Hi there,
I'm using Freesurfer version 5.1.0 to automatically define labels for left and right V1 using the method outlined in Hinds et al.
To do this I add the -label-v1 flag to my recon-all command line.
The problem is that this always fails with the following error visible in the .out file:
------------------------------------------------------------------- mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label lh.v1.invivo.label lh v1.invivo.reg V1_average /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label
output surface = v1.invivo.reg painting output onto subject 240211-50. processing subject V1_average... MRISreadVertexPosition(white): could not open file /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.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 -------------------------------------------------------------------
The problem seems to be with the current version of mris_spherical_average - if I modify the command line above to explicitly execute the old (4.4.0) version of mris_spherical_average then I do not get this error and the script completes without problems.
I'd be grateful of any advice/help on this.
Best Wishes,
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
Hi Krish
sounds like the processing of the subject was not finished. Can you run recon-all -s <subject> -make all
then rerun the hinds stuff?
cheers Bruce
On Wed, 6 Jul 2011, Krish Singh wrote:
Hi there, I'm using Freesurfer version 5.1.0 to automatically define labels for left and right V1 using the method outlined in Hinds et al.
To do this I add the -label-v1 flag to my recon-all command line.
The problem is that this always fails with the following error visible in the .out file:
mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label lh.v1.invivo.label lh v1.invivo.reg V1_average /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label
output surface = v1.invivo.reg painting output onto subject 240211-50. processing subject V1_average... MRISreadVertexPosition(white): could not open file /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.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
The problem seems to be with the current version of mris_spherical_average - if I modify the command line above to explicitly execute the old (4.4.0) version of mris_spherical_average then I do not get this error and the script completes without problems.
I'd be grateful of any advice/help on this.
Best Wishes,
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
Hi Bruce,
I have previously tried a completely clean recon-all and got the same problem, but I did not use "-make all". I'll try that.
One thing I'm not sure if you noticed, though:
If you look at the extract of the .out file I sent (between the ---- below), you can see that the 5.1.0 version of mris_spherical_average crashes when trying to load a file called lh.white from the surf subdirectory in the V1_average (i.e. not from my data).
The 4.4.0 version of mris_spherical_average, when run on the same data as part of the -label-v1 pipeline, does not throw this error.
It's odd that it tries to load this file because, from what I can see, the V1_average subject provided in 5.1.0 (and 4.4.0) does not have any white surface reconstructions?
Many thanks,
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 6 Jul 2011, at 15:15, Bruce Fischl wrote:
Hi Krish
sounds like the processing of the subject was not finished. Can you run recon-all -s <subject> -make all
then rerun the hinds stuff?
cheers Bruce
On Wed, 6 Jul 2011, Krish Singh wrote:
Hi there, I'm using Freesurfer version 5.1.0 to automatically define labels for left and right V1 using the method outlined in Hinds et al. To do this I add the -label-v1 flag to my recon-all command line. The problem is that this always fails with the following error visible in the .out file:
mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label lh.v1.invivo.label lh v1.invivo.reg V1_average /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label output surface = v1.invivo.reg painting output onto subject 240211-50. processing subject V1_average... MRISreadVertexPosition(white): could not open file /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.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
The problem seems to be with the current version of mris_spherical_average - if I modify the command line above to explicitly execute the old (4.4.0) version of mris_spherical_average then I do not get this error and the script completes without problems. I'd be grateful of any advice/help on this. Best Wishes, 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
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.
hmmmm, we'll take a look On Wed, 6 Jul 2011, Krish Singh wrote:
Hi Bruce, I have previously tried a completely clean recon-all and got the same problem, but I did not use "-make all". I'll try that.
One thing I'm not sure if you noticed, though:
If you look at the extract of the .out file I sent (between the ---- below), you can see that the 5.1.0 version of mris_spherical_average crashes when trying to load a file called lh.white from the surf subdirectory in the V1_average (i.e. not from my data).
The 4.4.0 version of mris_spherical_average, when run on the same data as part of the -label-v1 pipeline, does not throw this error.
It's odd that it tries to load this file because, from what I can see, the V1_average subject provided in 5.1.0 (and 4.4.0) does not have any white surface reconstructions?
Many thanks,
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 6 Jul 2011, at 15:15, Bruce Fischl wrote:
Hi Krish sounds like the processing of the subject was not finished. Can you run recon-all -s <subject> -make all then rerun the hinds stuff? cheers Bruce On Wed, 6 Jul 2011, Krish Singh wrote: Hi there, I'm using Freesurfer version 5.1.0 to automatically define labels for left and right V1 using the method outlined in Hinds et al. To do this I add the -label-v1 flag to my recon-all command line. The problem is that this always fails with the following error visible in the .out file: ------------------------------------------------------------------- mris_spherical_average -osurf v1.invivo.reg -n -o 240211-50 label lh.v1.invivo.label lh v1.invivo.reg V1_average /cubric/scratch/CCGG/Freesurf/240211-50/label/lh.v1.prob.label output surface = v1.invivo.reg painting output onto subject 240211-50. processing subject V1_average... MRISreadVertexPosition(white): could not open file /cubric/scratch/CCGG/Freesurf/V1_average/surf/lh.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 ------------------------------------------------------------------- The problem seems to be with the current version of mris_spherical_average - if I modify the command line above to explicitly execute the old (4.4.0) version of mris_spherical_average then I do not get this error and the script completes without problems. I'd be grateful of any advice/help on this. Best Wishes, 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 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
-
Bruce Fischl -
Krish Singh