----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Anastasia,
Is it okay to run my DTI data on Freesurfer 5.3 when all my recon-all scripts for the structural data were run in Freesurfer 5.0?
And I can download the tracula program straight from the tracula Wiki? And it will work for Linux?
Thanks so much!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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 Emily - You can't download tracula separately from the rest of freesurfer, you'll have to download freesurfer 5.3. It works on any platform that the rest of freesurfer works.
The one thing that tracula uses from the freesurfer recon is the aparc+aseg.mgz. I have never tried running tracula with an aparc+aseg.mgz from 5.0, so I cannot tell you if it'll work, but you can certainly try.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
Hello Anastasia,
Is it okay to run my DTI data on Freesurfer 5.3 when all my recon-all scripts for the structural data were run in Freesurfer 5.0?
And I can download the tracula program straight from the tracula Wiki? And it will work for Linux?
Thanks so much!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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.
Hello,
I am running into the following error when I try to run trac-all:
set: No match. ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several attempts at debugging it.
I was wondering if you had any suggestions? Attached is my dmrirc_single_subject configuration.
I am brand new to freesurfer and tracula and would appreciate any guidance you can give me!
Thanks!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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 Emily - You're using "*" to specify all the dicom files in the series. You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This dmrirc looks like it might have been adapted from an older version of the tutorials. If so, I highly recommend downloading the latest version of everything.
Hope this helps, a.y
On Mon, 21 Oct 2013, ebelleau@uwm.edu wrote:
Hello,
I am running into the following error when I try to run trac-all:
set: No match. ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several attempts at debugging it.
I was wondering if you had any suggestions? Attached is my dmrirc_single_subject configuration.
I am brand new to freesurfer and tracula and would appreciate any guidance you can give me!
Thanks!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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 anastasia, I work with Emily. the wild card she used i*.MRDC.1 specifies only the first dicom image. the dicoms are in the format:
i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc
so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom image
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 10:09:13 AM Subject: Re: [Freesurfer] Tracula Error
Hi Emily - You're using "*" to specify all the dicom files in the series. You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This dmrirc looks like it might have been adapted from an older version of the tutorials. If so, I highly recommend downloading the latest version of everything.
Hope this helps, a.y
On Mon, 21 Oct 2013, ebelleau@uwm.edu wrote:
Hello,
I am running into the following error when I try to run trac-all:
set: No match. ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several attempts at debugging it.
I was wondering if you had any suggestions? Attached is my dmrirc_single_subject configuration.
I am brand new to freesurfer and tracula and would appreciate any guidance you can give me!
Thanks!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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
The problem is that the command "set dcmlist = (i*.MRDC.1)" is executed as soon as it is read. So this will end up with an empty dcmlist, because there are no files named i*.MRDC.1 in the current directory.
On Tue, 22 Oct 2013, Jon Wieser wrote:
Hi anastasia, I work with Emily. the wild card she used i*.MRDC.1 specifies only the first dicom image. the dicoms are in the format:
i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc
so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom image
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 10:09:13 AM Subject: Re: [Freesurfer] Tracula Error
Hi Emily - You're using "*" to specify all the dicom files in the series. You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This dmrirc looks like it might have been adapted from an older version of the tutorials. If so, I highly recommend downloading the latest version of everything.
Hope this helps, a.y
On Mon, 21 Oct 2013, ebelleau@uwm.edu wrote:
Hello,
I am running into the following error when I try to run trac-all:
set: No match. ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several attempts at debugging it.
I was wondering if you had any suggestions? Attached is my dmrirc_single_subject configuration.
I am brand new to freesurfer and tracula and would appreciate any guidance you can give me!
Thanks!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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
according to the tracula wiki:
http://freesurfer.net/fswiki/FsTutorial/Tracula
the program should look in the directory specified by "dcmroot" to look for the dicom list
excerpt from the wiki page:
Step 5: Specify the location of diffusion DICOM files
set dcmroot = $TUTORIAL_DATA/diffusion_tutorial Use this variable to specify the directory under which the diffusion DICOM files for all subjects can be found.
Step 6: Specify the list of input DWIs
set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-000017-000001.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu, "ebelleau" ebelleau@uwm.edu Sent: Tuesday, October 22, 2013 12:24:22 PM Subject: Re: [Freesurfer] Tracula Error
The problem is that the command "set dcmlist = (i*.MRDC.1)" is executed as soon as it is read. So this will end up with an empty dcmlist, because there are no files named i*.MRDC.1 in the current directory.
