU8KkXDZlD12Q*217nh2wJ_qnB1qlhoBnzo_piSFvSQm3tqdVng0Ux7-C0VmV6R2U0n_ERXbjgFNzRU8h7HZ8c3QGR-eTl5v8MPbp41xJg*24__;JSUlJSUlJSUlJSUlJSUlJQ!!GNU8KkXDZlD12Q!89skkf_Lm13yv7_QFBwFmWXhPZlHjpkRJHmrPbBKqs4PjGH-twbVaAm-SlGU0hOdduIgWNglpGU2tBqcyqEUUcAqEQ$>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1prHPT9TOIzH-UewmHUF6AtgiV2z8jXLhDLvBqUFareRyeZIhuL2p0oqBTpr-7PmonPlGJot6AUXm5Avl78UjcFzMas9f0LAbfEZrlwEM9cmvET0H8S9CJuPwiTMkVJtAnyhT1Q3FUIOMtgcxHhRGisNPHqiuHAzleisiKtb7uUG6U1C4yhp9pa6LigbuTtsiUuBow0pNM-3gV900ZWhpzPoKb_AzsMUewlvH1KhL1W0MBE18GicrGoRS9jlxQTEzCf_h3VVECSOsH2_VmKGGIOsycZeydTmRFurUZybKbJvRr99ndUqa5mVwy7T5872Xj4osXV-WOy1O5DMsnUJaWA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1ZX8Uw1WEK2lmrJXpmO220vDD_0yz-jR5bPO6nea6DS1jA4jBpc6_R9iwROF1Hl7MtB6zONggGsZZNmiE5lEVb2a6MztcGXwA4lMLNPkmLjrf9mUrHXdKp2-BwYd6hrojEwqi-JPczIe9N-ni1MCywKxXEa61wBBYIiF4M233N2-9ZVqzVlbST07tdIg8HBzKDm31l1et_m3EKLV4a7wqi7cI2SdN-QEteyGNO2L6STX5C3R0OtNId99t18z0fWkP6T7At31M3z8K03fUbS61sbsf_6QC0kFNRONIicEkFw1hEofcS4FVgjiF9CA7GUGsLjercEPLEv_AzKdEEKnYkg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!GNU8KkXDZlD12Q!89skkf_Lm13yv7_QFBwFmWXhPZlHjpkRJHmrPbBKqs4PjGH-twbVaAm-SlGU0hOdduIgWNglpGU2tBqcyqF0CZg52g$>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
