Re: [Freesurfer] mris_divide_parcellation color table error
I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. Best, Tina From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:02 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error p.s. can you send me the splittable text file ? I seem to have deleted it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 _ ___ UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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. splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_divide_parcellation color table error (fwd)
Yes it worked. Thank you that is exactly what I needed. Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 30, 2013 12:36 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error (fwd) Hi Tina is this (attached) more what you wanted? If so, then I think you want to use mris_make_face_parcellation instead of mris_divide_parcellation. I can't remember what they used in that paper, but in mris_divide_parcellation I try to have the different units within a parcel have similar colors (which evidentally fails when you split it so finely) Bruce On Thu, 30 May 2013, Tina Jeon wrote: I am running version 5.3- the latest version. I also tried running the codes on v5.0 and got the same result. Is there any way I can change the color table so that the colors of the parcellation are unique? Thanks, Tina -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:41 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error Sure On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: The colors are visually different by a shade then loop every 4 or so colors. I think the color table may be running on a loop? I can send the annot and surface file if you need that as well. Best, Tina From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, May 29, 2013 8:02 PM To: Tina Jeon Subject: Re: [Freesurfer] mris_divide_parcellation color table error p.s. can you send me the splittable text file ? I seem to have deleted it. I'll try to test it out tomorrow On Thu, 30 May 2013, Tina Jeon wrote: Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg$FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010 -03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 _ ___ UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ 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. splittable.txt ___ 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] mris_divide_parcellation color table error
Yes same result as with freeview. Sent from my iPhone On May 29, 2013, at 7:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Tina Did you try visualizing it in tksurfer? Bruce On May 29, 2013, at 7:22 PM, Tina Jeon tina.j...@utsouthwestern.edumailto:tina.j...@utsouthwestern.edu wrote: Hello freesurfers, I am trying to create a figure similar to the Hagmann et al 2008 paper with 998 rois overlaid onto the surface, however, I am finding that there is no random, unique color for each parcellation unit like described in the help file for mris_divide_parcellation. I have attached a snapshot of my annotation file overlaid onto the surface, as you can see, the color iterates the same/similar color for a particular label. Can you tell me what I am doing wrong? Is there a pre-existing atlas as described in the Hagmann paper? My input: mris_ca_label –t ./FreeSurferColorLUT.txt subject_name lh ./lh.sphere.reg $FREESURFER_HOME/average/lh.curvature.buckner40.filled.desikan_killany.2010-03-25.gcs ./lh.aparc.998rois.annot mris_divide_parcellation subject_name lh ./lh.aparc.998rois.annot ./splittable.txt ./lh.annotation.998rois_26.annot Many thanks, Tina Jeon, MS UT Southwestern Medical Center ‘14 UT Southwestern Medical Center The future of medicine, today. neonate_buckner40_atlas.png splittable.txt ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] problem with alignment of labeling files generated from the rh.area file
Doug can you answer this? The vertex indices can be fixed with matlab but more importantly I need to know why there is a slight offset in vertex coordinates. Thank you! Tina Jeon -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, May 23, 2013 10:57 AM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem with alignment of labeling files generated from the rh.area file hmmm, then I would have thought that they would have vertex indices =0. Maybe Doug knows? On Thu, 23 May 2013, Tina Jeon wrote: I generated the labeling file from the corresponding numbers in base file. The ctx-rh-bankssts was generated from mris_annotation2label with input -a2005. This is the file with -1 vertex numbers. In theory these files should be the same. On May 23, 2013, at 10:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina how did you create it? If the vertex indices are -1 it means they are not assigned, and when you load it into tksurfer it will sample them onto the surface. You can then save it it will write the new vertex numbers into the label file. Not sure about the offset though. Bruce On Thu, 23 May 2013, Tina Jeon wrote: Hello Freesurfers, I have created labeling files from a subject using the area file (previously named base). The label file corresponds to the freesurfer generated cortical label, ctx-rh-bankssts, which I have attached in this email. The labeling files should be the same, however, there are some discrepancies in the files: 1). There is a slight offset in the vertices. 