External Email - Use Caution Thanks for pointing that out! That seems to be working. Jim
On Thu, Dec 28, 2023 at 6:53 PM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > This is from Freesurfer wiki - > https://secure-web.cisco.com/1CkNjrY48pCUahVqRgpWm_wWr-VT402BvZ0Y61vf5NBHE08gelDHJOnnrnONbPXLIsRUSgn-e1KlQ28-1bqlh2D9mdfR4oz5K2DcAapaDi_kIRYa9oOGpUGPN7HBgvT7nsrqBOhDSS1cOpeZ1vlmzNwZczc-cKlN2aymuKdjRBszVXj6pSIzy284SpTKycNB0Fu9kYvlF9WMrQLPBazYr7itkxhkOU3JWMD4-UoiVa9TbyhR71UonTZDQK57ox2IABmOi_Byg-ahMf7rWMa3NdavabkZhRt_6s9jZZE9ooyzXY-aFh0m-UBLCJJ5H-q_XO5-sie0nuzq8b8Z2HV6a3Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUserContributions%2FFAQ > > *Q. I have already skull-stripped data. Can I submit it to recon-all?* > > A: If your skull-stripped volume does not have the cerebellum, then no. If > it does, then yes, however you will have to run the data a bit differently. > > First you must run only -autorecon1 like this: > *recon-all -autorecon1 -noskullstrip -s <subjid>* > > Then you will have to make a symbolic link or copy T1.mgz to > brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. > Finally, open this brainmask.mgz file and check that it looks okay (there > is no skull, cerebellum is intact; use the sample subject *bert* that > comes with your FreeSurfer installation to make sure it looks comparable). > From there you can run the final stages of recon-all: > *recon-all -autrecon2 -autorecon3 -s <subjid>* > > Hope it helps. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *James Hengenius > *Sent:* Thursday, December 28, 2023 5:06 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] Recon-all failing with pre-skullstripped input > data (mri_em_register can't find brainmask.mgz) > > > > * External Email - Use Caution * > > Hello FS experts, > > > > I downloaded some anatomical data. I have defaced full images and > pre-skullstripped images for each participant. I tried the defaced images > first, but FS skullstripping looks a little off (possibly because the > defacing hides bits of the cranium in some images and causes problems in > mri_watershed). So I would like to use the pre-skullstripped files as my > initial inputs. > > > > I have placed the pre-skullstripped file for each participant in > $SUBJECTS_DIR/$subjid/mri/orig/. Each participant's skullstripped input > volume is named 001.mgz. > > > > I then submit the following command in a script to my slurm queue (after > setting appropriate FS env vars), where the script input ${1} is the > $subjid mentioned above: > > > > recon-all \ > -subject ${1} \ > -all \ > -openmp 40 \ > -noskullstrip > > > > The output log from FS ends with the following error. The > function mri_em_register seems to be looking for brainmask.mgz, and fails > to open it. If the input image is already extracted from the skull, do I > need to manually call it brainmask.mgz rather than 001.mgz? Or am I missing > something else in my function call (like order of flags)? Does > -noskullstrip need to come before -openmp, for example? > > > > Thanks! > > Jim H. > > > > End of recon-all output: > > > > writing output to T1.mgz > 3D bias adjustment took 1 minutes and 20 seconds. > @#@FSTIME 