[Freesurfer] Creating a .gca file
Hello experts, I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to create a atlas using previous registered subjects. It does not complete the mri_ca_normalize phase and stops there. It shows pbsubmit: Command not found as error. Please correct me. Also attaching the rebuild_gca_atlas file. Thanks Pradeep Kumar Mahato rebuild_gca_atlas.csh Description: C-Shell script ___ 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.
Re: [Freesurfer] Creating a .gca file
Hi Pradeep pbsubmit is a wrapper script for submitting a job to a PBS cluster. If you don't have a cluster you should just run the commands that it runs. cheers Bruce On Mon, 19 Jan 2015, pradeep mahato wrote: Hello experts, I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to create a atlas using previous registered subjects. It does not complete the mri_ca_normalize phase and stops there. It shows pbsubmit: Command not found as error. Please correct me. Also attaching the rebuild_gca_atlas file. Thanks Pradeep Kumar Mahato ___ 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.
Re: [Freesurfer] creating a gca file from .mgz files
The command line to get the aseg was: Mri_convert -rt nearest -c file containing all valued label masks.nii.gz aseg.mgz Fslmaths was used to match label values to the colour lut and combine them all into one file. Thanks, Jeff On 2012-09-05, at 1:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what is your mri_convert command line? On Wed, 5 Sep 2012, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train
Re: [Freesurfer] creating a gca file from .mgz files
and when you say it is way off what do you mean? Is the intensity volume conformed in the same way? On Thu, 6 Sep 2012, Jeff Thompson wrote: The command line to get the aseg was: Mri_convert -rt nearest -c file containing all valued label masks.nii.gz aseg.mgz Fslmaths was used to match label values to the colour lut and combine them all into one file. Thanks, Jeff On 2012-09-05, at 1:05 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what is your mri_convert command line? On Wed, 5 Sep 2012, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training
Re: [Freesurfer] creating a gca file from .mgz files
I don't think you actually want to do the full conformation as that will change the type to uchar, which is probably what is messing up your values. Instead, try this mri_vol2vol --mov aseg.mgz --targ orig.mgz --regheader --interp nearest --precision int --o aseg.conf.mgz doug On 09/05/2012 12:47 PM, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz
Re: [Freesurfer] creating a gca file from .mgz files
what is your mri_convert command line? On Wed, 5 Sep 2012, Jeff Thompson wrote: Hello, I got mri_ca_train to complete and to produce a .gca file, which looks to be what is expected after splitting it up into means/labels/priors files. The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz file to replace the norm.mgz file, and it seemed to work in mri_ca_train. I am now having trouble with the aseg.mgz file in mri_normalize. It states that the aseg.mgz file needs to be conformed. When I conform the image the label values are way off. I tried the mri_convert conform with the rt nearest , but the label values seemed to still be off. The file I have has dimensions of : ~0.6 , 0.6 , 1.0 mm and 256x256x90. Any recommendations to solve this problem? Thank you, Jeff Thompson Subject: Re: [Freesurfer] creating a gca file from .mgz files From: ni...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: fis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Date: Wed, 29 Aug 2012 19:56:09 -0400 i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
Re: [Freesurfer] creating a gca file from .mgz files
Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that. Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate
Re: [Freesurfer] creating a gca file from .mgz files
i think there should be an error log that outputs the errors that mri_ca_train found. or you can run mri_ca_train with the -check flag. it performs checks looking for voxels that are in the wrong hemisphere, based on the talairach registration. for mri_convert, be sure to include the flag -rt nearest which overrides the default resample type of 'interpolate', which is not appropriate for labeled volumes. n. On Wed, 2012-08-29 at 18:20 -0300, Jeff Thompson wrote: Hello, Still getting the bus error when running mri_ca_train. I tried running it after I conformed the manually labelled volume as well. I've been working on getting rebuild_gca_atlas.csh to work. I don't know how to get the labelled volume to conform when converting the labelled volume to .mgz with mri_convert without throwing all of the label values off. This resulted in a lot of errors when running rebuild_gca_atlas.csh and gave an error stating ERROR: mri_ca_train check found 1 subjects with bad labels! Thanks, Jeff Thompson __ CC: freesurfer@nmr.mgh.harvard.edu From: fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Date: Tue, 28 Aug 2012 20:12:45 -0400 To: jeff_rthomp...@hotmail.com Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file
