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Hi,
We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error:
mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
and the end of its output:
<...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory -----
It is the same error reported in these emails:
https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q...
but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace:
... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ...
Any thoughts on how to proceed? Thanks,
-syam
Hi Syam, it looks like fspalm is not creating the correct command line for mri_surfcluster (the --in should be an output of palm, not the fsaverage surface). Can you send the full terminal output? doug
On 3/25/2020 9:13 AM, Syam Gadde wrote:
External Email - Use CautionHi,
We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error:
mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
and the end of its output:
<...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory
It is the same error reported in these emails:
https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q...
but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace:
... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ...
Any thoughts on how to proceed? Thanks,
-syam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Actually I was just sending an example command to demonstrate the same error. I'll see if I can get the actual command fspalm was running.
-syam
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, March 27, 2020 10:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
Hi Syam, it looks like fspalm is not creating the correct command line for mri_surfcluster (the --in should be an output of palm, not the fsaverage surface). Can you send the full terminal output? doug
On 3/25/2020 9:13 AM, Syam Gadde wrote:
External Email - Use CautionHi,
We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error:
mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
and the end of its output:
<...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory
It is the same error reported in these emails:
https://urldefense.com/v3/__https://www.mail-archive.com/search?l=freesurfer...
but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace:
... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ...
Any thoughts on how to proceed? Thanks,
-syam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
External Email - Use Caution
This is the actual command that fails:
mri_surfcluster --in rh.50to50.glmdir//con_nonpos/sig.mgh --mask rh.50to50.glmdir//mask.mgh --cwsig rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.mgh --sum rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary --ocn rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh --annot aparc --cwpvalthresh .05 --o rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh --no-fixmni --csd rh.50to50.glmdir//csd/--perm-resid.j001-con_nonpos.csd --csdpdf rh.50to50.glmdir//con_nonpos/--perm-resid.pdf.dat --vwsig rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.mgh --vwsigmax rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.max.dat --oannot rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.annot --surf white
Output is:
Creating CDFs from CSD files csd->threshsign = 0 thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ hemi = rh srcid = rh.50to50.glmdir//con_nonpos/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh MGH ocnid = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh MGH sumfile = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 0 Found 149926 vertices in mask Found 149926 vertices in mask Found 149926 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm
1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread(<D8>^Y$<91><FC>^?): could not open file ---------------------------------------------------- Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory
When I removed the --vwsigmax option and ran the old version, it runs to completion, and the following line:
MRISread(<D8>^Y$<91><FC>^?): could not open file
does not show up in the output.
-syam
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Syam Gadde syam.gadde@duke.edu Sent: Friday, March 27, 2020 11:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
External Email - Use Caution
Actually I was just sending an example command to demonstrate the same error. I'll see if I can get the actual command fspalm was running.
-syam
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, March 27, 2020 10:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
Hi Syam, it looks like fspalm is not creating the correct command line for mri_surfcluster (the --in should be an output of palm, not the fsaverage surface). Can you send the full terminal output? doug
On 3/25/2020 9:13 AM, Syam Gadde wrote:
External Email - Use CautionHi,
We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error:
mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
and the end of its output:
<...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory
It is the same error reported in these emails:
https://urldefense.com/v3/__https://www.mail-archive.com/search?l=freesurfer...
but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace:
... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ...
Any thoughts on how to proceed? Thanks,
-syam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
External Email - Use Caution
Just to update, I found another version of mri_surfcluster that you (Doug) linked from the archives, with a build date of April 3, 2019, and that apparently worked just fine. I'm not sure where I got the one I downloaded. Sorry for the red herrings!
-syam
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Syam Gadde syam.gadde@duke.edu Sent: Friday, March 27, 2020 12:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
External Email - Use Caution
This is the actual command that fails:
mri_surfcluster --in rh.50to50.glmdir//con_nonpos/sig.mgh --mask rh.50to50.glmdir//mask.mgh --cwsig rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.mgh --sum rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary --ocn rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh --annot aparc --cwpvalthresh .05 --o rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh --no-fixmni --csd rh.50to50.glmdir//csd/--perm-resid.j001-con_nonpos.csd --csdpdf rh.50to50.glmdir//con_nonpos/--perm-resid.pdf.dat --vwsig rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.mgh --vwsigmax rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.max.dat --oannot rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.annot --surf white
Output is:
Creating CDFs from CSD files csd->threshsign = 0 thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ hemi = rh srcid = rh.50to50.glmdir//con_nonpos/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh MGH ocnid = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh MGH sumfile = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 0 Found 149926 vertices in mask Found 149926 vertices in mask Found 149926 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm
1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread(<D8>^Y$<91><FC>^?): could not open file ---------------------------------------------------- Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory
When I removed the --vwsigmax option and ran the old version, it runs to completion, and the following line:
MRISread(<D8>^Y$<91><FC>^?): could not open file
does not show up in the output.
-syam
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Syam Gadde syam.gadde@duke.edu Sent: Friday, March 27, 2020 11:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
External Email - Use Caution
Actually I was just sending an example command to demonstrate the same error. I'll see if I can get the actual command fspalm was running.
-syam
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Friday, March 27, 2020 10:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
Hi Syam, it looks like fspalm is not creating the correct command line for mri_surfcluster (the --in should be an output of palm, not the fsaverage surface). Can you send the full terminal output? doug
On 3/25/2020 9:13 AM, Syam Gadde wrote:
External Email - Use CautionHi,
We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error:
mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
and the end of its output:
<...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000;
Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory
It is the same error reported in these emails:
https://urldefense.com/v3/__https://www.mail-archive.com/search?l=freesurfer...
but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace:
... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ...
Any thoughts on how to proceed? Thanks,
-syam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.com/v3/__https://mail.nmr.mgh.harvard.edu/mailman/listinf...
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Syam Gadde