Hello FS experts,
I’m trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this?
best,
Jon
Hi Jon
usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce On Sat, 1 Feb 2014, Jonathan Holt wrote:
Hello FS experts,
I’m trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this?
best,
Jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive.
These are the last 50 or so lines of the output before it stops:
mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh... ERROR: failure writing /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2
I'm confused as to why it's looking for a nameless .mgh file, or perhaps that is normal. This is my first usage for make_average_subject.
Jon
On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Jon
usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce
On Sat, 1 Feb 2014, Jonathan Holt wrote:
Hello FS experts,
I'm trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this?
best,
Jon _______________________________________________ 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 Jon
can you include your entire command line so we can see it?
thanks Bruce
On Mon, 3 Feb 2014, Jonathan Holt wrote:
Bruce, I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive.
These are the last 50 or so lines of the output before it stops:
mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average /tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh, -1): could not open file
Applying LTAtransformInterp (resample_type 1) writing to/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh... ERROR: failure writing/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2
I'm confused as to why it's looking for a nameless .mgh file, or perhaps that is normal. This is my first usage for make_average_subject.
Jon
On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jon
usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce On Sat, 1 Feb 2014, Jonathan Holt wrote: Hello FS experts, I’m trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this? best, Jon
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.
All,
[1]+ Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ >&test.log
On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Jon
can you include your entire command line so we can see it?
thanks Bruce
On Mon, 3 Feb 2014, Jonathan Holt wrote:
Bruce,
I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive.
These are the last 50 or so lines of the output before it stops:
mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/ LONG_STUDY_2/average /tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh, -1): could not open file
Applying LTAtransformInterp (resample_type 1) writing to/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/ LONG_STUDY_2/average/tmp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh... ERROR: failure writing/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/ LONG_STUDY_2/average/tmp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2
I'm confused as to why it's looking for a nameless .mgh file, or perhaps that is normal. This is my first usage for make_average_subject.
Jon
On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jon
usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce On Sat, 1 Feb 2014, Jonathan Holt wrote: Hello FS experts, I'm trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this? best, Jon
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.
and can you send us the output? On Mon, 3 Feb 2014, Jonathan Holt wrote:
All, [1]+ Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ >&test.log
On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jon
can you include your entire command line so we can see it? thanks Bruce On Mon, 3 Feb 2014, Jonathan Holt wrote: Bruce, I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive. These are the last 50 or so lines of the output before it stops:mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average
/tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writingto/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/ma ke _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh... ERROR: failurewriting/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/t mp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2 I'm confused as to why it's looking for a nameless .mgh file, or perhaps that is normal. This is my first usage for make_average_subject. Jon On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Jon usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce On Sat, 1 Feb 2014, Jonathan Holt wrote: Hello FS experts, I’m trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this? best, Jon _______________________________________________ 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 you are, attached!
On Mon, Feb 3, 2014 at 3:54 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
and can you send us the output?
On Mon, 3 Feb 2014, Jonathan Holt wrote:
All,
[1]+ Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ >&test.log
On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Jon
can you include your entire command line so we can see it? thanks Bruce On Mon, 3 Feb 2014, Jonathan Holt wrote: Bruce, I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive. These are the last 50 or so lines of the output before it stops:mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/ LONG_STUDY_2/average
/tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writingto/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/ LONG_STUDY_2/average/tmp/ma ke _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh. .. ERROR: failurewriting/net/data4/ALSSCI/FreeSurfer201211/ FreeSurfer/LONG_STUDY_2/average/t mp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2
I'm confused as to why it's looking for a nameless .mgh file, or perhaps that is normal. This is my first usage for make_average_subject. Jon On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Jon usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce On Sat, 1 Feb 2014, Jonathan Holt wrote: Hello FS experts, I'm trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this? best, Jon _______________________________________________ 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.
Remove the forward slash at the end of each subject name doug
On 02/03/2014 04:04 PM, Jonathan Holt wrote:
Here you are, attached!
On Mon, Feb 3, 2014 at 3:54 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
and can you send us the output? On Mon, 3 Feb 2014, Jonathan Holt wrote: All, [1]+ Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ >&test.log On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Jon can you include your entire command line so we can see it? thanks Bruce On Mon, 3 Feb 2014, Jonathan Holt wrote: Bruce, I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive. These are the last 50 or so lines of the output before it stops: mghWrite(/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average /tmp/make_average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writingto/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/tmp/ma ke _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh... ERROR: failurewriting/net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2/average/t mp/make _average_vol-tmp-28460/orig-s_090803sk.long.SKtemplate/.mgh /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/LONG_STUDY_2 I'm confused as to why it's looking for a nameless .mgh file, or perhaps that is normal. This is my first usage for make_average_subject. Jon On Sat, Feb 1, 2014 at 5:54 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Jon usually that means that either the partition is full or you don't have permission. If that's not the case you will need to give us more details Bruce On Sat, 1 Feb 2014, Jonathan Holt wrote: Hello FS experts, I’m trying to make an average subject and I had an unfortunate error during the mri_convert stage, specifically an mghWrite error. I failed to save the output so I cannot recall the exact details, are there any specific things I should be looking out for to prevent this? best, Jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Jonathan Holt