Re: [Freesurfer] Jacobian mri_cvs_register
Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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] Jacobian mri_cvs_register
I got an error using the mri_jacobina. The function returns: The input morph originated from a tm3d (mri_cvs_register file). GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000 mri_jacobian: could not read input morph /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d The command is provided below: mri_jacobian -tm3d /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro af...@imperial.ac.uk wrote: Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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] bad freesurfer segmentation
Hi Doety that is a very low contrast-to-noise image. Can you give us more details on the acquisition? The matrix was 256x256, what is the slice thickness? And the other parameter (sequence name? TR/TR/flip angle? acceleration?) cheers Bruce On Thu, 10 Jul 2014, Doety Prins wrote: Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256. I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? Thanks in advance, Doety ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Creating own atlas
Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ 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 own atlas
Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Jacobian mri_cvs_register
Hi, You should use the final m3z file. The -tm3d flag just indicates that the file was created by mri_cvs_register. Lilla On Fri, 11 Jul 2014, André Ribeiro wrote: I got an error using the mri_jacobina. The function returns: The input morph originated from a tm3d (mri_cvs_register file). GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000 mri_jacobian: could not read input morph /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d The command is provided below: mri_jacobian -tm3d /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro af...@imperial.ac.uk wrote: Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 own atlas
Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 own atlas
Hi Brianna yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] bad freesurfer segmentation
the 2mm slice thickness is going to be problematic and is probably why you lose so much cortical constrast. Typically we don't recommend using anything more than 1.5 and really no reason these days not to get closer to 1mm (for example, you can get a very nice 1.25mmx1.25x1mm mprage in a bit over 2 minutes) cheers Bruce On Fri, 11 Jul 2014, Doety Prins wrote: slice thickness: 2 mm Repetition time: 25 ms (I think this might have caused the low contrast) flip angle: 30 degrees I'm sorry, can't find any data on acceleration Doety On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety that is a very low contrast-to-noise image. Can you give us more details on the acquisition? The matrix was 256x256, what is the slice thickness? And the other parameter (sequence name? TR/TR/flip angle? acceleration?) cheers Bruce On Thu, 10 Jul 2014, Doety Prins wrote: Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256. I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? Thanks in advance, Doety ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bad freesurfer segmentation
slice thickness: 2 mm Repetition time: 25 ms (I think this might have caused the low contrast) flip angle: 30 degrees I'm sorry, can't find any data on acceleration Doety On 11 jul. 2014, at 15:10, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety that is a very low contrast-to-noise image. Can you give us more details on the acquisition? The matrix was 256x256, what is the slice thickness? And the other parameter (sequence name? TR/TR/flip angle? acceleration?) cheers Bruce On Thu, 10 Jul 2014, Doety Prins wrote: Hi Bruce, Thanks for your reply. In my previous e-mail I already tried to attach one of my subjects, but got the response that the message was too big, and therefore it was rejected. So how should I upload the image? The images are T1-weighted, 3D, acquired with a 3T scanner, resolution 256 256. I discovered that FSL does a proper segmentation on this subjects, so I was looking for a way to import these segments from FSL into the Freesurfer pipeline, but I didn't succeed so far. I used the white matter segment from FSL as wm.mgz (in a subject in which I already ran recon-all), I used mri_vol2vol to get this segment in the right space, and normalized with mri_normalize. Then I rerun recon-all with -autorecon2-wm. But it gives me the error message: 'ERROR: mri_segment-MRIcheckVolDims: volume1 depth=160 != volume2 depth=256.' So apparently, the wm.mgz still doesn't have the right size. Do you have any experience with this? Or any ideas about this? Best regards, Doety On 9 jul. 2014, at 15:00, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the segmentation of my T1 scans, as both the white surface and the pial surface are placed incorrectly (see attached images). This seems to me to be a too big difference with what it should look like, that I think could not be fixed with the standard troubleshooting strategies. Do you have any solutions for this? Is it for instance possible to make changes to the recon-all script to shift the surfaces? Thanks in advance, Doety ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Creating own atlas
Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas? Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer? Thanks, Brianna On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 own atlas
Hi Brianna if you upload a subject that is not doing well I'll take a look. Have you tried the -bigventricles flag? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas? Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer? Thanks, Brianna On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Jacobian mri_cvs_register
Thank you for the explanation but in that case there are two things that seems odd. First, in the mri_cvs_register I kept all the files and therefore the combined_toIBSR_02_elreg_afteraseg-norm.tm3d file was not removed. If I try to replicate this file through the createMorph --out fullCVSmorph.tm3d --template template.mgz --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z morph el_reg_toTEMPLATE.tm3d the file produced is different from the one previously created by the program (and gives far worse registration results when used with the applyMorph). Is something wrong here? Second, even if the two files gave the same results wouldn’t this fullCVSmorph.tm3d (otherwise called combined_toIBSR_02_elreg_afteraseg-norm.tm3d) have both information from *afteraseg-norm.m3z and el_reg_toTEMPLATE.tm3d, and therefore the Jacobian applied solely to the nlalign-afteraseg-norm.m3z would not match. Lastly, am I right assuming the combined_toIBSR_02_elreg_afteraseg-norm.tm3d is the last registration (and most accurate) performed by mri_cvs_register? Regards, Andre Santos Ribeiro On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi, You should use the final m3z file. The -tm3d flag just indicates that the file was created by mri_cvs_register. Lilla On Fri, 11 Jul 2014, André Ribeiro wrote: I got an error using the mri_jacobina. The function returns: The input morph originated from a tm3d (mri_cvs_register file). GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000 mri_jacobian: could not read input morph /home/afs13/Documents/data/ test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d The command is provided below: mri_jacobian -tm3d /home/afs13/Documents/data/ test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro af...@imperial.ac.uk wrote: Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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 own atlas
I have not tried that yet - when would I enter this flag? During the initial recon-all coding or later? Thanks, Brianna On Fri, Jul 11, 2014 at 10:49 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna if you upload a subject that is not doing well I'll take a look. Have you tried the -bigventricles flag? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas? Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer? Thanks, Brianna On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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
Re: [Freesurfer] Creating own atlas
it's a flag to recon-all. Run recon-all -help and you should find it On Fri, 11 Jul 2014, Brianna Damadian wrote: I have not tried that yet - when would I enter this flag? During the initial recon-all coding or later? Thanks, Brianna On Fri, Jul 11, 2014 at 10:49 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna if you upload a subject that is not doing well I'll take a look. Have you tried the -bigventricles flag? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas? Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer? Thanks, Brianna On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hello, I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? Thanks, Brianna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Jacobian mri_cvs_register
Hi, First, in the mri_cvs_register I kept all the files and therefore the combined_toIBSR_02_elreg_afteraseg-norm.tm3d file was not removed. If I try to replicate this file through the createMorph --out fullCVSmorph.tm3d --template template.mgz --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z morph el_reg_toTEMPLATE.tm3d the file produced is different from the one previously created by the program (and gives far worse registration results when used with the applyMorph). Is something wrong here? No, there is nothing wrong. In the above command you are just not composing the right files. I assume that you have run the default mri_cvs_register command. In that case there are two non-linear registration steps one aided by aseg info and one by intensities. In the above you are skipping the morph created by the former so that is why you are not getting the same combined output. Instead of morph el_reg_toTEMPLATE.tm3d you would need to use morph combined*aseg.tm3d Second, even if the two files gave the same results wouldn’t this fullCVSmorph.tm3d (otherwise called combined_toIBSR_02_elreg_afteraseg-norm.tm3d) have both information from *afteraseg-norm.m3z and el_reg_toTEMPLATE.tm3d, and therefore the Jacobian