Hi Doug,

Here is output of uname -a: Linux thalamos.nimh.nih.gov 3.10.0-1127.13.1.e17.x96-64 #1 SMP 2020 x86-64 x86-64 GNU/Linux. For the second command: Centos Linux release 7.8.2003 (Core).

My system has the newest AFNI installed, do you think that could be the cause of the problem?

Thanks for your help!

Xiaomin

From: Douglas N. Greve
Sent: Thursday, July 23, 2020 11:00 AM
To: Xiaomin Yue
Subject: Re: FW: [Freesurfer] mri_fieldsign error

No, sorry, When I run it on my system it works. If I can't replicate the problem, I can't fix it. I don't know why you get it and I don't. Can you send me your system specs, ie,
- run uname -a
- the contents of /etc/redhat-release (if it exists)

On 7/23/2020 9:42 AM, Xiaomin Yue wrote:

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Any ideas?

Thanks,

Xiaomin

From: Xiaomin Yue
Sent: Tuesday, July 21, 2020 12:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_fieldsign error

        External Email - Use Caution

I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel fedora’ with the same “segmentation fault (core dumped)” error.

Thanks,

Xiaomin

From: Xiaomin Yue
Sent: Friday, July 17, 2020 6:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_fieldsign error

        External Email - Use Caution

Yes. I will try it on a real Linux box and let you know.

Thanks,

Xiaomin

From: Douglas N. Greve
Sent: Friday, July 17, 2020 5:32 PM
To: Xiaomin Yue; Freesurfer support list
Subject: Re: [Freesurfer] mri_fieldsign error

No, it does not. The only other problem I can think of is that it has something to do with WSL. Do you have a real linux box you can try it on?

On 7/17/2020 5:24 PM, Xiaomin Yue wrote:
External Email - Use Caution

HI Doug,

Sorry for the slow response. I got the same “segmentation fault (core dumped)” error when running the left hemi. I tested it multiple times. Does this function create a detailed log I can send to you?

Thanks,

Xiaomin

From: Douglas N. Greve
Sent: Friday, July 17, 2020 1:07 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_fieldsign error

I was not able to replicate this on my CentOS7 linux box. You sent me left hemi data, so I ran the command below

mri_fieldsign --fs fieldsign.71.nii.gz --polar LOO.wedge.polar.lh.real.nii.gz LOO.wedge.polar.lh.imag.nii.gz --eccen LOO.ring.eccen.lh.real.nii.gz LOO.ring.eccen.lh.imag.nii.gz --s LOO --hemi lh --sphere

But I also noticed that the command that you gave below is for the right hemi. Do you know if the left hemi works?

On 7/11/2020 1:43 PM, Xiaomin Yue wrote:
        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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