Can you send the recon-all.log file?

On 10/9/2020 12:47 PM, Kathy L. Pearson wrote:

     External Email - Use Caution

No, it does not exist, and my question is why not in 7.1.0 when it is created with the same two commands in 5.3.0?

Thanks,

Kathy

...

Douglas N. Greve Fri, 09 Oct 2020 05:49:32 -0700 does that file exist?

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From: Kathy L. Pearson Sent: Thursday, October 8, 2020 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: surf pial_lgi not created in version 7.1.0

In freesurfer version 5.3.0, I can successfully run: recon-all -autorecon-all -mprage -s $subj -qcache -localGI recon-all -s $subj -qcache -measure pial_lgi

However, the same commands with 7.1.0 give an error after this last of a number of generated statements and no surf/*pial_lgi output: mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find subjects/147608/surf/lh.pial_lgi

Is a new command needed for version 7.1.0?

Thanks,

Kathy Pearson

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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This was resolved for me by copying from: 5.3.0/matlab/freesurfer_read_surf.m to: 7.1.0/matlab/freesurfer_read_surf.m

Before the copy, here is the difference:

diff 5.3.0/matlab/freesurfer_read_surf.m 7.1.0/matlab/freesurfer_read_surf.m

63d62 < % $Revision: 1.2 $ $Date: 2011/02/07 21:47:40 $ 71d69 < ver = '$Revision: 1.2 $ $Date: 2011/02/07 21:47:40 $';

where the 7.1.0 files does not have the ver string assignment though it's still referenced on line 70 and fails. There I assume the result from the MATLAB ver command cannot be parsed as a string.

cat -n 7.1.0/matlab/freesurfer_read_surf.m | head -70 | tail -1

70 fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

This is the original error from recon-all.log:

...

Warning: Input argument must be a string.

In ver at 41

In freesurfer_read_surf at 70 In find_corresponding_center_FSformat at 26 Error using fprintf Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

Kathy Pearson

________________________________________ From: Kathy L. Pearson kathy.pearson@colorado.edu Sent: Monday, October 19, 2020 6:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: surf pial_lgi not created in version 7.1.0

I am getting this error near the tail of the 7.1.0 recon-all.log file just before exit: ERROR: find_corresponding_center_FSformat did not complete successfully!

At this link from May 13: https://secure-web.cisco.com/1H8AMDJGjoaHX6eaKCFT2xE-ACbjSllNjv09F_JjrEcEUef... I see that you have posted in reference to a similar question: https://secure-web.cisco.com/1xjmPynA224fZS8oQlIMV5RGT_s0q2Arf3gz8JTt4nmahpF...

If this is different from the 7.1.0 distribution's file in the matlab directory May 11 10:04 find_corresponding_center_FSformat.m please let me know what authentication login/password combination is needed to access this to see if it will fix my errors.

Is this file updated in the newer 7.1.1?

Thanks,

Kathy

Douglas N. Greve Mon, 19 Oct 2020 07:42:01 -0700 Can you send the recon-all.log file?

______________________________________ From: Kathy L. Pearson kathy.pearson@colorado.edu Sent: Friday, October 9, 2020 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: surf pial_lgi not created in version 7.1.0

No, it does not exist, and my question is why not in 7.1.0 when it is created with the same two commands in 5.3.0?

Thanks,

Kathy

Douglas N. Greve Fri, 09 Oct 2020 05:49:32 -0700 does that file exist?

________________________________________ From: Kathy L. Pearson Sent: Thursday, October 8, 2020 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: surf pial_lgi not created in version 7.1.0

In freesurfer version 5.3.0, I can successfully run: recon-all -autorecon-all -mprage -s $subj -qcache -localGI recon-all -s $subj -qcache -measure pial_lgi

However, the same commands with 7.1.0 give an error after this last of a number of generated statements and no surf/*pial_lgi output: mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find subjects/147608/surf/lh.pial_lgi

Is a new command needed for version 7.1.0?