applied solely to the nlalign-afteraseg-norm.m3z would not match. It is correct. The jacobians of fullCVSmorph.tm3d and nlalign-afteraseg-norm.m3z will not match. I am a bit confused about whey you think they should. Lastly, am I right assuming the combined_toIBSR_02_elreg_afteraseg-norm.tm3d is the last registration (and most accurate) performed by mri_cvs_register? Yes. In the most current FS version though we use the m3z files as we are trying to phase out the tm3d format. Lilla On Fri, Jul 11, 2014 at 3:11 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi, You should use the final m3z file. The -tm3d flag just indicates that the file was created by mri_cvs_register. Lilla On Fri, 11 Jul 2014, André Ribeiro wrote: I got an error using the mri_jacobina. The function returns: The input morph originated from a tm3d (mri_cvs_register file). GCAMread(/home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d): invalid version # 0.000 mri_jacobian: could not read input morph /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d The command is provided below: mri_jacobian -tm3d /home/afs13/Documents/data/test_freesurfer_reg/combined_toIBSR_02_elreg_aseg.tm3d /home/afs13/Documents/data/test_freesurfer_reg/brain.mgz /home/afs13/Documents/data/test_freesurfer_reg/test_jac.nii.gz Regards, Andre Santos Ribeiro PhD Student, Imperial College London On Fri, Jul 11, 2014 at 11:09 AM, André Ribeiro af...@imperial.ac.uk wrote: Thank you! Didn't realized that function existed. Regards, Andre Santos Ribeiro On Thu, Jul 10, 2014 at 4:59 PM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Andre You can run: mri_jacobian -tm3d 3d morph template volume output volume --Lilla On Thu, 10 Jul 2014, André Ribeiro wrote: Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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] Hippocampal Subsectioning
Hi, I was doing a hippocampal subsectioning https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran volume_in_number_of_voxels Right-Hippocampus right_presubiculum right_CA1 right_CA2_3 right_fimbria right_subiculum right_CA4_DG right_hippocampal_fissure ESZC063088.863806.93270.49527.04580.9615662.38 5160.47419.635 ESZC094474.984175.63495.299507.35610.4166002.32 5415.3764.783 ESZC173714.853549.983803.8510407.2236.3766100.06 5702.51498.232 ESZC192747.233018.232794.957421.49385.8454304.76 4006.76320.488 ESZC203651.644114.272849.188566.68679.9615988.08 4780.1270.116 ESZS043969.073151.292902.78127.18124.0435183.18 4956.47160.333 ESZS073839.453542.613582.489566.92644.8365774.21 5276.71308.941 ESZS143224.984186.212500.167324.79532.7775247.57 4348.97140.18 ESZS163153.163417.782777.058924.38917.1625016.83 5038.98129.952 ESZS173358.733223.232767.348336.61346.6285224.47 4779.15275.812 ___ 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] create label from binary .mgh file
Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] create label from binary .mgh file
Hi Lars this would be pretty simple to do in matlab, but I'm not sure if we have anything do to it otherwise (Doug might) cheers Bruce On Fri, 11 Jul 2014, Lars M. Rimol wrote: Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] Correlation coeffecient
Hi Freesurfer experts I am trying to obtain correlation coefficients for significant clusters and found a previous post about this, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html but the MATLAB function link within this post is dead? any help is greatly appreciated thanks, Chris ___ 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] Hippocampal Subsectioning
Hi Joshua, the measurements are in voxels, so you need to multiply them by 0.125 (which is 0.5^3) to obtain values in mm3. Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Joshua S nitrosomonas...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, July 11, 2014 5:46:59 PM Subject: [Freesurfer] Hippocampal Subsectioning Hi, I was doing a hippocampal subsectioning on a data set. Previously recon-all -all was used, and then I did recon-all -hippo-subfields. I then used the script kvlQuantifyHippocampalSubfieldSegmentations.sh to find the volume of the hippocampus and its sub parts. I was confused as to the data I was getting out. The hippocampus seems to large. The voxel size is 0.5 mm * 0.5 mm * 0.5 mm so the hippocampal areas seem to large. Also the subunits of the hippocampus are larger than the actual hippocampus which again does not make sense. I attached one of the output files Thank you for any replies, From Joshua Segaran ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] create label from binary .mgh file
use mri_cor2label with the --surf option On 07/11/2014 01:36 PM, Bruce Fischl wrote: Hi Lars this would be pretty simple to do in matlab, but I'm not sure if we have anything do to it otherwise (Doug might) cheers Bruce On Fri, 11 Jul 2014, Lars M. Rimol wrote: Hi, Is there a way to take a binary .mgh file (surface file with 163842 vertices containing 1 or 0) and create a label such that the ones in the input file == the label? For instance, to create a label from a p-map. I tried using mri_cor2label based on previous responses on the mailing list, but that seems to produce volumes and I'm not really sure what it does anyway... Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Correlation coeffecient