2). A reduced number of vertices in the .label file created from the area file. 3). The vertex numbers are numbered -1. Our goal is to overlay a custom atlas onto a cortical surface generated from amira in freesurfer. Can you please tell how to transform the labeling files so that I can successfully overlay them? I have attached all three files for you. rh.rh_label_2001.label is the labeling file created from the base file, rh.ctx-rh-bankssts.label is the label from freesurfer and the rh.base file I have sent to Bruce the file is too large. When I overlay the rh.rh_label_2001.label and other labels generated from the base file, only parts of the temporal lobe are overlayed. Thank you in advance, Tina Jeon 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] problem with alignment of labeling files generated from the rh.area file
I generated the labeling file from the corresponding numbers in base file. The ctx-rh-bankssts was generated from mris_annotation2label with input -a2005. This is the file with -1 vertex numbers. In theory these files should be the same. On May 23, 2013, at 10:28 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Tina how did you create it? If the vertex indices are -1 it means they are not assigned, and when you load it into tksurfer it will sample them onto the surface. You can then save it it will write the new vertex numbers into the label file. Not sure about the offset though. Bruce On Thu, 23 May 2013, Tina Jeon wrote: Hello Freesurfers, I have created labeling files from a subject using the area file (previously named base). The label file corresponds to the freesurfer generated cortical label, ctx-rh-bankssts, which I have attached in this email. The labeling files should be the same, however, there are some discrepancies in the files: 1). There is a slight offset in the vertices. 2). A reduced number of vertices in the .label file created from the area file. 3). The vertex numbers are numbered -1. Our goal is to overlay a custom atlas onto a cortical surface generated from amira in freesurfer. Can you please tell how to transform the labeling files so that I can successfully overlay them? I have attached all three files for you. rh.rh_label_2001.label is the labeling file created from the base file, rh.ctx-rh-bankssts.label is the label from freesurfer and the rh.base file I have sent to Bruce the file is too large. When I overlay the rh.rh_label_2001.label and other labels generated from the base file, only parts of the temporal lobe are overlayed. Thank you in advance, Tina Jeon 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
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
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
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
[Freesurfer] conversion from ascii to surface
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. ___ 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 base file question
Doug or any freesurfer experts can you please answer this question it is quite urgent: I have created some manual cortical labels in freesurfer using tksurfer. The .labels file containing the vertices of the cortical labels does not correspond to the labels of the pial surface even though they were drawn on the pial. I noticed however, that they do correspond to the lh.base.mgh and rh.base.mgh file that was created with an older version of freesurfer. These files contain coordinates and their corresponding label in the look up table. My guess is that the base file is an intermediate surface between the white and gray. The question is why do the vertices in the manual labels not correspond to the those in the pial surface? Alternatively, since the lh.base.mgh and rh.base.mgh are no longer apart of the recon-all process is there another name in to which it is called? The command to make the cortical label is: mri_label2vol--label labelname.label --temp brainmask.mgz --o labelname.nii.gz --identity --proj frac 0 1 .1 --subject subject_id --hemi lh The command(s) to make the base file an ascii file is: mri_annotation2label --subject # --hemi *h --seg #/surf/*h.base.mgh --outdir junk mris_convert -c *h.base.mgh #/surf/*h.white #/surf/*h.base.asc Thank you, Tina Jeon -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 12:50 PM To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer base file question Hi Tina, sorry no one got to your first email. Sometimes emails do fall through the cracks, so always feel free to repost. It is not clear to me what command you are running or what you are trying to do. Can you supply more detail? doug On 04/02/2012 11:55 AM, Tina Jeon wrote: Hi Doug could you please answer these questions that I posted on the listserv. Your help would be much appreciated to an upcoming project on cortical development. Thank you. I noticed that the newest version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? i.e. called a different name? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon -- -- UT Southwestern Medical Center The future of medicine, today. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] Freesurfer base file question
