A few more questions
1. How much memory do you have on your system? You can find it from the first line of /proc/meminfo It should be something like "MemTotal: 131781468 kB"
2. What environmental limits do you have? Send the result of the "limit" unix command
3. I put a new version of mri_fieldsign here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fieldsign. Can you run this version and send me the terminal output? Also, if you can run it outside of your bash script, it would be better.
On 7/24/2020 9:44 AM, Xiaomin Yue wrote:
External Email - Use Caution
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 mailto:dgreve@mgh.harvard.edu *Sent: *Thursday, July 23, 2020 11:00 AM *To: *Xiaomin Yue mailto:yuexm@hotmail.com *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:
* External Email - Use Caution * Any ideas? Thanks, Xiaomin *From: *Xiaomin Yue <mailto:yuexm@hotmail.com> *Sent: *Tuesday, July 21, 2020 12:36 PM *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *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 <mailto:yuexm@hotmail.com> *Sent: *Friday, July 17, 2020 6:07 PM *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *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 <mailto:dgreve@mgh.harvard.edu> *Sent: *Friday, July 17, 2020 5:32 PM *To: *Xiaomin Yue <mailto:yuexm@hotmail.com>; Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *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 <mailto:dgreve@mgh.harvard.edu> *Sent: *Friday, July 17, 2020 1:07 PM *To: *freesurfer@nmr.mgh.harvard.edu <mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.