Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1):
processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory
As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist.
I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'."
Any help you can provide would be greatly appreciated!
Thanks in advance,
Andrew
-- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu
Hi Andrew,
Glad it's not just me! I'm still not sure whether this is a generic problem with version 5.1.0 (which I use) or a local problem.
I can only find a rather inelegant hack. What I do is complete the recon-all (5.1.0) and then run a bunch of steps using mris_spherical_average from version 4.4.0:
Here's what I do <stuff in angle brackets is for you to fill in>
cd $SUBJECTS_DIR <PATH TO VERSION 4.4.0>/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <SUBJECTNAME> label rh.v1.invivo.label rh v1.invivo.reg V1_average ./<SUBJECTNAME>/label/rh.v1.prob.label <PATH TO VERSION 4.4.0>/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <SUBJECTNAME> label lh.v1.invivo.label lh v1.invivo.reg V1_average ./<SUBJECTNAME>/label/lh.v1.prob.label threshold_labelfile_at0p8 ./<SUBJECTNAME>/label/lh.v1.prob.label ./<SUBJECTNAME>/label/lh.v1.predict.labe threshold_labelfile_at0p8 ./<SUBJECTNAME>/label/rh.v1.prob.label ./<SUBJECTNAME>/label/rh.v1.predict.label mris_anatomical_stats -l ./<SUBJECTNAME>/label/lh.v1.predict.label <SUBJECTNAME> lh >> ./<SUBJECTNAME>/stats/hinds_v1_lh mris_anatomical_stats -l ./<SUBJECTNAME>/label/rh.v1.predict.label <SUBJECTNAME> rh >> ./<SUBJECTNAME>/stats/hinds_v1_rh
This seems to work, but I'm not sure if there is any fall-out from mixing versions. (Note you need to link or copy a version of V1_average into your SUBJECTS_DIR first)
Good luck!
Krish
-- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd@cardiff.ac.uk
On 11 Nov 2011, at 22:04, Andrew Bock wrote:
Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1):
processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory
As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist.
I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'."
Any help you can provide would be greatly appreciated!
Thanks in advance,
Andrew
-- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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.
Dear Dr. Bock,
I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark
2011/11/11 Andrew Bock abock@u.washington.edu
Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1):
processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/ subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory
As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist.
I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'."
Any help you can provide would be greatly appreciated!
Thanks in advance,
Andrew
-- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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.
try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem
cheers Bruce On Tue, 12 Jun 2012, Anders Hougaard wrote:
Dear Dr. Bock, I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark
2011/11/11 Andrew Bock abock@u.washington.edu Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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.
Here is the hack I use, taken from Krish's previous post. I hope this helps:
cd $SUBJECTS_DIR recon-all -s <subject> -label_v1 /usr/local/freesurfer4.5/freesurfer/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <subject> label rh.v1.invivo.label rh v1.invivo.reg V1_average ./<subject>/label/rh.V1.prob.label /usr/local/freesurfer4.5/freesurfer/bin/mris_spherical_average -osurf v1.invivo.reg -n -o <subject> label lh.v1.invivo.label lh v1.invivo.reg V1_average ./<subject>/label/lh.V1.prob.label threshold_labelfile_at_0p8 ./<subject>/label/lh.V1.prob.label ./<subject>/label/lh.V1.predict.label threshold_labelfile_at_0p8 ./<subject>/label/rh.V1.prob.label ./<subject>/label/rh.V1.predict.label mris_anatomical_stats -l ./<subject>/label/lh.V1.predict.label <subject> lh >> ./<subject>/stats/hinds_V1_lh mris_anatomical_stats -l ./<subject>/label/rh.V1.predict.label <subject> rh >> ./<subject>/stats/hinds_V1_rh
Andrew
On Tue, Jun 12, 2012 at 9:48 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem
cheers Bruce
On Tue, 12 Jun 2012, Anders Hougaard wrote:
Dear Dr. Bock,
I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark
2011/11/11 Andrew Bock abock@u.washington.edu Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/**subjects/V1_average/surf/rh.**white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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/**compliancelinehttp://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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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.
Hi Bruce,
That actually seems to do the trick. Thank you very much!
Best, Anders
2012/6/12 Bruce Fischl fischl@nmr.mgh.harvard.edu
try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem
cheers Bruce
On Tue, 12 Jun 2012, Anders Hougaard wrote:
Dear Dr. Bock,
I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark
2011/11/11 Andrew Bock abock@u.washington.edu Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/**subjects/V1_average/surf/rh.**white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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/**compliancelinehttp://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.
