External Email - Use Caution        

Hi All,

 

Just in case the below poster was missed.

 

Thanks,

Xiaomin

 

From: Xiaomin Yue
Sent: Saturday, July 11, 2020 1:43 PM
To: Freesurfer support list
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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