Re: [Freesurfer] QDEC and Hippocampal subfields
Hi Marcos, the hippocampal subfield volumes are single values for each subject and hemisphere, so you cannot display them on the brain surface. Cheers, /Eugenio On Thu, May 16, 2013 6:22 pm, Marcos Martins da Silva wrote: Hi, Doug Thank you for your answer. Well I guess that after I read your both tutorials for group analysis (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis ) I mistook the concepts of qdec.table.dat and FSGD. My fault. Following the QDEC tutorial I saw we could import aseg data to qdec.table.dat after pressing generate stats data tables button. So I was wondering if I could do the same from hippo-subfields data. Importing is faster and more precise than make the table by hand. Well the hippo-subfield pipeline creates several files such as posterior_left_subiculum.mgz on for each subfield and side. As far as I know you can: 1- run kvlQuantifyPosteriorProbabilityImages to output the volume in voxels 2- visualize the subfield segmentations with freeview loading nu.mgz and the posterior* files as p-labels. Following QDEC tutorial we could generate a display showing the correlation between cortical thickness (or volume) and age for example. I would like to a similar analysis with hippo-subfields and get a display showing the correlations of the hippo-subfields and age. So, just for an example, perhaps I could notice that subiculum volume decreases with age but hippocampal fissure increases with age. I guess I could analyze the data from hippo-subfields in a statistical package to get numbers and graphics but it would be great if I could see that as a surface like we do with cortical data. Cheers, Marcos Em Qui, 2013-05-16 Ã s 11:56 -0400, Douglas N Greve escreveu: Hi Marcos, On 05/15/2013 08:32 PM, Marcos Martins da Silva wrote: Hi, freesurfers I have two questions: 1- Is there a way to use QDEC to analyze data from hippocampal subfields created by recon-all -s subj -hippo-subfields? That is, I know I can manually put data from posterior* files when making the FSGD file but it would be great if I could import it like I do from aseg.stats. when you say you want analyze the hippo subfields in QDEC, do you mean you want to include them as regressors?If so, you will need to add them to your QDEC table. BTW, QDEC does not needan FSGD file. 2- Assuming all data from my subjects are already are already in the FSGD, I understand I can select cortical thickness or volume as dependent variable and inspect the correlations between cortical thickness and age, for example. But I could not find how to define a hippocampal subfield volume as a dependent variable. Is that possible? This way I could display correlations between a subfield volume and age or gender. I have not used the hippo subfields yet, and I'm embarrassed to say that I don't know what exactly it outputs. If there is a stats file there, you can run asegstats2table to create a table file, then use the table as input to mri_glmfit (use the --table option). doug Thank you, Marcos ___ 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 - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. ___ 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] conversion from ascii to surface
Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 __ __ UT Southwestern Medical Center The future of medicine, today. 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] T or Z values in QDEC
Dear Freesurfer list members, Within QDEC I have found a number of clusters that show significantly different cortical thickness and local gyrification between two groups. The cluster summary exhibits the p value, coordinates and other information regarding the cluster, however I wanted to report the t or z values and was unsure in finding or computing this from QDEC. The p-value must be computed from one of these scores but I could not find it to be reported in any of the output. Searching on the mailing list and tutorials, I could not find an easy solution to this. Thanks for your time and I look forward to hearing back. All the best, Philip Kelly ___ 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] T or Z values in QDEC
Dear Freesurfer list members, Within QDEC I have found a number of clusters that show significantly different cortical thickness and local gyrification between two groups. The cluster summary exhibits the p value, coordinates and other information regarding the cluster, however I wanted to report the t or z values and was unsure in finding or computing this from QDEC. The p-value must be computed from one of these scores but I could not find it to be reported in any of the output. Searching on the mailing list and tutorials, I could not find an easy solution to this. Thanks for your time and I look forward to hearing back. All the best, Philip Kelly ___ 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] conversion from ascii to surface
Hi Tina can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote: Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 __ __ UT Southwestern Medical Center The future of medicine, today. 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] conversion from ascii to surface
Hi Tina how did you create the ascii file? The problem is that some of the faces contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). cheers Bruce On Fri, 17 May 2013, Tina Jeon wrote: Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error. Thank you Bruce, Cheers, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote: Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 _ _ __ UT Southwestern Medical Center The future of medicine, today. 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] issue with pial surface in orbitofrontal cortex
Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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 attachment: pial2.png___ 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] issue with pial surface in orbitofrontal cortex
Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] conversion from ascii to surface
I created the ascii file directly from amira, which from what I understand is 0 based. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:15 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina how did you create the ascii file? The problem is that some of the faces contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). cheers Bruce On Fri, 17 May 2013, Tina Jeon wrote: Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error. Thank you Bruce, Cheers, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote: Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 _ _ __ UT Southwestern Medical Center The future of medicine, today. 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] conversion from ascii to surface