Glad to hear it Bruce
On Jun 13, 2012, at 7:30 AM, Anders Hougaard ahougaard@dadlnet.dk wrote:
Hi Bruce,
That actually seems to do the trick. Thank you very much!
Best, Anders
2012/6/12 Bruce Fischl fischl@nmr.mgh.harvard.edu try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem
cheers Bruce
On Tue, 12 Jun 2012, Anders Hougaard wrote:
Dear Dr. Bock, I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark
2011/11/11 Andrew Bock abock@u.washington.edu Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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.
Dear Freesurfers,
I am now encountering a new error with the Hinds V1 procedure:
I am still using the same version (5.1.0) and nothing has changed, except that I have been doing some cross-hemispheric registration for some of the subjects (not this one).
using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 1.000 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /Applications/freesurfer/subjects/t05/surf/lh.sphere... reading template parameterization from /Applications/freesurfer/subjects/V1_average/label/lh.v1.invivo.tif... mrisReadTriangleFile(/Applications/freesurfer/subjects/t05/surf/lh.smoothwm): surface doesn't match /Applications/freesurfer/subjects/t05/surf/lh.sphere
Any suggestions?
All the best, Anders
2012/6/13 Anders Hougaard ahougaard@dadlnet.dk
Hi Bruce,
That actually seems to do the trick. Thank you very much!
Best, Anders
2012/6/12 Bruce Fischl fischl@nmr.mgh.harvard.edu
try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem
cheers Bruce
On Tue, 12 Jun 2012, Anders Hougaard wrote:
Dear Dr. Bock,
I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark
2011/11/11 Andrew Bock abock@u.washington.edu Hello,
I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/**subjects/V1_average/surf/rh.**white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 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/**compliancelinehttp://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.
Hi Anders
usually this means you did some editing but didn't complete the rerunning of the recon-all process. Try running it with -make all
cheers Bruce On Fri, 8 Mar 2013, Anders Hougaard wrote:
Dear Freesurfers, I am now encountering a new error with the Hinds V1 procedure:
I am still using the same version (5.1.0) and nothing has changed, except that I have been doing some cross-hemispheric registration for some of the subjects (not this one).
using inflated surface for initial alignment using n_averages = 4096 l_dist = 10.000 using l_parea = 1.000 $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from /Applications/freesurfer/subjects/t05/surf/lh.sphere... reading template parameterization from /Applications/freesurfer/subjects/V1_average/label/lh.v1.invivo.tif... mrisReadTriangleFile(/Applications/freesurfer/subjects/t05/surf/lh.smoothwm ): surface doesn't match /Applications/freesurfer/subjects/t05/surf/lh.sphere
Any suggestions?
All the best, Anders
2012/6/13 Anders Hougaard ahougaard@dadlnet.dk Hi Bruce, That actually seems to do the trick. Thank you very much!
Best, Anders
2012/6/12 Bruce Fischl fischl@nmr.mgh.harvard.edu try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem
cheers Bruce On Tue, 12 Jun 2012, Anders Hougaard wrote: Dear Dr. Bock, I get the same error in FS 5.1.0 when running recon-all -s <subject> -label_v1. Did you find a solution? Best regards, Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark 2011/11/11 Andrew Bock <abock@u.washington.edu> Hello, I am having a similar problem to one described on the freesurfer mail archive, where I receive the following error when trying to identify V1 using the Hinds method (i.e. recon-all -s <subject> -label_v1): processing subject V1_average... MRISreadVertexPosition(white): could not open file /usr/local/freesurfer/subjects/V1_average/surf/rh.white No such file or directory MRISreadOriginalProperties: could not read surface file white No such file or directory could not read surface positions from white No such file or directory As Prof. Krish Singh indicated in July, it appears the problem occurs when trying to open rh.white (or lh.white) from the surf subdirectory in V1_average, which doesn't exist. I have run recon-all -s <subject> -make all, but it returns "make: Nothing to be done for `all'." Any help you can provide would be greatly appreciated! Thanks in advance, Andrew -- Andrew Bock, Ph.D. Department of Psychology University of Washington Seattle, WA 98195 Tel: 206.543.3817 Fax: 206.685.3157 abock@u.washington.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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.
freesurfer@nmr.mgh.harvard.edu
-
Anders Hougaard -
Andrew Bock -
Bruce Fischl -
Krish Singh