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
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
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
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 $FREESURFER_HOME/FreeSurferColorLUT.txt) * priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn
Re: [Freesurfer] creating a gca file from .mgz files
Hopefully that doesn't scale the values I will make sure it doesn't. When running mri_ca_train by itself after changing to float the next error was the Bus error. When running rebuild_gca_atlas.csh I was having problems with pbsubmit, but after avoiding that it seems to be stuck with mri_ca_train. Date: Tue, 28 Aug 2012 17:02:51 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files does that scale the values? Hopefully not. It sounds like things don't fail after you changed to float until you get the pbsubmit problem, correct? On Tue, 28 Aug 2012, Jeff Thompson wrote: To change to type Float I used: fslmaths Alloybrain_mask_LUTComplete.nii.gz -thr 0 Alloybrain_mask_LUTComplete_float.nii.gz -odt float I will try some other methods for changing the data type, but if that isn't the issue are there other cases of getting similar errors from mri_ca_train? thanks, Jeff Date: Tue, 28 Aug 2012 16:37:19 -0400 From: fis...@nmr.mgh.harvard.edu To: jeff_rthomp...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] creating a gca file from .mgz files how did you change the type to float? Make sure it doesn't scale the inputs if that is the segmentation volume. rebuild_gca_atlas.csh uses our compute cluster queueing system which is what the pbsubmit script is. You'll need to modify it to use whatever cluster you are using or to run them in series cheers Bruce On Tue, 28 Aug 2012, Jeff Thompson wrote: Hello, When running the mri_ca_train I am getting a Bus error near the beginning of it. 'bash-3.2$ 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
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.
[Freesurfer] creating labels, new atlas
Hello, How can tksurfer be used to create label files for the purpose of making a new atlas, if that atlas is needed to create the surface files needed to view the brain in tksurfer? Would people use FSL to create the masks, and convert them into what is needed for freesurfer or is there another way? 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.
Re: [Freesurfer] creating labels, new atlas
I found this info on the tksurfer webpage. The label file format is interchangable with TkMedit. You can create a label in TkSurfer, save it, and load it in TkMedit, or vice versa. Jeff Thompson From: jeff_rthomp...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: creating labels, new atlas Date: Thu, 23 Aug 2012 10:48:46 -0300 Hello, How can tksurfer be used to create label files for the purpose of making a new atlas, if that atlas is needed to create the surface files needed to view the brain in tksurfer? Would people use FSL to create the masks, and convert them into what is needed for freesurfer or is there another way? 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.
[Freesurfer] GCA file for non-human recon-all use
Hello, I have a few questions that I hope can be answered: Q1:How can '.label' files be turned into the necessary '.gca' file needed for the recon-all pipeline. Starting for the first step in auto-recon2.What else other than the '.label' files would be needed to create this '.gca' file? Q2: How to get the seg_edited.mgz file? I would want to use this file in the rebuild_gca_atas.csh script. Q3:Can the rebuild_gca_atlas.csh script be used to make a replacement for the RB_all_2008-03-26.gca file from the average folder? Q4:Is there a way to avoid needing the .gca file if cortical thickness measurements is the only goal?Or could there be a limited number of labels needed incorporated into the .gca file for this goal. Ex. Just Cerebral cortex ROI's. Thank you for any help, 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.
Re: [Freesurfer] Creating and using an atlas from scratch
Hi,I have run talairach_avi with the template I have made, and an input file that is manually skull stripped. I ran: talairach_avi --i input.nii.gz --atlas avgeragetemplate --xfm talairach_avitest.xfmI had put the averagetemplate.nii.gz file in the average folder in freesurfer for this to work. I also have averagetemplate.4dfp.hdr , averagetemplate.4dfp.img , averagetemplate.4dfp.mat in the average folder.Running this creates talsrcimg.hdr, talsrcimg.img, talsrcimg.mat in the folder where I ran the script. However in the talairach_avi log it gives an error saying /Applications/freesurfer/average/averagetemplate.4dfp.ifh does not exist! How can I create this file?I found a brief note in a mailing list that mentioned analyzeto4dfp talsrcimg -O0 -y:$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Sat Dec 31 03:27:10 2011 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 However, I don't know what I need to run this. Will I need to install analyze and 4dfp to be able to run analyzeto4dfp? Or is there another way to get this averagetemplate.4dfp.ifh file?Thanks,-Jeff ___ 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] analyzeto4dfp to get a talsrcimg.4dfp.ifh file
Hi,I have run talairach_avi with the template I have made, and an input file that is manually skull stripped. I ran: talairach_avi --i input.nii.gz --atlas avgeragetemplate --xfm talairach_avitest.xfmI had put the averagetemplate.nii.gz file in the average folder in freesurfer for this to work. I also have averagetemplate.4dfp.hdr , averagetemplate.4dfp.img , averagetemplate.4dfp.mat in the average folder.Running this creates talsrcimg.hdr, talsrcimg.img, talsrcimg.mat in the folder where I ran the script. However in the talairach_avi log it gives an error saying /Applications/freesurfer/average/averagetemplate.4dfp.ifh does not exist! How can I create this file?I found a brief note in a mailing list that mentioned analyzeto4dfp talsrcimg -O0 -y:$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Sat Dec 31 03:27:10 2011 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 However, I don't know what I need to run this. Will I need to install analyze and 4dfp to be able to run analyzeto4dfp? Or is there another way to get this averagetemplate.4dfp.ifh file?Thanks,-Jeff ___ 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] MCSRCH ERROR
Hi - Was there ever a solution found for this? I am currently having the same problem. Thanks, Jeff Thompson Can you send us e recon-all.log file? On Aug 8, 2011, at 4:30 AM, Irwin, William WIrwin at memory.ucsf.edu wrote: Hi- I’m at a bit of a loss as to how to address and/or fix these errors. The native input images are very good quality; the conversion to T1.mgz is fine; the brainmask.mgz is good, a bit of dura remained at the parietal/occipital region (very common); otherwise, the skull stripping is very clean. The recon-all “finished” but with errors as expected. Processing “continued” to the end, but there is no output except in /mri and /touch. Doing: #@# Skull Stripping First under “Computing MAP estimate using 3481 samples...” IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10327.2 tol 0.10 Then several of the same under “EM alignment process ...” IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 3 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 4 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 5 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 017: -log(p) = 1145822.4 tol 0.00 Then again at “Computing MAP estimate using 2772 samples...” IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 7006.0 tol 0.10 IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 838978.4 tol 0.00 Thanks, Wil William Irwin | Brain Imaging Coordinator UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wirwin at memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816 ___ 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.
