Hello,
Is there any way to extract a three dimensional coordinate representation of the different brain regions (i.e., their centroids) that freesurfer is estimating the cortical thickness of?
Any help is appreciated and apologies if this question has been answered before.
regards, David
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster?
I have attached my dmrirc file as well as the files needed for it to run on the cluster.
Thanks,
Emily
Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster?
a.y
On Wed, 5 Mar 2014, ebelleau@uwm.edu wrote:
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster?
I have attached my dmrirc file as well as the files needed for it to run on the cluster.
Thanks,
Emily
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off of the cluster, but one of my colleagues was able to run his data off of our cluster ( the whole pathway including bedpost) without any problem. However he (Jon Wieser) made an individual dmrirc configuration file script for every subject and then made sure each one got assigned to a different processor in another script.
Thanks,
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:02:14 PM Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster?
a.y
On Wed, 5 Mar 2014, ebelleau@uwm.edu wrote:
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster?
I have attached my dmrirc file as well as the files needed for it to run on the cluster.
Thanks,
Emily
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.
Hello,
I recently modified my script so that it would work on a cluster. I had been running it successfully locally but am now having some trouble on the cluster. The only thing I changed in the dmrirc script were some pathways. However, I keep getting an error of must specify as many dicoms as subjects. I did not change any dicom numbers in this once successfully working script.
Attached is my script. Any thoughts?
Thanks,
Emily
----- Original Message ----- From: ebelleau@uwm.edu To: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:25:00 PM Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off of the cluster, but one of my colleagues was able to run his data off of our cluster ( the whole pathway including bedpost) without any problem. However he (Jon Wieser) made an individual dmrirc configuration file script for every subject and then made sure each one got assigned to a different processor in another script.
Thanks,
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:02:14 PM Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster?
a.y
On Wed, 5 Mar 2014, ebelleau@uwm.edu wrote:
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster?
I have attached my dmrirc file as well as the files needed for it to run on the cluster.
Thanks,
Emily
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 Emily - Replace "sub238/DTI/i*.MRDC.1" with a single file name.
a.y
On Thu, 13 Mar 2014, ebelleau@uwm.edu wrote:
Hello,
I recently modified my script so that it would work on a cluster. I had been running it successfully locally but am now having some trouble on the cluster. The only thing I changed in the dmrirc script were some pathways. However, I keep getting an error of must specify as many dicoms as subjects. I did not change any dicom numbers in this once successfully working script.
Attached is my script. Any thoughts?
Thanks,
Emily
----- Original Message ----- From: ebelleau@uwm.edu To: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:25:00 PM Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Anastasia,
We use SLURM.
I have not personally yet run bedpost off of the cluster, but one of my colleagues was able to run his data off of our cluster ( the whole pathway including bedpost) without any problem. However he (Jon Wieser) made an individual dmrirc configuration file script for every subject and then made sure each one got assigned to a different processor in another script.
Thanks,
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:02:14 PM Subject: Re: [Freesurfer] Running Tracula on a cluster
Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster?
a.y
On Wed, 5 Mar 2014, ebelleau@uwm.edu wrote:
Hello,
I plan on running a batch of subjects (around 80) on a computer cluster.
I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist?
However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster?
I have attached my dmrirc file as well as the files needed for it to run on the cluster.
Thanks,
Emily
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.
There is not an easy way. Start by converting the annotation to a segmentation (mri_annotation2label with --seg output). Binarize the label you are interested in (mri_binarize --i annotseg.mgh --match 2021 --o rh-pericalcarine.mgh), then run mri_surfcluster --in rh-pericalcarine.mgh --thmin .5 --centroid (and other necessary args). The 2021 value is obtained from $FREESURFER_HOME/FreeSurferColorLUT.txt doug
On 03/05/2014 02:03 PM, David Phillips wrote:
Hello,
Is there any way to extract a three dimensional coordinate representation of the different brain regions (i.e., their centroids) that freesurfer is estimating the cortical thickness of?
Any help is appreciated and apologies if this question has been answered before.
regards, David _______________________________________________ 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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Anastasia Yendiki -
David Phillips -
Douglas N Greve -
ebelleau＠uwm.edu