On Tue, 22 Oct 2013, Jon Wieser wrote:
Hi anastasia, I work with Emily. the wild card she used i*.MRDC.1 specifies only the first dicom image. the dicoms are in the format:
i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc
so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom image
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 10:09:13 AM Subject: Re: [Freesurfer] Tracula Error
Hi Emily - You're using "*" to specify all the dicom files in the series. You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This dmrirc looks like it might have been adapted from an older version of the tutorials. If so, I highly recommend downloading the latest version of everything.
Hope this helps, a.y
On Mon, 21 Oct 2013, ebelleau@uwm.edu wrote:
Hello,
I am running into the following error when I try to run trac-all:
set: No match. ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several attempts at debugging it.
I was wondering if you had any suggestions? Attached is my dmrirc_single_subject configuration.
I am brand new to freesurfer and tracula and would appreciate any guidance you can give me!
Thanks!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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
It's the * and its interpretation by the unix shell that does this, so it has nothing to do with tracula.
When you run this command: set dcmlist = (i*.MRDC.1) you're telling unix to find all files that match this pattern and to make the dcmlist variable equal to the list of files. If it doesn't find any files like this (and it'll look in the current directory unless you specify the full path), then dcmlist will be empty.
When you run this command: set dcmlist = (i727056.MRDC.1) you're telling unix to make the dcmlist variable equal to the string i727056.MRDC.1, so it won't search to find any files.
Does this make sense?
On Tue, 22 Oct 2013, Jon Wieser wrote:
according to the tracula wiki:
http://freesurfer.net/fswiki/FsTutorial/Tracula
the program should look in the directory specified by "dcmroot" to look for the dicom list
excerpt from the wiki page:
Step 5: Specify the location of diffusion DICOM files
set dcmroot = $TUTORIAL_DATA/diffusion_tutorial Use this variable to specify the directory under which the diffusion DICOM files for all subjects can be found.
Step 6: Specify the list of input DWIs
set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-000017-000001.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu, "ebelleau" ebelleau@uwm.edu Sent: Tuesday, October 22, 2013 12:24:22 PM Subject: Re: [Freesurfer] Tracula Error
The problem is that the command "set dcmlist = (i*.MRDC.1)" is executed as soon as it is read. So this will end up with an empty dcmlist, because there are no files named i*.MRDC.1 in the current directory.
On Tue, 22 Oct 2013, Jon Wieser wrote:
Hi anastasia, I work with Emily. the wild card she used i*.MRDC.1 specifies only the first dicom image. the dicoms are in the format:
i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc
so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom image
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 10:09:13 AM Subject: Re: [Freesurfer] Tracula Error
Hi Emily - You're using "*" to specify all the dicom files in the series. You should specify just one file.
BTW, do you have the latest version of freesurfer and the tutorials? This dmrirc looks like it might have been adapted from an older version of the tutorials. If so, I highly recommend downloading the latest version of everything.
Hope this helps, a.y
On Mon, 21 Oct 2013, ebelleau@uwm.edu wrote:
Hello,
I am running into the following error when I try to run trac-all:
set: No match. ERROR: must specify as many DWI dicoms as subjects
I have taken my script and examined it line by line and have made several attempts at debugging it.
I was wondering if you had any suggestions? Attached is my dmrirc_single_subject configuration.
I am brand new to freesurfer and tracula and would appreciate any guidance you can give me!
Thanks!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: ebelleau@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:53:29 PM Subject: Re: [Freesurfer] Tracula
Hi Emily - The first version of tracula was in freesurfer 5.1. However, I would *highly* recommend using the newer version of tracula, now in 5.3, as it has improvements in both performance and speed.
The processing in trac-all is supposed to happen in parallel for each of the subjects included in the configuration file, if you run trac-all on a cluster. However, not all clusters have the same set-up, and you may have to make modifications for it to work on your cluster, with the help of your cluster admins. There should be previous questions on this in this list's email archives. Let me know if you have any other questions.
a.y
On Thu, 10 Oct 2013, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@uwm.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 10, 2013 3:14:06 PM Subject: Tracula
Hello,
I had a question regarding batch processing in trac all.
When you batch process and put in multiple subjects in your subject list in your configuration file, are the subjects run parallel or serial?
Also, I am having a hard time finding the linux version of tracula that is compatible with Freesurfer version 5.0 (assuming it exists)?
Thank you so much and I appreciate your guidance as I am brand new to freesurfer and tracula.
Emily _______________________________________________ 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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
ebelleau＠uwm.edu -
Jon Wieser