Hi freesurfers,
I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error
"Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames
Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"
I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan.
Anyone run into this problem and were able to fix it?
Thanks in advance,
Marissa
Each input file should have one frame. What sequence did you run on the scanner? This usually happens when someone collected a multiecho mprage. If so, then compute the rms of the multiple echoes and run recon-all on that
On 02/22/2016 11:29 AM, Marissa Pifer wrote:
Hi freesurfers,
I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error
"Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames
Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"
I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan.
Anyone run into this problem and were able to fix it?
Thanks in advance,
Marissa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Marissa
why does it have multiple frames? What kind of acquisition was it? If you know which frame is the correct one you can always extract it, for example
cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig mv 001.mgz two_frames.mgz mri_convert -nth 0 two_frames.mgz 001.mgz
Bruce
On Mon, 22 Feb 2016, Marissa Pifer wrote:
Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error
"Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames
Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"
I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan.
Anyone run into this problem and were able to fix it?
Thanks in advance,
Marissa
Bruce,
I'm not sure why it has multiple frames. It was a spin echo, T1 weighted structural MRI. I input the command you suggested and recon-all is running now.
Thank you for your help!
Marissa
On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marissa
why does it have multiple frames? What kind of acquisition was it? If you know which frame is the correct one you can always extract it, for example
cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig mv 001.mgz two_frames.mgz mri_convert -nth 0 two_frames.mgz 001.mgz
Bruce
On Mon, 22 Feb 2016, Marissa Pifer wrote:
Hi freesurfers,
I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error
"Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames
Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64
recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016"
I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan.
Anyone run into this problem and were able to fix it?
Thanks in advance,
Marissa
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.
But is that the right frame to use? I would check with whoever collected the data and get it sorted out before diving into an analysis.
On 02/22/2016 02:34 PM, Marissa Pifer wrote:
Bruce,
I'm not sure why it has multiple frames. It was a spin echo, T1 weighted structural MRI. I input the command you suggested and recon-all is running now.
Thank you for your help!
Marissa
On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Marissa why does it have multiple frames? What kind of acquisition was it? If you know which frame is the correct one you can always extract it, for example cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig mv 001.mgz two_frames.mgz mri_convert -nth 0 two_frames.mgz 001.mgz Bruce On Mon, 22 Feb 2016, Marissa Pifer wrote: Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error "Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016" I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan. Anyone run into this problem and were able to fix it? Thanks in advance, Marissa _______________________________________________ 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.
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Absolutely, I've contacted them about it, and if it is not the right one, I can use the other. There are only 2 frames so I can narrow it down at least.
Marissa
On Mon, Feb 22, 2016 at 3:46 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
But is that the right frame to use? I would check with whoever collected the data and get it sorted out before diving into an analysis.
On 02/22/2016 02:34 PM, Marissa Pifer wrote:
Bruce,
I'm not sure why it has multiple frames. It was a spin echo, T1 weighted structural MRI. I input the command you suggested and recon-all is running now.
Thank you for your help!
Marissa
On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Marissa why does it have multiple frames? What kind of acquisition was it? If you know which frame is the correct one you can always extract it, for example cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig mv 001.mgz two_frames.mgz mri_convert -nth 0 two_frames.mgz 001.mgz Bruce On Mon, 22 Feb 2016, Marissa Pifer wrote: Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error "Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames!/Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz
has 2 frames Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016" I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan. Anyone run into this problem and were able to fix it? Thanks in advance, Marissa _______________________________________________ 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.
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