External Email - Use Caution
I don’t see freeview directly linking against libXm.so from Motif, though it does link against X windows libraries like libXmu.so and libX11.so. You can see this with the “ldd” command (some examples in screenshot below). I don't think the RPM installer for freesurfer installs any Motif libraries. I don't have any Motif libraries installed on my CentOS 7.7 image running under WSL that runs freeview/freesurfer. Now it could be you installed some packages on your system that installed Motif and/or also maybe changed the X windows distribution libraries (as used by freeview). - R..
On Jul 9, 2020, at 12:54, Xiaomin Yue <yuexm@hotmail.com> wrote: External Email - Use Caution Hi, Here is the command I used in the freeview 3.0: freeview – f $SUBJECTS_DIR/LOO/surf/lh.inflated. lh.inflated was created using FS7.1. The freeview display is attached in this email. The inflated brain is displayed correctly when I run the same command in freeview 2.0. (see attached). Thanks,Xiaomin From: fsbuildSent: Thursday, July 9, 2020 1:56 AMTo: freesurfer@nmr.mgh.harvard.eduCc: yuexm@hotmail.comSubject: Re: [Freesurfer] freeview 3.0 External Email - Use Caution Hello Xiaomin, It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment. - R. On Jul 8, 2020, at 12:08, Xiaomin Yue <yuexm@hotmail.com> wrote: External Email - Use Caution Dear all, The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color. The Freeview is currently running under WSL and was running without a problem until I updated libXm4. Is there a particular library file associated with libXm4 the Freeview needs to run without this problem? ThanksXiaomin_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0%C2%A0%3Cf... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks for your response. Why does freeview 2 work?
Thanks, Xiaomin
From: fsbuildmailto:fsbuild@contbay.com Sent: Thursday, July 9, 2020 10:20 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: yuexm@hotmail.commailto:yuexm@hotmail.com Subject: Re: [Freesurfer] freeview 3.0
External Email - Use Caution I don’t see freeview directly linking against libXm.so from Motif, though it does link against X windows libraries like libXmu.so and libX11..so. You can see this with the “ldd” command (some examples in screenshot below). I don't think the RPM installer for freesurfer installs any Motif libraries. I don't have any Motif libraries installed on my CentOS 7.7 image running under WSL that runs freeview/freesurfer.
Now it could be you installed some packages on your system that installed Motif and/or also maybe changed the X windows distribution libraries (as used by freeview).
- R.
On Jul 9, 2020, at 12:54, Xiaomin Yue yuexm@hotmail.com wrote:
External Email - Use Caution
Hi,
Here is the command I used in the freeview 3.0: freeview – f $SUBJECTS_DIR/LOO/surf/lh.inflated. lh.inflated was created using FS7.1. The freeview display is attached in this email. The inflated brain is displayed correctly when I run the same command in freeview 2.0. (see attached).
Thanks, Xiaomin
From: fsbuildmailto:fsbuild@contbay.com Sent: Thursday, July 9, 2020 1:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: yuexm@hotmail.commailto:yuexm@hotmail.com Subject: Re: [Freesurfer] freeview 3.0
External Email - Use Caution Hello Xiaomin,
It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment.
- R.
On Jul 8, 2020, at 12:08, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Dear all,
The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color. The Freeview is currently running under WSL and was running without a problem until I updated libXm4. Is there a particular library file associated with libXm4 the Freeview needs to run without this problem?
Thanks Xiaomin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<freeview2_inflated.jpg><freeview3_inflated.jpg>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Xiaomin,
Freeview 2 was built against much older Qt and VTK libraries. But unfortunately we still do not know why the new version has problem with libXm4. Is there any way you can revert back to your previous libXm? From the screenshot you sent it appears to be some kind of rendering artifact, which could result from a lot of factors, such as incompatible libraries or graphics card driver.
Ruopeng
On Jul 9, 2020, at 10:38 PM, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Thanks for your response. Why does freeview 2 work?
Thanks, Xiaomin
From: fsbuildmailto:fsbuild@contbay.com Sent: Thursday, July 9, 2020 10:20 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: yuexm@hotmail.commailto:yuexm@hotmail.com Subject: Re: [Freesurfer] freeview 3.0
External Email - Use Caution
I don’t see freeview directly linking against libXm.so from Motif, though it does link against X windows libraries like libXmu.so and libX11..so. You can see this with the “ldd” command (some examples in screenshot below). I don't think the RPM installer for freesurfer installs any Motif libraries. I don't have any Motif libraries installed on my CentOS 7.7 image running under WSL that runs freeview/freesurfer.