something is wrong as there should be no vertex indices 12721 On Fri, 17 May 2013, Tina Jeon wrote: I created the ascii file directly from amira, which from what I understand is 0 based. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:15 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina how did you create the ascii file? The problem is that some of the faces contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). cheers Bruce On Fri, 17 May 2013, Tina Jeon wrote: Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error. Thank you Bruce, Cheers, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote: Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 _ _ __ UT Southwestern Medical Center The future of medicine, today. 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] issue with pial surface in orbitofrontal cortex
Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] conversion from ascii to surface
Great! I subtracted the vertices by one and now it works. Appreciate your help and fast responses. Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:37 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface something is wrong as there should be no vertex indices 12721 On Fri, 17 May 2013, Tina Jeon wrote: I created the ascii file directly from amira, which from what I understand is 0 based. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:15 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina how did you create the ascii file? The problem is that some of the faces contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). cheers Bruce On Fri, 17 May 2013, Tina Jeon wrote: Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error. Thank you Bruce, Cheers, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote: Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 ___ _ _ _ __ UT Southwestern Medical Center The future of medicine, today. 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] conversion from ascii to surface
sure. Glad it worked out Bruce On Fri, 17 May 2013, Tina Jeon wrote: Great! I subtracted the vertices by one and now it works. Appreciate your help and fast responses. Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:37 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface something is wrong as there should be no vertex indices 12721 On Fri, 17 May 2013, Tina Jeon wrote: I created the ascii file directly from amira, which from what I understand is 0 based. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 9:15 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina how did you create the ascii file? The problem is that some of the faces contain vertex numbers that are you of range. Note that the vertex indices in the face list must be 0-based, not 1-based. Your file specifies 12722 vertices, but then lists some faces as having vertex number 12722 (which is out of bounds by 1). cheers Bruce On Fri, 17 May 2013, Tina Jeon wrote: Here it is. I tried changing the name to lh.pial_neo024.asc but there was the same segmentation error. Thank you Bruce, Cheers, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Friday, May 17, 2013 8:57 AM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] conversion from ascii to surface Hi Tina can you send me the ascii file? Note that we assume in many places that the surface files start with a hemisphere specifier, so your output should probably be lh.neo024_2_pial or something like that. I doubt that's why it's crashing though Bruce On Fri, 17 May 2013, Tina Jeon wrote: Dear Bruce, Yes I have, My input: mris_convert ./neo024_2_lh.pial.asc ./neo024_2_lh.pial Segmentation fault Can you lead me as to why there is an error? Thank you, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 16, 2013 5:49 PM To: Tina Jeon Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] conversion from ascii to surface Hi Tina try mris_convert cheers Bruce On Thu, 16 May 2013, Tina Jeon wrote: Dear Doug, Nick, and all, I am trying to convert a surface from Amira to freesurfer in order to visualize a parcellated neonate brain. I have the freesurfer ascii files (white/pial) and need to convert those into surfaces that can be read by tksurfer. Do you have any suggestions for how I could do the conversion? Thank you in advance! All the best Tina Jeon PhD Candidate UT Southwestern Medical Center ‘14 ___ _ _ _ __ UT Southwestern Medical Center The future of medicine, today. 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] recon-all error: Correcting Defect 2
v5.0.0 On May 16, 2013, at 2:18 PM, Bruce Fischl wrote: Hi Sudhin what FS version are you running? Bruce On Thu, 16 May 2013, Sudhin A. Shah wrote: Hi, I got the following error: CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Thanks, S ___ 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] issue with pial surface in orbitofrontal cortex
When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com: Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
what is your command line? You are probably better off setting gray_hi, gray_low, wm_hi, wm_low, etc... Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com: Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] TRACULA outputs out of expected range
Hi Ali - The last row of your gradient table is 0 0 0. And yet, based on the b-value table, it is supposed to correspond to a diffusion-weighted volume with b=800. So there must have been a diffusion-encoding gradient vector that was applied to acquire that volume, and you need to find out what that gradient vector was and put it in that line. Also, some of the lines in the gradient table follow the Xe-Y notation and some don't. I don't know if this will cause a problem, it's possible that it might depending on the platform. In any case, it's good to be consistent to be safe. Hope this helps, a.y On Mon, 6 May 2013, Ali Ezzati wrote: Hi Anastasia, I think I still have the previous problem of out of range outputs. For example: based on literature ( your previous TRACULA-bases articles) the expected range of mean FA value is around 0.4-0.5, but the average FA for my data is 0.7-0.8. The same is true with MD, RD, AD values. Comparative analysis between groups is not promising too. This makes me think something is going wrong with my analysis/settings, although I get no error during processing. I can only think of settings in .dmricr or bvec file to be a source of error, so I have attached a sample of them for one of the subjects to this email. I would be grateful if you could take a look at them and let me know if they are as expected. There are 3 .bvec files inside the dmri folder: 1- dwi_orig.mghdti.bvecs 