External Email - Use Caution
Hi Doug,
The file LOO.tar.gz has been uploaded to transfer/incoming directory on the ftp server. Please let me know what else you need to solve this problem.
Thanks, Xiaomin
From: Douglas N. Grevemailto:dgreve@mgh.harvard.edu Sent: Wednesday, July 15, 2020 11:15 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_fieldsign error
I don't know what is going wrong here. One simple thing to check is to make sure that all the input files have the same number of vertices as the surface. If that is the case, then upload the subject and input files using the instructions below
From the linux command line,
Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file.
On 7/15/2020 11:07 AM, Xiaomin Yue wrote:
External Email - Use Caution Hi All,
Just in case the below poster was missed.
Thanks, Xiaomin
From: Xiaomin Yuemailto:yuexm@hotmail.com Sent: Saturday, July 11, 2020 1:43 PM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_fieldsign error
External Email - Use Caution Hi Doug,
I used FS 7.1 under WSL to analyze retinotopy data. Since the ring and wedge were presented at a different frequency, the data had to be analyzed separately for each condition. To get the field sign, I had to use the mri_fieldsign function to combine polar and eccen data. However, an error happened with running mri_fieldsign: “Segmentation fault (core dumped)”. The following is the command-line output.
Thanks for your help! Xiaomin
cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala cmdline mri_fieldsign --fs LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO --hemi rh --sphere sysname Linux hostname DESKTOP-SVDQE4Q machine x86_64 user xiaominyue eccen real ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz eccen imag ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz patch (null) subject LOO hemi rh fwhm -1.000000 nsmooth -1 fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz usenew 1 Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere Using spherical coordinates Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Complex Ripping Zeros Rot (rad): 0 0 surfer: compute_fieldsign2() dthresh = 1.5 shape = 1 nvertices = 153801 0 0 45452 0.03 33.2224 1018 1000 39160 21.33 -18.3959 2055 2000 44734 43.26 33.0783 3148 3000 49793 65.38 0.653687 4344 4000 38626 88.16 16.7555 5529 5000 54149 110.12 -4.90118 6706 6000 61599 133.36 -5.74607 7971 7000 50134 155.88 -17.5589 9165 8000 34182 178.05 -18.9387 10591 9000 59682 200.70 -4.60514 12034 10000 63856 223.18 -4.4884 13297 11000 41007 245.62 27.3489 14938 12000 27365 267.70 -1.40077 16684 13000 23615 289.10 -0.518007 18048 14000 47088 309.37 18.7017 19798 15000 21060 330.11 15.9458 21681 16000 33067 350.27 -11.1953 23173 17000 28744 371.48 -6.18747 25112 18000 27738 392.41 -6.93845 26953 19000 20538 414.47 2.99349 28903 20000 80583 435.98 -0.338512 30319 21000 16251 459.83 -45.2313 32174 22000 17139 483.36 -2.31642 34093 23000 13307 507.02 19.1461 36170 24000 17826 530.65 -10.7575 37683 25000 69324 555.78 -6.17011 39666 26000 14043 583.29 -10.5151 41746 27000 76017 609.92 -0.0112556 43986 28000 84646 636.28 1.24722 46088 29000 9763 664.26 12.7035 48326 30000 92161 694.30 2.03416 50431 31000 99884 724.91 1.20525 ./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault (core dumped) mri_fieldsign --fs $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s $subjname --hemi $hemi --sphere
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