Re: [Freesurfer] creating a gca file from .mgz files
Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directoryreading T1 data from subject's mri/norm.mgz directorytraining on 1 subject and writing results to single_oneAlloy.gcagcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 4***processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgzBus error'Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that.Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please
Re: [Freesurfer] creating a gca file from .mgz files
how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that. Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
Re: [Freesurfer] creating a gca file from .mgz files
To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that. Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn
Re: [Freesurfer] creating a gca file from .mgz files
does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that. Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability
Re: [Freesurfer] creating a gca file from .mgz files
Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that. Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we
Re: [Freesurfer] creating a gca file from .mgz files
Oh, so you still got a bus error? I didn't realize that. Make sure the seg volumes are ok On Aug 28, 2012, at 6:10 PM, Jeff Thompson jeff_rthomp...@hotmail.com wrote: Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ mri_ca_train -parc_dir Alloybrain_mask_LUTComplete_float.mgz -T1 norm.mgz Alloy single_oneAlloy.gcareading segmentation from subject's mri/Alloybrain_mask_LUTComplete_float.mgz directory reading T1 data from subject's mri/norm.mgz directory training on 1 subject and writing results to single_oneAlloy.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *** processing subject Alloy, 1 of 1... reading input 0: Desktop/freesurfer/subjects/Alloy/mri/norm.mgz Bus error ' Previously it was giving an error saying that :mri_ca_train: segmentation file Desktop/freesurfer/subjects/Buddha/mri/Alloybrain_mask_LUTComplete.nii.gz is not type UCHAR or FLOAT So I changed the file type to float to get rid of that. Any ideas? When I run rebuild_gca_atlas.csh it gives a pbsubmit command not found error. If I have a cluster to use, but am able to just load everything onto it and then run it, can I comment out all of the pbsubmit lines? Thank you for all the help, Jeff Date: Mon, 27 Aug 2012 12:00:13 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer
Re: [Freesurfer] creating a gca file from .mgz files
Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson 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 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.
Re: [Freesurfer] creating a gca file from .mgz files
Hi Jefff you can give mri_ca_normalize a flag to tell it to use a manual segmentation instead of the gca. Try -seg manual seg volume. Then the gca name won't matter - it should ignore it. You could use label2label I guess, although if it's accurate across brains then you probably don't need it and can just build the gca from a handful of brains instead of the dozens we need for humans cheers Bruce On Mon, 27 Aug 2012, Jeff Thompson wrote: Hello, Okay, but from looking at the recon-all pipeline it looks like to generate the norm.mgz file the .gca atlas is needed first. If I create the seg_edited.mgz file from my manually labelled file can I use that in rebuild_gca_atlas.csh to generate the .gca atlas? This would incorporate the mri_ca_train, is that correct? The other question I have is regarding mri_label2label. If I have manually labelled one brain from my set, can I use mri_label2label to convert these labels to other dog brains in my set if they have been registered to the first brain used? Thank you, Jeff Thompson Date: Sat, 25 Aug 2012 11:11:46 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] creating a gca file from .mgz files Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson 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 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.
Re: [Freesurfer] creating a gca file from .mgz files
Hi Jeff it's more complicated than that. You need a .mgz volume for every subject you want to train on that contains the labels, and an accompanying intensity volume (we usually use the norm.mgz for this purpose). Then we extract statistics to create the .gca across these subjects using mri_ca_train cheers Bruce On Thu, 23 Aug 2012, Jeff Thompson wrote: From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this: mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgz where: * means -- the mean intensity of the most likely label * labels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson ___ 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] creating a gca file from .mgz files
From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this:mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgzwhere:means -- the mean intensity of the most likely labellabels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson ___ 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.