2- bvecs.norot 3- bvecs The first 2 files are the same as my input .bvec file (bvecs.norot is rotated to 3 rows instead of 3 columns). File 3 -bevecs- is different from the other 2 files. Thank you again for your help, Ali From: Ali Ezzati Sent: Friday, May 03, 2013 11:54 AM To: Anastasia Yendiki Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] TRACULA outputs out of expected range Hi Anastasia, Thank you for your response. I think I figured out what was the problem: The delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise the program fails to reshape it correctly. In my case the delimiter was , and the program was reading only the 1st column of it. I have one more question: I know that FA values might differ from study to study and from MRI to MRI, but what is a reasonable range for that after analysis with Tracula? In your study (20011) the range was ~ 0.3-0.6. But for in elderly population the average is around 0.2 higher. Does it sound normal to you? I was not able to find any study using your method in elderly population for comparison. Thank you, Ali From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Tuesday, April 30, 2013 3:11 PM To: Ali Ezzati Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA outputs out of expected range Hi Ali - This is unusual. It may have something to do with system settings. Can you send an example of the two versions of the bvecs files that have the different values? Thanks, a.y On Mon, 29 Apr 2013, Ali Ezzati wrote: Hello Experts, I would be grateful if you could help me with this problem: I was able to run all steps of TRACULA on several subjects without any error message, but all the final outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA values for all tracts are 1). I tried to identify the source of this problem... clearly FA values in dmri/dtifit_FA, which is an output of prep step are all out of range. The only source of error that I can think of is .bvecs file. My input .bvecs files are in 3 columns, exactly as described in the manual. There are two .bvecs file in the dmri folder. one is dwi_orig.mghdti.bvecs which is exactly the same as my input .bvecs file and the other one's name is just bvecs, which has completely different values. Could this be the source of my problem? or something else is causing this. Thank you, Ali 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] incomplete forceps
Hi Benjamin - This means that the initial guess for the path based on the atlas average is way off, due to poor alignment between your subject and the atlas subejcts. Ways to get around this is to look into the options for registration, whether diffusion-to-anatomical or anatomical-to-atlas, and to increase the number of control points used for fminor. Hope this helps, a.y On Mon, 6 May 2013, Roschinski, Benjamin wrote: Dear Freesurfer experts, we have a problem with the forceps. After the first trac-all we had a forcpes minor with a really unusually structure so we tried to fix it with an rerun of the trac-all. The result was a forceps minor with a third thigh in the sagittal axis. We did a second rerun and now the forceps minor normalized. Our problem is that we don´t know if we should do more trac-all reruns by other patients with difficult tracula or how we should interpret this result. Do you have any ideas to solve this? The second problem is that we have many many tracula results with incomplete forcepes minor or major. We know that the forcepes are the most difficult tracts because of the curvature but do you have some ideas to fix that problem? Kind regards Benjamin ___ 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] DTI metrics along the whole tract?
Hi Celine - Since 5.2, there are 2 types of measures in the pathstats.byvoxel.txt file: The value at every point along the trajectory sampled at roughly the center of the bundle, or the value at every point along the trajectory averaged over the width of the bundle. Sorry, there are no other measures available at this point. If I understand correctly, you would like to see something like a profile of the measure of interest at every point along the trajectory? a.y On Mon, 6 May 2013, cel...@nmr.mgh.harvard.edu wrote: Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine ___ 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] T or Z values in QDEC
Hi Philip, the p-value for the cluster is not computed from a t or z. It is computed from a simulation in which random noise is generated on the surface, smoothed, clustered. The maximum cluster size is found. This is repeated 1 times to give a list of 1 cluster sizes. The p-value for a given cluster in your analysis equals the number of clusters in the list whose area is greater divided by 1. dopug On 5/17/13 9:46 AM, Kelly, Philip wrote: Dear Freesurfer list members, Within QDEC I have found a number of clusters that show significantly different cortical thickness and local gyrification between two groups. The cluster summary exhibits the p value, coordinates and other information regarding the cluster, however I wanted to report the t or z values and was unsure in finding or computing this from QDEC. The p-value must be computed from one of these scores but I could not find it to be reported in any of the output. Searching on the mailing list and tutorials, I could not find an easy solution to this. Thanks for your time and I look forward to hearing back. All the best, Philip Kelly ___ 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] tracula error
Hi Skyler - How does the brain mask look like? Any major chunks of brain missing in the area of the left uncinate? That's the tract where the error occurs, and based on this info in the log file, I'm guessing it's a masking issue: [...] INFO: Rejected 4221 streamlines for straying off mask INFO: Rejected 2 streamlines for reversing direction INFO: Rejected 9 streamlines as length outliers INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) [...] Hope this helps, a.y On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote: Hi all, We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. Thank you in advance! Skyler ___ 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] Tracula problem
Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist
Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)
Thanks,
a.y
On Wed, 15 May 2013, Hoptman, Matthew wrote:
Hi all,
I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is
that
version very different from the newer 5.3?). If I run
trac-preproc -c dmrirc –prep,
I get:
mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info
I don’t know why it would look for COR-.info in the subjects’ root directory.
I’m
attaching my dmrirc file in case that helps.
Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine
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Re: [Freesurfer] data analysis
Hi Benjamin - The tractography algorithm running under the hood hasn't changed from 5.1 to 5.2, but the way the initial guess for the path is chosen that's fed into the algorithm has changed. Also several defaults for the registration method, number of samples, number of control points have changed. So I'd check what those parameters were for your 5.1 and 5.2 results, and if one of those configuration choices seems to work better, use that. But just to be safe, I'd use the same version for all subjects, simply b/c it's possible that some libraries with which the code was compiled may have changed between freesurfer 5.1 and 5.2 and you don't want to introduce that kind of variability. Hope this helps, a.y On Thu, 16 May 2013, Roschinski, Benjamin wrote: Dear Freesurfer users and experts, for the first time we used TRACULA 5.1.0 to visualize the tracts of our test persons and now we did the update to TRACULA 5.2.0. We did a rerun of the trac-all logarithm for all test persons in order to achieve better TRACULA results. At one point we had patient with good TRACULA outputs (all tracts are complete) by using 5.1.0 but the same person had a worse TRACULA output by using 5.2.0. There have also bin test persons that recieve good tract result with TRACULA 5.2.0. than with 5.1.0. Now we would like to know if we can use TRACULA 5.1.0 data for one person with good tracts and for another person TRACULA 5.2.0 data with good tracts as well but both with worse tracts when using the different TRACULA version? Summarizing we would like to know if we can mix the data analysis with data from TRACULA 5.1.0 and 5.2.0? Kind regards Benjamin PS: I have sent you another message on the sixth of May. Can you help me with this problem as well? ___ 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] issue with pial surface in orbitofrontal cortex
mri_segment \ -v \ -fillv \ -fillbg \ -wlo 104 \ -ghi 118 \ -whi 140 \ -n 4 \ -keep \ brain.mgz wm.mgz The pial surface in the rest of the brain is ok, it is only the orbitofrontal/piriform cortex that is problematic. I now wanted to add -p 0.7. Caspar 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu: what is your command line? You are probably better off setting gray_hi, gray_low, wm_hi, wm_low, etc... Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com: Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] any way to parallelize Tracula?
Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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 MAC installation
Hi I am having trouble with the license file. I created in Freesurfer a file named .license but I cannot open this and copy the license. where and how should I put the 3 lines license? I tried to test my freesurfer installation with Bert but I got as answer command non found. Please help BW Flavia ___ 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] any way to parallelize Tracula?
Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**__** __ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Tracula longitudinal nan values for highest probability path
Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them nan-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do? E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point: 63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33 And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan Thanks for your help!! :) Best, Vincent ___ 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] any way to parallelize Tracula?
Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. _ _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ___ 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ 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 MAC installation
Hello Flavia, The .license file should be placed in the /Applications/freesurfer directory. To load freesurfer, you must open the terminal type the following : setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh -Zeke On 05/17/2013 12:49 PM, Flavia Niccolini wrote: Hi I am having trouble with the license file. I created in Freesurfer a file named .license but I cannot open this and copy the license. where and how should I put the 3 lines license? I tried to test my freesurfer installation with Bert but I got as answer command non found. Please help BW Flavia ___ 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] issue with pial surface in orbitofrontal cortex
and what happens? Can you send the full screen output? On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: mri_segment \ -v \ -fillv \ -fillbg \ -wlo 104 \ -ghi 118 \ -whi 140 \ -n 4 \ -keep \ brain.mgz wm.mgz The pial surface in the rest of the brain is ok, it is only the orbitofrontal/piriform cortex that is problematic. I now wanted to add -p 0.7. Caspar 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu: what is your command line? You are probably better off setting gray_hi, gray_low, wm_hi, wm_low, etc... Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com: Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
filling ventricles filling basal ganglia using white lolim = 104.0 using gray hilim = 118.0 using white hilim = 140.0 running border classification 4 times preserving editing changes in output volume... using 70% threshold mri_read(): couldn't determine type of file /.../.700 mri_segment: could not read source volume from .700 ../mri/brain.mgz: Permission denied if I add a -i to the input volume, it says flag not recognized. to get a floating point number into my tcsh script, I am using `echo 7/10 | bc -l` according to this previous discussion on the mailing list, there should be a fix available somewhere: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html Thanks, Caspar 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu: and what happens? Can you send the full screen output? On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: mri_segment \ -v \ -fillv \ -fillbg \ -wlo 104 \ -ghi 118 \ -whi 140 \ -n 4 \ -keep \ brain.mgz wm.mgz The pial surface in the rest of the brain is ok, it is only the orbitofrontal/piriform cortex that is problematic. I now wanted to add -p 0.7. Caspar 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu: what is your command line? You are probably better off setting gray_hi, gray_low, wm_hi, wm_low, etc... Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com: Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ 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
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