try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m On 07/11/2014 01:51 PM, Chris Wertz wrote: Hi Freesurfer experts I am trying to obtain correlation coefficients for significant clusters and found a previous post about this, https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html but the MATLAB function link within this post is dead? any help is greatly appreciated thanks, Chris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Temporal lobe reconstruction problem
Hi James if you upload a problem subject we will take a look (the whole subject dir please) cheers Bruce On Fri, 11 Jul 2014, james pardon wrote: Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James ___ 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] exporting movies from freeview
Hi Freesurfer Team, I have a 4D volume mask of MRI mask values over time - which I can view frame by frame within Freeview. Is there any way to export this in movie form out of freeview so I can play it back independently of the interface? Thank you. Best Regards, Pavitra ___ 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] exporting movies from freeview
Hi Pavitra, In Freeview, go to File - Save Movie Frames. For the fly through option select Frame. There is no command line option for this feature yet, but hopefully soon. -Louis On Fri, 11 Jul 2014, pavit...@nmr.mgh.harvard.edu wrote: Hi Freesurfer Team, I have a 4D volume mask of MRI mask values over time - which I can view frame by frame within Freeview. Is there any way to export this in movie form out of freeview so I can play it back independently of the interface? Thank you. Best Regards, Pavitra ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Group differences in pc1 (longitudinal stage2)
Dear FS list, (dear Martin!) I have a longitudinal design, 3 groups, 2 timepoints, and I created three different QDEC tables (two groups at a time) in order to be able to compare each pair of groups in terms of percentage change from pre to post (what's referred to as pc1 in the first stage of the two-stage-model). I look at thickness, area and lGI as dependent variables. Group is a categorical factor of interest, gender as the other categorical factor (not interested in its effect), and age as (continuous) nuisance. I'm interested in the contrast Does the average ..., accounting for gender, differ between G1 and G2? Say that, for some analysis (e.g. group 1 vs group 2, thickness, LH) I get a certain cluster that survives the MonteCarlo Null-Z correction. If the cluster is redish, I take it to mean that group 1 has a higher signed value of pc1 than group 2, and vice-versa if the cluster is blueish. However, because pc1 is (I think) a signed statistic, i.e. is negative for thickness decrease and positive for thickness increase, this makes me unsure how to interpret the stage2 (cross-sectional) result. As I understand it, having a significant red cluster in the group comparison can mean either of these 3 scenarios: 1. Both groups have pc10 2. G1 has pc10 and G2 has pc10 3. Both groups have pc10 ..but that the pc1 of G1 is always greater, as a signed number, than that of G2, since that is what defines the cluster. The problem is that, when I run the same analysis but keeping only subjects of one group in at one time, i.e. for each group separately and looking at the contrast Does the average ... differ from zero?, in most cases I don't get the same cluster that appeared in the group comparison. My question is therefore: can a cluster appearing in the between-groups analysis be trusted if the same (or similar) cluster does *not *appear in each of the two within-groups (one-sample test) analyses? And if the latter analysis produces null results but the former does have sig clusters, does it still make sense to look at the sign of each group's mean pc1 in order to find the effect of the longitudinal treatment (atrophy or increase), even if that group in fact did not have a pc1 that was significantly different from zero? Many thanks for your help! Tudor ___ 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] Tutorial Installation Issue
Hi all, I have a question regarding the installation of the buckner tutorial dataset. I have been able to download and unzip the tutorial data, but it seems only partially downloaded. In the readme, I see that there are supposed to be 3 subfolders to the dataset: group_study, tutorial_subjs, and raw, but my download only contains one subfolder (tutorial_subjs). I have tried downloading multiple times in multiple ways without a change in results. Is anyone aware of what might be causing this? Thank you! Kathryn Kundrod ___ 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] [FreeSurfer] Importing DICOM Files