Now it could be you installed some packages on your system that installed Motif and/or also maybe changed the X windows distribution libraries (as used by freeview).
- R.
On Jul 9, 2020, at 12:54, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Hi,
Here is the command I used in the freeview 3.0: freeview – f $SUBJECTS_DIR/LOO/surf/lh.inflated. lh.inflated was created using FS7.1. The freeview display is attached in this email. The inflated brain is displayed correctly when I run the same command in freeview 2.0. (see attached).
Thanks, Xiaomin
From: fsbuildmailto:fsbuild@contbay.com Sent: Thursday, July 9, 2020 1:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: yuexm@hotmail.commailto:yuexm@hotmail.com Subject: Re: [Freesurfer] freeview 3.0
External Email - Use Caution Hello Xiaomin,
It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment.
- R.
On Jul 8, 2020, at 12:08, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Dear all,
The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color. The Freeview is currently running under WSL and was running without a problem until I updated libXm4. Is there a particular library file associated with libXm4 the Freeview needs to run without this problem?
Thanks Xiaomin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<freeview2_inflated.jpg><freeview3_inflated.jpg>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Ruopeng,
Thanks for taking time to answer my question. I wish I can revert back to the early version of libraries Freeview uses. Is there a way to figure out version number of libraries asccoated with Freeview? If not, I has to stick with freeview 2.
Thanks, Xiaomin
From: Wang, Ruopengmailto:RWANG4@mgh.harvard.edu Sent: Friday, July 10, 2020 9:08 AM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview 3.0
Hi Xiaomin,
Freeview 2 was built against much older Qt and VTK libraries. But unfortunately we still do not know why the new version has problem with libXm4. Is there any way you can revert back to your previous libXm? From the screenshot you sent it appears to be some kind of rendering artifact, which could result from a lot of factors, such as incompatible libraries or graphics card driver.
Ruopeng
On Jul 9, 2020, at 10:38 PM, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Thanks for your response. Why does freeview 2 work?
Thanks, Xiaomin
From: fsbuildmailto:fsbuild@contbay.com Sent: Thursday, July 9, 2020 10:20 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: yuexm@hotmail.commailto:yuexm@hotmail.com Subject: Re: [Freesurfer] freeview 3.0
External Email - Use Caution I don’t see freeview directly linking against libXm.so from Motif, though it does link against X windows libraries like libXmu.so and libX11..so. You can see this with the “ldd” command (some examples in screenshot below). I don't think the RPM installer for freesurfer installs any Motif libraries. I don't have any Motif libraries installed on my CentOS 7.7 image running under WSL that runs freeview/freesurfer.
Now it could be you installed some packages on your system that installed Motif and/or also maybe changed the X windows distribution libraries (as used by freeview).
- R.
On Jul 9, 2020, at 12:54, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Hi,
Here is the command I used in the freeview 3.0: freeview – f $SUBJECTS_DIR/LOO/surf/lh.inflated. lh.inflated was created using FS7.1. The freeview display is attached in this email. The inflated brain is displayed correctly when I run the same command in freeview 2.0. (see attached).
Thanks, Xiaomin
From: fsbuildmailto:fsbuild@contbay.com Sent: Thursday, July 9, 2020 1:56 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Cc: yuexm@hotmail.commailto:yuexm@hotmail.com Subject: Re: [Freesurfer] freeview 3.0
External Email - Use Caution Hello Xiaomin,
It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment.
- R.
On Jul 8, 2020, at 12:08, Xiaomin Yue <yuexm@hotmail.commailto:yuexm@hotmail.com> wrote:
External Email - Use Caution
Dear all,
The Freeview (3.0) coming with fs 7.1 can not show any surface brain (inflated, pial, white) in a solid color. The Freeview is currently running under WSL and was running without a problem until I updated libXm4. Is there a particular library file associated with libXm4 the Freeview needs to run without this problem?
Thanks Xiaomin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<freeview2_inflated.jpg><freeview3_inflated.jpg>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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Is the fMRI data in there somewhere? I can't find it
On 7/15/2020 2:21 PM, Xiaomin Yue wrote:
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. Greve mailto:dgreve@mgh.harvard.edu *Sent: *Wednesday, July 15, 2020 11:15 AM *To: *freesurfer@nmr.mgh.harvard.edu mailto: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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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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Douglas N. Greve -
fsbuild -
Wang, Ruopeng -
Xiaomin Yue