Hi Caspar can you include the command line and all the output? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: filling ventricles filling basal ganglia using white lolim = 104.0 using gray hilim = 118.0 using white hilim = 140.0 running border classification 4 times preserving editing changes in output volume... using 70% threshold mri_read(): couldn't determine type of file /.../.700 mri_segment: could not read source volume from .700 ../mri/brain.mgz: Permission denied if I add a -i to the input volume, it says flag not recognized. to get a floating point number into my tcsh script, I am using `echo 7/10 | bc -l` according to this previous discussion on the mailing list, there should be a fix available somewhere: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html Thanks, Caspar 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu: and what happens? Can you send the full screen output? On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: mri_segment \ -v \ -fillv \ -fillbg \ -wlo 104 \ -ghi 118 \ -whi 140 \ -n 4 \ -keep \ brain.mgz wm.mgz The pial surface in the rest of the brain is ok, it is only the orbitofrontal/piriform cortex that is problematic. I now wanted to add -p 0.7. Caspar 2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu: what is your command line? You are probably better off setting gray_hi, gray_low, wm_hi, wm_low, etc... Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com: Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well. Peace, Matt. On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Caspar yes, that might help. There are expert opts for this. Sorry, I have almost no experience analyzing monkey brains at .5mm, so I'm really not sure what to advise you. Perhaps one of the other people on list who have done a bunch can comment? Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, I tried adding control points in the white matter in that region, however, it does not seem to fix the issue. Also, the brainmask.mgz does not seem to exclude this part of the brain, so that is not the problem either. I am attaching another screenshot (horizontal 119) to illustrate the problem. White matter pixel values range from the high 80ies to 100 in this area. Included grey matter pixel values are in the low 80ies. Excluded grey matter pixel values range from the low 60ies to low 70ies. Would it make sense to re-run mri_segment with a different threshold? Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar is the closest white matter captured by the white surface? What is the intensity of voxels there? If 110 you could try putting control points in them and seeing if that helps (that is, in the closest voxels that are entirely white matter). Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce, ok. But in theory, what would you recommend to get around the darkening issue? Unfortunately, I do not have a field map available for this data set. Or should I not expect to get a pial surface in this area since the white matter is not discernable? There are five slices without clear white matter (original voxel size 0.5x0.5x0.5 mm). Thanks, Caspar 2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar if it's primate I don't think I'm going to be able to help - you'll need someone more familiar with primate anatomy sorry Bruce On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, yes, it is primate data. I just dropped an archive on your FTP server in transfer/incoming. Thanks! Caspar 2013/5/16 Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
mri_segment: could not read source volume from .700
../mri/brain.mgz: Permission denied
if I add a -i to the input volume, it says flag not recognized.
to get a floating point number into my tcsh script, I am using `echo
7/10 | bc -l`
according to this previous discussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what happens? Can you send the full screen output?
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
what is your command line? You are probably better off setting gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html),
but now it does not recognize the -i flag.
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Hard to fix if that is the receive field and you don't have another
image
like a T2w to remove it with. Perhaps mri_normalize can be tuned to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I have
almost no experience analyzing monkey brains at .5mm, so I'm really
not
sure what to advise you. Perhaps one of the other people on list who
have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I tried adding control points in the white matter in that region,
however, it does not seem to fix the issue. Also, the brainmask.mgz
does not seem to exclude this part of the brain, so that is not the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate
the
problem.
White matter pixel values range from the high 80ies to 100 in this
area.
Included grey matter pixel values are in the low 80ies.
Excluded grey matter pixel values range from the low 60ies to low
70ies.
Would it make sense to re-run mri_segment with a different
threshold?
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
is the closest white matter captured by the white surface? What is
the
intensity of voxels there? If 110 you could try putting control
points in
them and seeing if that helps (that is, in the closest voxels that
are
entirely white matter).
Bruce
On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
ok.
But in theory, what would you recommend to get around the
darkening
issue? Unfortunately, I do not have a field map available for
this
data set.
Or should I not expect to get a pial surface in this area since
the
white matter is not discernable?
There are five slices without clear white matter (original voxel
size
0.5x0.5x0.5 mm).
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
if it's primate I don't think I'm going to be able to help -
you'll
need
someone more familiar with primate anatomy
sorry
Bruce
On Thu, 16 May 2013, Caspar M.
Schwiedrzik wrote:
Hi Bruce and Matt,
yes, it is primate data. I just dropped an archive on your FTP
server
in transfer/incoming.
Thanks!
Caspar
2013/5/16 Matt Glasser m...@ma-tea.com:
Is the brain extraction removing that part of
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
mri_segment: could not read source volume from .700
../mri/brain.mgz: Permission denied
if I add a -i to the input volume, it says flag not recognized.
to get a floating point number into my tcsh script, I am using `echo
7/10 | bc -l`
according to this previous discussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what happens? Can you send the full screen output?
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to
add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
what is your command line? You are probably better off setting
gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
html),
but now it does not recognize the -i flag.
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Hard to fix if that is the receive field and you don't have
another
image
like a T2w to remove it with. Perhaps mri_normalize can be tuned
to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I
have
almost no experience analyzing monkey brains at .5mm, so I'm
really
not
sure what to advise you. Perhaps one of the other people on list
who
have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I tried adding control points in the white matter in that
region,
however, it does not seem to fix the issue. Also, the
brainmask.mgz
does not seem to exclude this part of the brain, so that is not
the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate
the
problem.
White matter pixel values range from the high 80ies to 100 in
this
area.
Included grey matter pixel values are in the low 80ies.
Excluded grey matter pixel values range from the low 60ies to
low
70ies.
Would it make sense to re-run mri_segment with a different
threshold?
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
is the closest white matter captured by the white surface?
What is
the
intensity of voxels there? If 110 you could try putting
control
points in
them and seeing if that helps (that is, in the closest voxels
that
are
entirely white matter).