Hi FreeSurfers, I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files. Here is the script I used: recon-all -s 142 \ -i $SUBJECTS_DIR/142/01.dcm I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work. Here is my output: ERROR: cannot find /home/mclem/freesurfer/testsubjects/142/01.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 Any thoughts on what I'm doing wrong? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center matthew.c...@utsouthwestern.edumailto:tabatha.mel...@utsouthwestern.edu UT Southwestern Medical Center The future of medicine, today. ___ 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] [FreeSurfer] Importing DICOM Files
Hi Matthew where are the dicoms located? Does that file exist? What happens if you do: ls -l /home/mclem/freesurfer/testsubjects/142/01.dcm cheers Bruce On Fri, 11 Jul 2014, Matthew Clem wrote: Hi FreeSurfers, I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files. Here is the script I used: recon-all -s 142 \ -i $SUBJECTS_DIR/142/01.dcm I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work. Here is my output: ERROR: cannot find /home/mclem/freesurfer/testsubjects/142/01.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 Any thoughts on what I'm doing wrong? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center matthew.c...@utsouthwestern.edu _ UT Southwestern Medical Center The future of medicine, today. ___ 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] [FreeSurfer] Importing DICOM Files
Hi Bruce, Thanks for your quick response. Here is what comes up when I enter ls -l /home/mclem/freesurfer/testsubjects/142/01.dcm: ls: cannot access /home/mclem/freesurfer/testsubjects/142/01.dcm: No such file or directory Originally, I copied the subject's folder (142) from a flash drive into the freesurfer folder - was I supposed to import them using the terminal? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center matthew.c...@utsouthwestern.edu UT Southwestern Medical Center The future of medicine, today. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, July 11, 2014 3:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Importing DICOM Files Hi Matthew where are the dicoms located? Does that file exist? What happens if you do: ls -l /home/mclem/freesurfer/testsubjects/142/01.dcm cheers Bruce On Fri, 11 Jul 2014, Matthew Clem wrote: Hi FreeSurfers, I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files. Here is the script I used: recon-all -s 142 \ -i $SUBJECTS_DIR/142/01.dcm I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work. Here is my output: ERROR: cannot find /home/mclem/freesurfer/testsubjects/142/01.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 Any thoughts on what I'm doing wrong? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center matthew.c...@utsouthwestern.edu _ UT Southwestern Medical Center The future of medicine, today. ___ 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] [FreeSurfer] Importing DICOM Files
Hi Matthew we don't care where they are, but you need to specificy the correct path for them to recon-all cheers Bruce On Fri, 11 Jul 2014, Matthew Clem wrote: Hi Bruce, Thanks for your quick response. Here is what comes up when I enter ls -l /home/mclem/freesurfer/testsubjects/142/01.dcm: ls: cannot access /home/mclem/freesurfer/testsubjects/142/01.dcm: No such file or directory Originally, I copied the subject's folder (142) from a flash drive into the freesurfer folder - was I supposed to import them using the terminal? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center matthew.c...@utsouthwestern.edu UT Southwestern Medical Center The future of medicine, today. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, July 11, 2014 3:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] Importing DICOM Files Hi Matthew where are the dicoms located? Does that file exist? What happens if you do: ls -l /home/mclem/freesurfer/testsubjects/142/01.dcm cheers Bruce On Fri, 11 Jul 2014, Matthew Clem wrote: Hi FreeSurfers, I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files. Here is the script I used: recon-all -s 142 \ -i $SUBJECTS_DIR/142/01.dcm I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work. Here is my output: ERROR: cannot find /home/mclem/freesurfer/testsubjects/142/01.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 Any thoughts on what I'm doing wrong? Thanks, Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center matthew.c...@utsouthwestern.edu _ UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] LME Longitudinal QDEC Table
Hello Freesurfer Experts,
I am performing a mass-univariate analyses using the LME toolbox for
longitudinal studies.
After running both mris_preproc and mri_surf2surf , I load the
lh.thickness_sm10.mgh file using
*[Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');*
Next, I run the following command:
*Qdec = fReadQdec('qdec.table.dat');*
However, it seems that the output is entirely in string format 166 x 1
cell. The first row reads as 'fsid fsid-base years group gender age' in
a single column.
Because of this, I am running into problems when I try to execute the
following steps:
*Qdec = rmQdecCol(Qdec,1);* (removes first column)
*sID = Qdec(2:end,1); (grabs the subjects' IDs)*
*Qdec = rmQdecCol(Qdec,1);* (removes the subjects'ID column)
*M = Qdec2num(Qdec);* (converts to a numeric matrix)
*[M,Y,ni] = sortData(M,1,Y,sID);* (sorts the data)
Your help will be greatly appreciated!
Many thanks.