No worries about that. I have created some manual cortical labels in freesurfer using tksurfer. The .labels file containing the vertices of the cortical labels does not correspond to the labels of the pial surface even though they were drawn on the pial. I noticed however, that they do correspond to the lh.base.mgh and rh.base.mgh file that was created with an older version of freesurfer. These files contain coordinates and their corresponding label in the look up table. My guess is that the base file is an intermediate surface between the white and gray. The question is why do the vertices in the manual labels not correspond to the those in the pial surface? Alternatively, since the lh.base.mgh and rh.base.mgh are no longer apart of the recon-all process is there another name in to which it is called? The command to make the cortical label is: mri_label2vol--label labelname.label --temp brainmask.mgz --o labelname.nii.gz --identity --proj frac 0 1 .1 --subject subject_id --hemi lh The command(s) to make the base file an ascii file is: mri_annotation2label --subject # --hemi *h --seg #/surf/*h.base.mgh --outdir junk mris_convert -c *h.base.mgh #/surf/*h.white #/surf/*h.base.asc Thank you, Tina Jeon -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 12:50 PM To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer base file question Hi Tina, sorry no one got to your first email. Sometimes emails do fall through the cracks, so always feel free to repost. It is not clear to me what command you are running or what you are trying to do. Can you supply more detail? doug On 04/02/2012 11:55 AM, Tina Jeon wrote: Hi Doug could you please answer these questions that I posted on the listserv. Your help would be much appreciated to an upcoming project on cortical development. Thank you. I noticed that the newest version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? i.e. called a different name? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon -- -- UT Southwestern Medical Center The future of medicine, today. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] base.mgh file
Freesurfer universe, I noticed that the newer version of freesurfer does not output a ?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table. Question: 1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on? 2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? My goal is to figure out which surface aligns with my manually created cortical labels for visualization. I am running version FSv5.0.0 on Centos4_x86_64 bit. Many thanks, Tina Jeon Biomedical Engineering Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center P: (214) 645-2892 F: (214) 645-2885 UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_vol2surf
I created the manual ROIs in tksurfer. Then saved them as label files, however, I ran into a problem when the manual ROI's only include a small number of voxels lining the cortical ribbon. The commands mri_label2vol and mri_vol2surf are NOT failing however when I try to visualize the volume with tkmedit I get this Application error when I try to scroll through slices: Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) What I think happened was the predefined label created in tksurfer is not a surface label, therefore does not work when I add projfrac-max. Can you suggest a work around based on my objectives of: 1). Creating a manual drawn surface label in volume and surface format 2). Having the surface label project to the entire cortical surface, not just a tiny sliver of voxels surrounding the white matter. Thank you for your help, Tina Graduate student Advanced Imaging Research Center UT Southwestern Medical Center -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 5:01 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf How did you create the manual ROIs? How is the label2vol command failing? Usually good to send the terminal output of a failing command too. doug Tina Jeon wrote: I want both the surface and volume. Sorry about the confusion. The command line is: mri_label2vol --label ./3t2234/label/15yr_lh_A1C_fs.label --temp ./3t2234/mri/brainmask.mgz --regheader 3t2234 --projfracmax 0 1 .1 --subject 3t2234 --hemi lh --o ./3t2234/label/15yr_lh_A1C_fs.mgz I am using a linux centos. I can send you my files if need be. Basically I would like my manual roi edits to project to the entire cortical ribbon. Thanks, Tina -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 4:12 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, I think I'm missing something. If you want a volume, why are you converting it to the surface? Also, make sure to send command-lines of commands that are failing. doug Tina Jeon wrote: Good to know, however I would like to display the volume, not the surface so that I can check to see if the label is covering the entire cortex, not just a small delegation of voxels around the pial surface. Is there a way I can visualize a volume file using tkmedit? I know mri_label2vol can convert the .label file to .mgz, however, I am still getting the same display error and the command is not recognizing the flag --projfrac-max -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:35 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf tkmedit only displays volumes. Use tksurfer for surfaces, something like tksurfer 3t2234 lh inflated -overlay ./3t2234/label/15yr_lh_A1C_new2.mgh doug Tina Jeon wrote: Using tkmedit -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:01 PM To: Tina Jeon Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf how are you trying to display it? On Mon, 12 Mar 2012, Tina Jeon wrote: I am still getting the same display error with using an mgh file. mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1 --hemi lh Any suggestions? Thank you, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 2:01 PM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, the problem may be with using nifti. Try an mgh file. Also, you'll probably want to use --projfrac-max 0 1 .1 doug Tina Jeon wrote: Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface
Re: [Freesurfer] mri_vol2surf
I am still getting the same display error with using an mgh file. mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1 --hemi lh Any suggestions? Thank you, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 2:01 PM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, the problem may be with using nifti. Try an mgh file. Also, you'll probably want to use --projfrac-max 0 1 .1 doug Tina Jeon wrote: Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) -- -- UT Southwestern Medical Center The future of medicine, today. -- -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] mri_vol2surf
Using tkmedit -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:01 PM To: Tina Jeon Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf how are you trying to display it? On Mon, 12 Mar 2012, Tina Jeon wrote: I am still getting the same display error with using an mgh file. mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1 --hemi lh Any suggestions? Thank you, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 2:01 PM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, the problem may be with using nifti. Try an mgh file. Also, you'll probably want to use --projfrac-max 0 1 .1 doug Tina Jeon wrote: Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) - - -- UT Southwestern Medical Center The future of medicine, today. - - -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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] mri_vol2surf
Good to know, however I would like to display the volume, not the surface so that I can check to see if the label is covering the entire cortex, not just a small delegation of voxels around the pial surface. Is there a way I can visualize a volume file using tkmedit? I know mri_label2vol can convert the .label file to .mgz, however, I am still getting the same display error and the command is not recognizing the flag --projfrac-max -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:35 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf tkmedit only displays volumes. Use tksurfer for surfaces, something like tksurfer 3t2234 lh inflated -overlay ./3t2234/label/15yr_lh_A1C_new2.mgh doug Tina Jeon wrote: Using tkmedit -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:01 PM To: Tina Jeon Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf how are you trying to display it? On Mon, 12 Mar 2012, Tina Jeon wrote: I am still getting the same display error with using an mgh file. mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1 --hemi lh Any suggestions? Thank you, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 2:01 PM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, the problem may be with using nifti. Try an mgh file. Also, you'll probably want to use --projfrac-max 0 1 .1 doug Tina Jeon wrote: Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) - - -- UT Southwestern Medical Center The future of medicine, today. - - -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_vol2surf
I want both the surface and volume. Sorry about the confusion. The command line is: mri_label2vol --label ./3t2234/label/15yr_lh_A1C_fs.label --temp ./3t2234/mri/brainmask.mgz --regheader 3t2234 --projfracmax 0 1 .1 --subject 3t2234 --hemi lh --o ./3t2234/label/15yr_lh_A1C_fs.mgz I am using a linux centos. I can send you my files if need be. Basically I would like my manual roi edits to project to the entire cortical ribbon. Thanks, Tina -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 4:12 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, I think I'm missing something. If you want a volume, why are you converting it to the surface? Also, make sure to send command-lines of commands that are failing. doug Tina Jeon wrote: Good to know, however I would like to display the volume, not the surface so that I can check to see if the label is covering the entire cortex, not just a small delegation of voxels around the pial surface. Is there a way I can visualize a volume file using tkmedit? I know mri_label2vol can convert the .label file to .mgz, however, I am still getting the same display error and the command is not recognizing the flag --projfrac-max -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:35 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf tkmedit only displays volumes. Use tksurfer for surfaces, something like tksurfer 3t2234 lh inflated -overlay ./3t2234/label/15yr_lh_A1C_new2.mgh doug Tina Jeon wrote: Using tkmedit -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:01 PM To: Tina Jeon Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf how are you trying to display it? On Mon, 12 Mar 2012, Tina Jeon wrote: I am still getting the same display error with using an mgh file. mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1 --hemi lh Any suggestions? Thank you, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 2:01 PM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf Hi Tina, the problem may be with using nifti. Try an mgh file. Also, you'll probably want to use --projfrac-max 0 1 .1 doug Tina Jeon wrote: Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) --- - - - -- UT Southwestern Medical Center The future of medicine, today. --- - - - -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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