Bruce
On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
ok.
But in theory, what would you recommend to get around the
darkening
issue? Unfortunately, I do not have a field map available for
this
data set.
Or should I not expect to get a pial surface in this area
since
the
white matter is not discernable?
There are five slices without clear white matter (original
voxel
size
0.5x0.5x0.5 mm).
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
if it's primate I don't think I'm going to be able to help -
you'll
need
someone more familiar with primate anatomy
sorry
Bruce
On Thu, 16 May 2013, Caspar M.
Schwiedrzik wrote:
Hi
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that not for version 4.5?
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
mri_segment: could not read source volume from .700
../mri/brain.mgz: Permission denied
if I add a -i to the input volume, it says flag not recognized.
to get a floating point number into my tcsh script, I am using `echo
7/10 | bc -l`
according to this previous discussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what happens? Can you send the full screen output?
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to
add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
what is your command line? You are probably better off setting
gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
html),
but now it does not recognize the -i flag.
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Hard to fix if that is the receive field and you don't have
another
image
like a T2w to remove it with. Perhaps mri_normalize can be tuned
to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I
have
almost no experience analyzing monkey brains at .5mm, so I'm
really
not
sure what to advise you. Perhaps one of the other people on list
who
have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I tried adding control points in the white matter in that
region,
however, it does not seem to fix the issue. Also, the
brainmask.mgz
does not seem to exclude this part of the brain, so that is not
the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate
the
problem.
White matter pixel values range from the high 80ies to 100 in
this
area.
Included grey matter pixel values are in the low 80ies.
Excluded grey matter pixel values range from the low 60ies to
low
70ies.
Would it make sense to re-run mri_segment with a different
threshold?
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
is the closest white matter captured by the white surface?
What is
the
intensity of voxels there? If 110 you could try putting
control
points in
them and seeing if that helps (that is, in the closest voxels
that
are
entirely white matter).
Bruce
On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
ok.
But in theory, what would you recommend to get around the
darkening
issue? Unfortunately, I do not have a field map available for
this
data set.
Or should I not expect to get a pial surface in this area
since
the
white matter is not discernable?
There are five slices without clear white matter (original
voxel
size
0.5x0.5x0.5 mm).
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
Try leaving out the -i and -seg
Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that not for version 4.5?
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
mri_segment: could not read source volume from .700
../mri/brain.mgz: Permission denied
if I add a -i to the input volume, it says flag not recognized.
to get a floating point number into my tcsh script, I am using `echo
7/10 | bc -l`
according to this previous discussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what happens? Can you send the full screen output?
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to
add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
what is your command line? You are probably better off setting
gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
html),
but now it does not recognize the -i flag.
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Hard to fix if that is the receive field and you don't have
another
image
like a T2w to remove it with. Perhaps mri_normalize can be tuned
to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I
have
almost no experience analyzing monkey brains at .5mm, so I'm
really
not
sure what to advise you. Perhaps one of the other people on list
who
have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I tried adding control points in the white matter in that
region,
however, it does not seem to fix the issue. Also, the
brainmask.mgz
does not seem to exclude this part of the brain, so that is not
the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate
the
problem.
White matter pixel values range from the high 80ies to 100 in
this
area.
Included grey matter pixel values are in the low 80ies.
Excluded grey matter pixel values range from the low 60ies to
low
70ies.
Would it make sense to re-run mri_segment with a different
threshold?
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
is the closest white matter captured by the white surface?
What is
the
intensity of voxels there? If 110 you could try putting
control
points in
them and seeing if that helps (that is, in the closest voxels
that
are
entirely white matter).
Bruce
On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
ok.
But in theory, what would you recommend to get around the
darkening
issue? Unfortunately, I do not have a field map available for
this
data set.
Or
Re: [Freesurfer] issue with pial surface in orbitofrontal cortex
Hi Bruce,
I only put them in because it was not working without them and that
was the solution in the previous discussion.
To summarize: Once I put in -p 0.7, mri_segment misinterprets 0.7 as
the input file name, no matter whether I use -i or not.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Try leaving out the -i and -seg
Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that not for version 4.5?
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file
mri_segment: could not read source volume from .700
-i: Command not found
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
mri_segment: could not read source volume from .700
../mri/brain.mgz: Permission denied
if I add a -i to the input volume, it says flag not recognized.
to get a floating point number into my tcsh script, I am using `echo
7/10 | bc -l`
according to this previous discussion on the mailing list, there
should be a fix available somewhere:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18824.html
Thanks, Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
and what happens? Can you send the full screen output?
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to
add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl fis...@nmr.mgh.harvard.edu:
what is your command line? You are probably better off setting
gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.
html),
but now it does not recognize the -i flag.
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Hard to fix if that is the receive field and you don't have
another
image
like a T2w to remove it with. Perhaps mri_normalize can be tuned
to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I
have
almost no experience analyzing monkey brains at .5mm, so I'm
really
not
sure what to advise you. Perhaps one of the other people on list
who
have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
Hi Bruce,
I tried adding control points in the white matter in that
region,
however, it does not seem to fix the issue. Also, the
brainmask.mgz
does not seem to exclude this part of the brain, so that is not
the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate
the
problem.