Best Regards,
Elijah
--
Elijah Mak, Gates Scholar
PhD Candidate *|* Psychiatry
University of Cambridge
Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Segmentation fault with mri_ca_train
Hello freesurfers, I am running into some sort of memory allocation issue when running mri_ca_train. I am simply using an intensity volume and a segmentation volume to create a GCA atlas. I keep getting this segmentation fault: 11, which is data allocation error. I have tried using all different environments and can't avoid it. The output is below: sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test /hearingbrain/Desktop/atlas_withSkull.gca reading T1 data from subject's mri/withSkull.mgz directory reading segmentation from subject's mri/seg_edited.mgz directory training on 1 subject and writing results to /Volumes/Macintosh HD/Users/hearingbrain/Desktop/atlas_withSkull.gca *** processing subject atlas_test, 1 of 1... reading input 0: /Applications/freesurfer/subjects/atlas_test/mri/withSkull.mgz gca width modified from 256 to 181 gca height modified from 256 to 217 gca depth modified from 256 to 181 Segmentation fault: 11 Any ideas? -MP ___ 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] Segmentation fault with mri_ca_train
Hi Mark have you tried conforming the inputs (making them all 256^3, 1mm iso and 8 bits/voxel)? Bruce On Fri, 11 Jul 2014, Mark Plantz wrote: Hello freesurfers, I am running into some sort of memory allocation issue when running mri_ca_train. I am simply using an intensity volume and a segmentation volume to create a GCA atlas. I keep getting this segmentation fault: 11, which is data allocation error. I have tried using all different environments and can't avoid it. The output is below: sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test /hearingbrain/Desktop/atlas_withSkull.gca reading T1 data from subject's mri/withSkull.mgz directory reading segmentation from subject's mri/seg_edited.mgz directory training on 1 subject and writing results to /Volumes/Macintosh HD/Users/hearingbrain/Desktop/atlas_withSkull.gca *** processing subject atlas_test, 1 of 1... reading input 0: /Applications/freesurfer/subjects/atlas_test/mri/withSkull.mgz gca width modified from 256 to 181 gca height modified from 256 to 217 gca depth modified from 256 to 181 Segmentation fault: 11 Any ideas? -MP ___ 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] Segmentation fault with mri_ca_train
Ahh, that did the trick. Thanks! On Fri, Jul 11, 2014 at 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Mark have you tried conforming the inputs (making them all 256^3, 1mm iso and 8 bits/voxel)? Bruce On Fri, 11 Jul 2014, Mark Plantz wrote: Hello freesurfers, I am running into some sort of memory allocation issue when running mri_ca_train. I am simply using an intensity volume and a segmentation volume to create a GCA atlas. I keep getting this segmentation fault: 11, which is data allocation error. I have tried using all different environments and can't avoid it. The output is below: sh-3.2# mri_ca_train -T1 withSkull.mgz -seg seg_edited.mgz atlas_test /hearingbrain/Desktop/atlas_withSkull.gca reading T1 data from subject's mri/withSkull.mgz directory reading segmentation from subject's mri/seg_edited.mgz directory training on 1 subject and writing results to /Volumes/Macintosh HD/Users/hearingbrain/Desktop/atlas_withSkull.gca *** processing subject atlas_test, 1 of 1... reading input 0: /Applications/freesurfer/subjects/atlas_test/mri/ withSkull.mgz gca width modified from 256 to 181 gca height modified from 256 to 217 gca depth modified from 256 to 181 Segmentation fault: 11 Any ideas? -MP ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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] transforming Base surfaces to Cross space
Dear All, For longitudinal data sets, is there a way that the lh.pial surface from the Base can be transformed into the brainmask.mgz space of a Cross so that it can be viewed with tkmedit on the Cross brainmask.mgz? Thanks, Paul ___ 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] Temporal lobe reconstruction problem
Hi Bruce, I have sent the link for a problem subject via a private message. Please note since MS causes hypointense lesions in white matter I have used an algorithm that fills hypointense lesions in WM with median intensity of normal appearing WM. Thanks James On Fri, Jul 11, 2014 at 11:19 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi James if you upload a problem subject we will take a look (the whole subject dir please) cheers Bruce On Fri, 11 Jul 2014, james pardon wrote: Hi all, On a few subjects with a specific pathology (MS) I cannot easily reconstruct temporal lobes. I think this issue comes up quite regularly on the mailing list, and I have tried to trouble shoot using control points, WM edits, even getting back to orig/001.mgz to correct areas that may seem the culprit for breaking surface reconstruction. Some subjects have gone through 7-8 runs of recon-all with different edits but still the problem persists in a few subjects in my study. I have also tried to use -mprage and -3T flags along the way to allow more liberal control point growing, despite an improvement in my results some of subjects still have very bad surface constructions. I have attached two snapshots to this email and I am happy to upload the complete subject folder if you need to take a look at them. As far as the SNR is concerned, I have designed my study based on recommended Freesurfer parameters a couple of years ago on 3T Siemens Trio with 32-channel receiver coil. A huge thank you for your previous helps, and thanks in advance for helping me with this new issue. James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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.
