Re: [Freesurfer] Problem with version of mri_surfcluster provided with fspalm
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-boun...@nmr.mgh.harvard.edu on behalf of Syam Gadde 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 1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; MRISread(^Y$<91>^?): could not open file Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory When I removed the --vwsigmax option and ran the old version, it runs to completion, and the following line: MRISread(^Y$<91>^?): could not open file does not show up in the output. -syam From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Syam Gadde 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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve 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 Caution > > 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 > 1.0 0.0 0.0 0.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0
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 1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; MRISread(^Y$<91>^?): could not open file Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white No such file or directory When I removed the --vwsigmax option and ran the old version, it runs to completion, and the following line: MRISread(^Y$<91>^?): could not open file does not show up in the output. -syam From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Syam Gadde 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-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve 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 Caution > > 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 > 1.0 0.0 0.0 0.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > Reading source surface > /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white > MRISread(x� 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/sea
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-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
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 Caution
>
> 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
> 1.0 0.0 0.0 0.0;
> 0.0 1.0 0.0 0.0;
> 0.0 0.0 1.0 0.0;
> 0.0 0.0 0.0 1.0;
>
> Reading source surface
> /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
> MRISread(x� 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*40nmr.mgh.harvard.edu&q=subject:*22*5C*5BFreesurfer*5C*5D*mri_surfcluster*ERROR*22&o=newest__;JSUlJSUlKysl!!OToaGQ!6icEV7Ijpg_iXl84kozP0KIV4fJUaOMqLJm_oi2GXBV86XgSCZYAPk2pXCLJTQMHJQ$
>
> 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^?): c
> ould not open file) = 37
> ...
>
> Any thoughts on how to proceed? Thanks,
>
> -syam
>
>
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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 Caution
>
> 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
> 1.0 0.0 0.0 0.0;
> 0.0 1.0 0.0 0.0;
> 0.0 0.0 1.0 0.0;
> 0.0 0.0 0.0 1.0;
>
> Reading source surface
> /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
> MRISread(x� 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=subject:%22%5C%5BFreesurfer%5C%5D+mri_surfcluster+ERROR%22&o=newest
>
> 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^?): 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
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[Freesurfer] Problem with version of mri_surfcluster provided with fspalm
External Email - Use Caution
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
1.0 0.0 0.0 0.0;
0.0 1.0 0.0 0.0;
0.0 0.0 1.0 0.0;
0.0 0.0 0.0 1.0;
Reading source surface
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white
MRISread(x�https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+mri_surfcluster+ERROR%22&o=newest
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^?): c
ould not open file) = 37
...
Any thoughts on how to proceed? Thanks,
-syam
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