Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Mareen,
You can do that in the "unsubscribe" section on the following page:
http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best,
-Zeke
On 10/21/2015 11:06 AM, Mareen Kussatz wrote:
hello, please delete mey e-mail from the list! Thank you Greets and Bye Bye Mareen Kussatz
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ 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.
Hi again,
Another advantage of using qcache in my case is that the file names are automatically generated and therefore standard.
Is there any risk (particularly for future compatibility) in using qcache? Did anyone had some problem with it?
Thanks in advance, Mathieu
Le 21/10/2015 18:07, Mathieu Dubois a écrit :
Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Mathieu
I don't see any reason we wouldn't continue to support it Bruce On Thu, 22 Oct 2015, Mathieu Dubois wrote:
Hi again,
Another advantage of using qcache in my case is that the file names are automatically generated and therefore standard.
Is there any risk (particularly for future compatibility) in using qcache? Did anyone had some problem with it?
Thanks in advance, Mathieu
Le 21/10/2015 18:07, Mathieu Dubois a écrit :
Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ 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.
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
Great, thanks for your answer.
Le 22/10/2015 17:08, Bruce Fischl a écrit :
Hi Mathieu
I don't see any reason we wouldn't continue to support it Bruce On Thu, 22 Oct 2015, Mathieu Dubois wrote:
Hi again,
Another advantage of using qcache in my case is that the file names are automatically generated and therefore standard.
Is there any risk (particularly for future compatibility) in using qcache? Did anyone had some problem with it?
Thanks in advance, Mathieu
Le 21/10/2015 18:07, Mathieu Dubois a écrit :
Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ 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.
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
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.
No, we will continue to support it
On 10/21/2015 11:13 PM, Mathieu Dubois wrote:
Hi again,
Another advantage of using qcache in my case is that the file names are automatically generated and therefore standard.
Is there any risk (particularly for future compatibility) in using qcache? Did anyone had some problem with it?
Thanks in advance, Mathieu
Le 21/10/2015 18:07, Mathieu Dubois a écrit :
Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ 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.
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
Great, thanks for your answer.
Le 22/10/2015 17:42, Douglas N Greve a écrit :
No, we will continue to support it
On 10/21/2015 11:13 PM, Mathieu Dubois wrote:
Hi again,
Another advantage of using qcache in my case is that the file names are automatically generated and therefore standard.
Is there any risk (particularly for future compatibility) in using qcache? Did anyone had some problem with it?
Thanks in advance, Mathieu
Le 21/10/2015 18:07, Mathieu Dubois a écrit :
Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ 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.
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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Mareen Kussatz -
Mathieu Dubois -
Z K