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Dear FreeSurfer Developers,
I'm trying to run recon-all using freesurfer 8.0.0. with the command "recon-all -s ${sub} -i ${sub}_T1w.nii.gz -T2 ${sub}_T2w.nii.gz -T2pial -all -qcache -hires -expert expert," and writing to you because I got the following error: ------------------ mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading 25 ** failed to open GIFTI XML file '25.gii' mrisReadGIFTIdanum: ERROR reading gifti 25.gii [INFO] read, cannot find 25, trying 25.gii ... error: No such file or directory error: mris_inflate: could not read surface file 25\00 Command exited with non-zero status 255 --------------------
I added "mris_inflate -n 25" as expert option, and, as far as I see, this error happened because recon-all does not reflect the expert option properly (should be "mris_inflate -no-save-sulc -n 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix" not "mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix"). I could run exactly the same recon-all command without error using freesurfer 7.4.1.
Could anyone kindly guide me on how to solve this issue?
Best regards,
Ikko
------------------- Ikko Kimura ikkok@drcmr.dk Postdoctoral researcher Neurophysics Group DRCMR, Copenhagen University Hospital - Amager and Hvidovre
This is a known error where it is filtering out the "-n" flag, and that causes an error. To get around it, you can download the current dev version and copy cp $DEV/bin/fsr-getxopts $FREESURFER/bin/fsr-getxopts that should fix it
On 12/10/2025 10:52 AM, Ikko Kimura wrote:
External Email - Use Caution Dear FreeSurfer Developers,
I'm trying to run recon-all using freesurfer 8.0.0. with the command "recon-all -s ${sub} -i ${sub}_T1w.nii.gz -T2 ${sub}_T2w.nii.gz -T2pial -all -qcache -hires -expert expert," and writing to you because I got the following error:
mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading 25 ** failed to open GIFTI XML file '25.gii' mrisReadGIFTIdanum: ERROR reading gifti 25.gii [INFO] read, cannot find 25, trying 25.gii ... error: No such file or directory error: mris_inflate: could not read surface file 25\00 Command exited with non-zero status 255
I added "mris_inflate -n 25" as expert option, and, as far as I see, this error happened because recon-all does not reflect the expert option properly (should be "mris_inflate -no-save-sulc -n 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix" not "mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix"). I could run exactly the same recon-all command without error using freesurfer 7.4.1.
Could anyone kindly guide me on how to solve this issue?
Best regards,
Ikko
Ikko Kimura ikkok@drcmr.dk Postdoctoral researcher Neurophysics Group DRCMR, Copenhagen University Hospital - Amager and Hvidovre
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
External Email - Use Caution
Thanks. Then, I'll download and try that one.
Best,
Ikko
On 24/12/2025 04:16, Douglas N. Greve wrote:
This is a known error where it is filtering out the "-n" flag, and that causes an error. To get around it, you can download the current dev version and copy cp $DEV/bin/fsr-getxopts $FREESURFER/bin/fsr-getxopts that should fix it
On 12/10/2025 10:52 AM, Ikko Kimura wrote:
External Email - Use Caution Dear FreeSurfer Developers,
I'm trying to run recon-all using freesurfer 8.0.0. with the command "recon-all -s ${sub} -i ${sub}_T1w.nii.gz -T2 ${sub}_T2w.nii.gz -T2pial -all -qcache -hires -expert expert," and writing to you because I got the following error:
mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading 25 ** failed to open GIFTI XML file '25.gii' mrisReadGIFTIdanum: ERROR reading gifti 25.gii [INFO] read, cannot find 25, trying 25.gii ... error: No such file or directory error: mris_inflate: could not read surface file 25\00 Command exited with non-zero status 255
I added "mris_inflate -n 25" as expert option, and, as far as I see, this error happened because recon-all does not reflect the expert option properly (should be "mris_inflate -no-save-sulc -n 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix" not "mris_inflate -no-save-sulc 25 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix"). I could run exactly the same recon-all command without error using freesurfer 7.4.1.
Could anyone kindly guide me on how to solve this issue?
Best regards,
Ikko
Ikko Kimura ikkok@drcmr.dk Postdoctoral researcher Neurophysics Group DRCMR, Copenhagen University Hospital - Amager and Hvidovre
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Ikko Kimura