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 Yue mailto:yuexm@hotmail.com *Sent: *Saturday, July 11, 2020 1:43 PM *To: *Freesurfer support list mailto: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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