2023:12:28:16:07:04 mri_normalize N 7 e 80.39 S 0.66 U 102.70 P > 128% M 581068 F 0 R 24411 W 0 c 32 w 229 I 0 O 0 L 1.00 1.38 9.22 > @#@FSLOADPOST 2023:12:28:16:08:25 mri_normalize N 7 1.99 1.66 8.64 > #------------------------------------- > #@# EM Registration Thu Dec 28 16:08:25 EST 2023 > /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri > > > mri_em_register -uns 3 -mask brainmask.mgz nu.mgz > /home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca > transforms/talairach.lta > > > setting unknown_nbr_spacing = 3 > using MR volume brainmask.mgz to mask input volume... > > > == Number of threads available to mri_em_register for OpenMP = 40 == > reading 1 input volumes... > logging results to talairach.log > reading > '/home/t/tpaus/jhengeni/fs_versions/7.4.1/freesurfer/average/RB_all_2020-01-02.gca'... > GCAread took 0 minutes and 1 seconds. > average std = 7.2 using min determinant for regularization = 5.2 > 0 singular and 884 ill-conditioned covariance matrices regularized > reading 'nu.mgz'... > error: > > *mghRead(/gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/mri/brainmask.mgz, > -1): could not open file^@ error: mri_em_register: could not open mask > volume brainmask.mgz. ^@* > @#@FSTIME 2023:12:28:16:08:25 mri_em_register N 7 e 1.42 S 0.25 U 1.43 P > 118% M 446804 F 0 R 108260 W 0 c 2 w 56 I 0 O 0 L 1.99 1.66 8.64 > @#@FSLOADPOST 2023:12:28:16:08:26 mri_em_register N 7 1.99 1.66 8.64 > Linux nia0918.scinet.local 3.10.0-1160.102.1.el7.x86_64 #1 SMP Tue Oct 17 > 15:42:21 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > > > recon-all -s 1000108_20252_2_0 exited with ERRORS at Thu Dec 28 16:08:26 > EST 2023 > > > For more details, see the log file > /gpfs/fs0/scratch/t/tpaus/jhengeni/subjects_dir_ukb/1000108_20252_2_0/scripts/recon-all.log > To report a problem, see *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > http://secure-web.cisco.com/1XCkDsdJWsMrlmodgOeNiymmGj76pqCRK08EtqMySvGrdmfw8h3NYTyJRqECei8g3O5Uwo5x2JTrz1r7lTmFseSAjfATObLVTGR0_zSK4kFPgOdT9FdzBlH1E96OvjKYM6zEdJsD0YW_TKtV7CgwEafYBK6EKBItOBmsrGdRjtVA6vSPFyzl0GoajATV4VtKWmLcVl9VXh6AgH91SXbjcVD-3UjU4CHiIGU_cGZ27KQzvOoROlWI3gpxUF-JmdxloX-WZ9DrifkTveWgsZetp7AbjDb2GrSQCjLsb1SN36hVdF834reZtB3Wi83ocl0V-0AS-CiWKoM_1L9QjniTMlQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting > <http://secure-web.cisco.com/1ywN1tDbl7MCg8OnWFYEA2Vcf-TaEWXJQlDYsrE7jJo4KqFgIlOWrzhzxDJm5uF11tgXR5fJi2W6vOuAdAAji5cdTjFimLnIGxtWSTB2-y5_HnBRRIRECgA43AhrDctzKRH546l4MaMTjVU30ZQUb5Jk54LqnNfWrh1gB0jsLHkHSgZBFmAXPrV3SIvbWFicYVt_Ebi8mCF-_Gi9xARjm2WPsG0bGNjIIC4gKMbRxQt_nSp83Y3Ik-tj4yEHQqrbfZSKxciUlXvG9xnPomANL8b4bFKfyM3zWmptSyMDvRAsv1F_SGfc8x8zU56LlZL2aPPLp5h3_wxXguFcFo2wxOQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1dhL_R8iRQqwTPDYS1_aBKmgCe1b1HGfzQLXsugQwbsu-lF5HK_ywvvt44-JA-uylpcfPRg3H1o6iiYtQC9H4HSy-XfhKh0cB7pNLe3weIH-2z6naLWPxNpBfMr0Vmf6KcbXhG00-t0ze1aO5J9LlR5GPI5hUMqfQG3ymSBkfK2RfmZ82esb7jOC_YkBr6y9B71gnTLgkx9sqH7pOEcsR0VAgEAP8R2tkCdqK_R-A07W1jdkUVA07hos8phJ4MMUHudWjh4uRjRfW9fAjHJs-z5_U7jiV7TULn15oVkQfZgZmEXMII9TFFlQd-ARZjbJgfh3LbxxCczQb_AXt6knbAA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. 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