[Freesurfer] mri_vol2surf
Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2surf error writing to nifti volume
Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freeview Surface Editing
Dear freesurfer experts, I am new to the freeview interface. How do I go about drawing a ROI on the surfaces to create my own label? Both the voxel edit and ROI edit buttons are not useful in this case. Thank you in advance, Tina Jeon PhD Candidate Advanced Imaging Research Center UT Southwestern Medical Center 2201 Inwood Rd Dallas, TX 75204 UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Converting an ascii file to a freesurfer volume file
Hello freesurfers, I am trying to convert a partially inflated surface .ply file created in afni to a freesurfer volume so that I can visualize the surfaces via tksurfer. Is there freesurfer command that converts text to volume, in essence the converse of mris_convert? And if not can you suggest a way that I can open the text file using a different graphical interface? Thank you in advance, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer DWI
Hello all, Can freesurfer be run on diffusion weighted images and/or B0 images? I am trying to obtain segmentation of the gray/white surfaces. Thanks, Tina Jeon ___ 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 to DTI space
Hello all, I am using surface tracking in FSL to align my freesurfer surfaces to my diffusion data. I am wondering if it were possible to use the freesurfer2fa.mat registration file as the registration input for mri_label2vol. The freesurfer2fa.mat was generated using FLIRT in FSL by registering the freesurfer conformed structural space to diffusion space. Ultimately I want to align the gyri and sulci volumes to the diffusion images I have. Is this a viable solution? Thanks in advance, Tina Jeon ___ 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] Label files for the Cortical Ribbon
Hello all! After creating some labeling files from aparc.a2005s.annot, I noticed that my sulci and gyri volumes generated from the .label files (i.e., after running mri_annotation2label and mri_label2vol) were only representing the outer layer of the white surface. Is there any way to generate .label files that include the entire cortical ribbon? Thanks, any help would be appreciated. Tina ___ 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] Label files for the Cortical Ribbon
Hello freesurfers! After creating some labeling files from aparc.a2005s.annot, I noticed that my sulci and gyri volumes generated from the .label files (i.e., after running mri_annotation2label and mri_label2vol) were only representing the outer layer of the white surface. Is there any way to generate .label files that include the entire cortical ribbon? Thanks, any help would be appreciated. Tina Jeon ___ 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] talairach
Hello freesurfer team, I am trying to run tkregister2 and I come up with this error message : No glx extension! register: ### tkoInitWindow(name) failed Any idea on what this could be from? Previously this command had worked. Thanks, Tina Jeon ___ 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] talairach to native space
Hello freesurfers, I am trying to align my T1W image in native space to the surface files (?h.pial, ?h.white, ?h.inflated, ?h.base) but it seems that they do no align perfectly. I thought the labeling information is in native space? However this does not seem to be the case because in the ascii files for the surfaces we found -120 in the coordinates but native space is [0,240] (i.e., without negatives). Is using tkregister2 the solution? Or using an affine registration matrix to transform the coordinates? Thanks in advance. Your help would be greatly appreciated. Tina Jeon ___ 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] Inflation Transformation
Hello FreeSurfers, I have inflated a couple surfaces less so that the gyri and sulci are more prominent on the surface using the parameters: mris_smooth -a 70 -n 70 -nw ./subj/surf/lh.white ./subj/surf/lh.smoothwm mris_inflate -n 5 ./subj/surf/lh.smoothwm ./subj/surf/lh.inflated mris_curvature -w -a 70 -thresh .999 -distances 10 10 ./subj/surf/lh.inflated Which seemed to do the trick, however, when I viewed the surfaces on the 3D surface generator Amira, I realized that inflating less caused the left and right surfaces to shift toward each other when viewed on the same coordinate system. The left and right surfaces must have been translated somewhere in the inflation process. How do I put them back into the correct coordinate space that the pial and white surfaces are? Thank you. Tina Jeon, M.S. Project Supervisor UT Southwestern Medical Center Advanced Imaging Research Center 2201 Inwood Road, NE 3.2 Dallas, Texas 75390-8568 Office (214) 645-2766 Fax (214) 645-2744 Cell (310) 592-1853 tina.j...@utsouthwestern.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
