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Dear Freesurfer experts,
While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors
gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248
It sounds like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space?
Thanks, Jiahe
set the TMPDIR env variable to point anywhere you want
On 06/04/2018 02:57 PM, Jiahe Zhang wrote:
External Email - Use Caution
Dear Freesurfer experts,
While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors
gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248
It sounds like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space?
Thanks, Jiahe
-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I tried both below and got the same error. setenv TMPDIR $my_tmp_dir setenv tmpdir $my_tmp_dir
Is doesn't seems like selxavg3-sess reads this env variable. Or am I missing something?
On Mon, Jun 4, 2018 at 5:56 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
set the TMPDIR env variable to point anywhere you want
On 06/04/2018 02:57 PM, Jiahe Zhang wrote:
External Email - Use CautionDear Freesurfer experts,
While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors
gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected
3257077248
It sounds like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space?
Thanks, Jiahe
-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
what version of fs are you running?
On 6/5/18 10:02 PM, Jiahe Zhang wrote:
External Email - Use Caution
I tried both below and got the same error. setenv TMPDIR $my_tmp_dir setenv tmpdir $my_tmp_dir
Is doesn't seems like selxavg3-sess reads this env variable. Or am I missing something?
On Mon, Jun 4, 2018 at 5:56 PM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
set the TMPDIR env variable to point anywhere you want On 06/04/2018 02:57 PM, Jiahe Zhang wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > While running selxavg3-sess on a large functional scan (7 Tesla, 768 > time points), I got these errors > > gzip: stdout: No space left on device > ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248 > > It sounds like there wasn't enough space on /tmp for an intermediate > file to be written. Is there any way I can override the default so the > intermediate file gets written to a location that does have enough > storage space? > > Thanks, > Jiahe > > > > -- > Jiahe Zhang > Ph.D. Candidate > Department of Psychology > Northeastern University > 617-373-2649 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
/usr/local/freesurfer/stable5_3_0/bin/freesurfer
On Wed, Jun 6, 2018 at 12:23 AM, Douglas Greve dgreve@mgh.harvard.edu wrote:
what version of fs are you running?
On 6/5/18 10:02 PM, Jiahe Zhang wrote:
External Email - Use CautionI tried both below and got the same error. setenv TMPDIR $my_tmp_dir setenv tmpdir $my_tmp_dir
Is doesn't seems like selxavg3-sess reads this env variable. Or am I missing something?
On Mon, Jun 4, 2018 at 5:56 PM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
set the TMPDIR env variable to point anywhere you want
On 06/04/2018 02:57 PM, Jiahe Zhang wrote:
External Email - Use CautionDear Freesurfer experts,
While running selxavg3-sess on a large functional scan (7 Tesla, 768 time points), I got these errors
gzip: stdout: No space left on device ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected
3257077248
It sounds like there wasn't enough space on /tmp for an intermediate file to be written. Is there any way I can override the default so the intermediate file gets written to a location that does have enough storage space?
Thanks, Jiahe
-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
oh, that functionality is only available in 6.0. In 5.3, the temp path is hard-coded. You can edit load_nifti.m to change the default path.
On 6/6/18 6:36 AM, Jiahe Zhang wrote:
External Email - Use Caution
/usr/local/freesurfer/stable5_3_0/bin/freesurfer
On Wed, Jun 6, 2018 at 12:23 AM, Douglas Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
what version of fs are you running? On 6/5/18 10:02 PM, Jiahe Zhang wrote:External Email - Use Caution I tried both below and got the same error. setenv TMPDIR $my_tmp_dir setenv tmpdir $my_tmp_dir Is doesn't seems like selxavg3-sess reads this env variable. Or am I missing something? On Mon, Jun 4, 2018 at 5:56 PM, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: set the TMPDIR env variable to point anywhere you want On 06/04/2018 02:57 PM, Jiahe Zhang wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > While running selxavg3-sess on a large functional scan (7 Tesla, 768 > time points), I got these errors > > gzip: stdout: No space left on device > ERROR: /tmp/tmp8187256.nii, read in 1669519272 voxels, expected 3257077248 > > It sounds like there wasn't enough space on /tmp for an intermediate > file to be written. Is there any way I can override the default so the > intermediate file gets written to a location that does have enough > storage space? > > Thanks, > Jiahe > > > > -- > Jiahe Zhang > Ph.D. Candidate > Department of Psychology > Northeastern University > 617-373-2649 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.-- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-2649
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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Douglas Greve -
Douglas N. Greve
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Jiahe Zhang