Thanks,

Kathy Pearson

External Email - Use Caution

Yes. On May 14, 2020, I downloaded: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz

Extracting: tar xzvf freesurfer-linux-centos7_x86_64-7.1.0.tar.gz freesurfer/matlab/freesurfer_read_surf.m gives a byte-size of 4947 with the content I have been describing that fails without these two lines:

% $Revision: 1.2 $ $Date: 2011/02/07 21:47:40 $ ver = '$Revision: 1.2 $ $Date: 2011/02/07 21:47:40 $';

Previous versions that all ran for me have byte size 5050 with those two lines.

Kathy Pearson

________________________________________

Douglas N. Greve Mon, 16 Nov 2020 07:55:22 -0800

I don't see that line in our 7.X versions. We did have that in development versions between 6 and 7 but we fixed it before version 7 release. Are you sure that it is in your 7.1 version?

________________________________________ From: Kathy L. Pearson kathy.pearson@colorado.edu Sent: Saturday, November 14, 2020 8:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: surf pial_lgi not created in version 7.1.0

This was resolved for me by copying from: 5.3.0/matlab/freesurfer_read_surf.m to: 7.1.0/matlab/freesurfer_read_surf.m

Before the copy, here is the difference:

diff 5.3.0/matlab/freesurfer_read_surf.m 7.1.0/matlab/freesurfer_read_surf.m

63d62 < % $Revision: 1.2 $ $Date: 2011/02/07 21:47:40 $ 71d69 < ver = '$Revision: 1.2 $ $Date: 2011/02/07 21:47:40 $';

where the 7.1.0 files does not have the ver string assignment though it's still referenced on line 70 and fails. There I assume the result from the MATLAB ver command cannot be parsed as a string.

cat -n 7.1.0/matlab/freesurfer_read_surf.m | head -70 | tail -1

70 fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

This is the original error from recon-all.log:

...

Warning: Input argument must be a string.

In ver at 41

In freesurfer_read_surf at 70 In find_corresponding_center_FSformat at 26 Error using fprintf Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

Kathy Pearson

________________________________________ From: Kathy L. Pearson kathy.pearson@colorado.edu Sent: Monday, October 19, 2020 6:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: surf pial_lgi not created in version 7.1.0

I am getting this error near the tail of the 7.1.0 recon-all.log file just before exit: ERROR: find_corresponding_center_FSformat did not complete successfully!

At this link from May 13: https://secure-web.cisco.com/1112xittgNPDDp8jonTXAcOxK4jdQ4UiVaINfgqifmb10_M... I see that you have posted in reference to a similar question: https://secure-web.cisco.com/11IxaRu4lLYDOHGA8SRYicnAPRqbDGlK_bGwg8CLB9ODigq...

If this is different from the 7.1.0 distribution's file in the matlab directory May 11 10:04 find_corresponding_center_FSformat.m please let me know what authentication login/password combination is needed to access this to see if it will fix my errors.

Is this file updated in the newer 7.1.1?

Thanks,

Kathy

Douglas N. Greve Mon, 19 Oct 2020 07:42:01 -0700 Can you send the recon-all.log file?

______________________________________ From: Kathy L. Pearson kathy.pearson@colorado.edu Sent: Friday, October 9, 2020 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: surf pial_lgi not created in version 7.1.0

No, it does not exist, and my question is why not in 7.1.0 when it is created with the same two commands in 5.3.0?

Thanks,

Kathy

Douglas N. Greve Fri, 09 Oct 2020 05:49:32 -0700 does that file exist?

________________________________________ From: Kathy L. Pearson Sent: Thursday, October 8, 2020 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: surf pial_lgi not created in version 7.1.0

In freesurfer version 5.3.0, I can successfully run: recon-all -autorecon-all -mprage -s $subj -qcache -localGI recon-all -s $subj -qcache -measure pial_lgi

However, the same commands with 7.1.0 give an error after this last of a number of generated statements and no surf/*pial_lgi output: mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find subjects/147608/surf/lh.pial_lgi

Is a new command needed for version 7.1.0?

Thanks,

Kathy Pearson