White matter pixel values range from the high 80ies to 100 in
this
area.
Included grey matter pixel values are in the low 80ies.
Excluded grey matter pixel values range from the low 60ies to
low
70ies.
Would it make sense to re-run mri_segment with a different
threshold?
Thanks, Caspar
2013/5/16 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Caspar
is the closest white matter captured by the white surface?
What is
the
intensity of voxels there? If 110 you could try putting
control
points in
them and seeing if that helps (that is, in the closest voxels
that
are
Re: [Freesurfer] any way to parallelize Tracula?
Hi Anastasia, I am operating on 5.1... I'm glad to know that there is such a huge difference in versions; and that there's so much gain in upgrading. I will look at the fsl_sub_mgh script, and I'll post back what I figure out (if anything), if other people are interested. Otherwise, it's vox clamantis en deserto... Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 1:02 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - The underlying script doing the job submission is called fsl_sub_mgh (a modification of fsl_sub). BTW, the -prior step should be about 70% less long and cumbersome in 5.2/5.3 than it was in 5.1. Which version are you running? a.y On Fri, 17 May 2013, Susan Kuo wrote: Hi Anastasia, I apologize for jumping in here, but I have run bedpostx parallelized on a cluster. Are there files that we can modify to run the script in parallel? I noticed the '-prior' step is particularly long and cumbersome. Thank you! Susie Kuo NIH On Fri, May 17, 2013 at 12:47 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Matt - Have you ever ran any parallelized FSL program (like bedpostx) on your SGE cluster? Our scripts have built on the FSL scripts, adding support for our PBS cluster, but in theory the SGE functionality is still there, so it should be possible to make it work. Of course practice is often somewhat more complicated than theory... a.y On Thu, 16 May 2013, Hoptman, Matthew wrote: Hi all, I have access to a cluster computer. Is there any way to parallelize tracula using SGE without having to make a unique dmrirc for each subject? If I could pass subject numbers to the dmrirc that would be great, for example. Thanks, Matt Matthew J. Hoptman, PhD Research Scientist V Nathan S. Kline Institute for Psychiatric Research Research Associate Professor in Psychiatry NYU School of Medicine IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**__** _ _ Conserve Resources. Print only when necessary. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] weighted DTI metrics for each section
Hi Freesurfer team I would have a question about the Tracula output. If I understand it correctly, the output of the file: pathstats.byvoxel.txt can give us a mean average of DTI metrics at each section of the tract. Is there a way to get the weighted_FA, AD RD and MD at each section? Thanks for your help. Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129 ___ 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] DTI metrics along the whole tract?
Hi Anastasia I am very sorry I didn't see this email so it may be a doubloon with my question I just post. Indeed I am interested in a profile of the DTI metrics along the tract. So if I take the average value of each section it can give me a kind of profile, and so I was just wondering if taking a weighted metrics would be possible in order to remove values that are a bit far from the highest probability of the tract. Thanks a lot! Celine Hi Celine - Since 5.2, there are 2 types of measures in the pathstats.byvoxel.txt file: The value at every point along the trajectory sampled at roughly the center of the bundle, or the value at every point along the trajectory averaged over the width of the bundle. Sorry, there are no other measures available at this point. If I understand correctly, you would like to see something like a profile of the measure of interest at every point along the trajectory? a.y On Mon, 6 May 2013, cel...@nmr.mgh.harvard.edu wrote: Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine ___ 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] Tracula problem
Hi Anastasia,
To follow up, yes, those files exist.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem
Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist
Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)
Thanks,
a.y
On Wed, 15 May 2013, Hoptman, Matthew wrote:
Hi all,
I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is
that
version very different from the newer 5.3?). If I run
trac-preproc -c dmrirc –prep,
I get:
mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info
I don’t know why it would look for COR-.info in the subjects’ root directory.
I’m
attaching my dmrirc file in case that helps.
Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
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It may contain confidential information which is legally privileged or
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e-mail in error or from someone who was not authorized to send it to you, you
are
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the e-mail.
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
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__
Conserve Resources. Print only when necessary.
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
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It may contain confidential information which is legally privilegedor
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protected by law. If you received this e-mail in error or from someone who is
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authorized to send it to you, you are strictly prohibited from reviewing,
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disseminating, distributing or copying the e-mail. PLEASE NOTIFY US
IMMEDIATELY OF
THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
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IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
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It may contain confidential information which is legally privileged or
otherwise
protected by law. If you received this e-mail in error or from someone who is
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disseminating, distributing or copying the e-mail. PLEASE NOTIFY US
IMMEDIATELY OF
THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for
your cooperation.
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.
Conserve Resources. Print only when necessary.
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in error
or from someone who is not authorized to send it to you, you are strictly
prohibited from reviewing, using, disseminating, distributing or copying the
e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE
THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally privileged
or otherwise protected by law. If you received this e-mail in error or from
someone who is not authorized to send it to you, you are strictly prohibited
from reviewing, using, disseminating, distributing or copying the e-mail.
PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
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[Freesurfer] FW: Tracula problem
Hi Anastasia,
I'm just forwarding a modified version of the email I'd sent you earlier to the
list so everyone can see it.
I solved this particular problem in a new dmrirc, but it seemed that I had to
modify trac-preproc to remove the ${dcmroot} in front of:
infile, b0mfile and b0pfile:
diff bin/trac-preproc bin/trac-preproc.orig
if ($#dcmroot 0) set infile = $infile
---
if ($#dcmroot 0) set infile = $dcmroot/$infile
259c259
endif
---
endif
296c296
set dcmfile = $b0mfile
---
set dcmfile = $dcmroot/$b0mfile
311c311
set dcmfile = $b0pfile
---
set dcmfile = $dcmroot/$b0pfile
But now it doesn't seem to loop through the subjects, so I'm doing them one at
a time (painful).
Also, if, as in my other question, I try to run this as a cluster job, I don't
know how I can substitute a new subject into subjlist. I have 64 subjects and
would like to do trac-all -prep -c dmri on all of them simultaneously. I have
used bedpostx in SGE, but there you can just write loop to get it to go through
your subjects.
If I could make the subject variable external to dmrirc, I could do easily
script the trac-all job to run in SGE, but I can't fiugre out how to pass it to
the trac-all command. Is there any way to pass the subject number directly to
the command?
Does this make sense?
Matt
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 12:31 PM
To: Hoptman, Matthew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula problem
Hi Matt - Can you source try this on the command line:
source dmrirc_53beta
echo $b0mlist
echo $b0plist
Are these filenames correct, do these files exist? This is how you define
them in your configuration file:
set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`)
set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`)
Thanks,
a.y
On Wed, 15 May 2013, Hoptman, Matthew wrote:
Hi all,
I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is
that
version very different from the newer 5.3?). If I run
trac-preproc -c dmrirc –prep,
I get:
mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
mri_convert /home/hoptman/freesurfer/subjects/c159032/
/home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz
corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info
I don’t know why it would look for COR-.info in the subjects’ root directory.
I’m
attaching my dmrirc file in case that helps.
Thanks,
Matt
Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine
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Re: [Freesurfer] QDEC and Hippocampal subfields
Hi, Eugenio Thank you for your answer. Em Sex, 2013-05-17 às 07:49 -0400, Juan Eugenio Iglesias escreveu: Hi Marcos, the hippocampal subfield volumes are single values for each subject and hemisphere, so you cannot display them on the brain surface. Cheers, /Eugenio On Thu, May 16, 2013 6:22 pm, Marcos Martins da Silva wrote: Hi, Doug Thank you for your answer. Well I guess that after I read your both tutorials for group analysis (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis and http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis ) I mistook the concepts of qdec.table.dat and FSGD. My fault. Following the QDEC tutorial I saw we could import aseg data to qdec.table.dat after pressing generate stats data tables button. So I was wondering if I could do the same from hippo-subfields data. Importing is faster and more precise than make the table by hand. Well the hippo-subfield pipeline creates several files such as posterior_left_subiculum.mgz on for each subfield and side. As far as I know you can: 1- run kvlQuantifyPosteriorProbabilityImages to output the volume in voxels 2- visualize the subfield segmentations with freeview loading nu.mgz and the posterior* files as p-labels. Following QDEC tutorial we could generate a display showing the correlation between cortical thickness (or volume) and age for example. I would like to a similar analysis with hippo-subfields and get a display showing the correlations of the hippo-subfields and age. So, just for an example, perhaps I could notice that subiculum volume decreases with age but hippocampal fissure increases with age. I guess I could analyze the data from hippo-subfields in a statistical package to get numbers and graphics but it would be great if I could see that as a surface like we do with cortical data. Cheers, Marcos Em Qui, 2013-05-16 Ã s 11:56 -0400, Douglas N Greve escreveu: Hi Marcos, On 05/15/2013 08:32 PM, Marcos Martins da Silva wrote: Hi, freesurfers I have two questions: 1- Is there a way to use QDEC to analyze data from hippocampal subfields created by recon-all -s subj -hippo-subfields? That is, I know I can manually put data from posterior* files when making the FSGD file but it would be great if I could import it like I do from aseg.stats. when you say you want analyze the hippo subfields in QDEC, do you mean you want to include them as regressors?If so, you will need to add them to your QDEC table. BTW, QDEC does not needan FSGD file. 2- Assuming all data from my subjects are already are already in the FSGD, I understand I can select cortical thickness or volume as dependent variable and inspect the correlations between cortical thickness and age, for example. But I could not find how to define a hippocampal subfield volume as a dependent variable. Is that possible? This way I could display correlations between a subfield volume and age or gender. I have not used the hippo subfields yet, and I'm embarrassed to say that I don't know what exactly it outputs. If there is a stats file there, you can run asegstats2table to create a table file, then use the table as input to mri_glmfit (use the --table option). doug Thank you, Marcos ___ 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 - Juan Eugenio Iglesias, PhD http://www.jeiglesias.com igles...@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A. 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
