[Freesurfer] mris_register problem: "No such file or directory"
Hi all, I received an error in one of the steps of recon-all. The error is "No such file or directory" at the end of one of the registration processes. The step was mris_register -curv. The command was: mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg I already checked that ../surf/lh.sphere and /average/lh.average.curvature.filled.buckner40.tif exist (and are readable). I also checked that the output directorry (../surf/ ) has the proper permisons to write. The version of mris_register is "stable5". Finally, the complete output message is (Please, note that the parts with <> have been edited by me for privacy reasons: # #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 /scripts mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /average/lh.average.curvature.filled.buckner40.tif... MRISregister() --- max_passes = 4 min_degrees = 0.50 max_degrees = 64.00 nangles = 8 tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.00 nfields 0 scale 0.00 desired_rms_height -1.00 momentum 0.95 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = -0.000, std = 0.575 curvature mean = 0.028, std = 0.935 curvature mean = -0.002, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 32.00, -64.00) sse = 463438.8, tmin=0.7880 d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, tmin=2.3467 d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, tmin=3.1967 d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8, tmin=4.0376 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 459815.2, tmin=4.8841 d=1.00 min @ (0.00, -0.25, 0.25) sse = 459808.6, tmin=5.7246 d=0.50 min @ (0.12, 0.38, -0.38) sse = 459786.2, tmin=6.5623 mrisComputeCorrelationTerm: delta is not finite at vno 0 MRISrigidBodyAlignGlobal() done 6.56 min No such file or directory Linux 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1398979 exited with ERRORS at Sun Aug 2 01:00:20 BST 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks in advance. ___ 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] mris_register problem: "No such file or directory"
Hi, Thanks for the quick answer. There was no error message in the previous steps. I started it with : mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere Although if the seed is the same, I am guessing that any non-deterministic process would have the same output. Is there a a way to automatically know if there was a problem in the sphere creation? Cheers. 2015-08-02 16:27 GMT+01:00 Bruce Fischl : > hmm, something seems to be wrong maybe the the ?h.sphere. Can you try > recreating it > cheers > Bruce > > On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: > > Hi all, >> >> I received an error in one of the steps of recon-all. The error is "No >> such >> file or directory" at the end of one of the registration processes. >> >> The step was mris_register -curv. The command was: >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> I already checked that ../surf/lh.sphere and >> /average/lh.average.curvature.filled.buckner40.tif exist (and are >> readable). I also checked that the output directorry (../surf/ ) has the >> proper permisons to write. >> >> The version of mris_register is "stable5". >> >> Finally, the complete output message is (Please, note that the parts with >> <> >> have been edited by me for privacy reasons: >> >> # >> #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 >> /scripts >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> using smoothwm curvature for final alignment >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ >> reading surface from ../surf/lh.sphere... >> reading template parameterization from >> /average/lh.average.curvature.filled.buckner40.tif... >> MRISregister() --- >> max_passes = 4 >> min_degrees = 0.50 >> max_degrees = 64.00 >> nangles = 8 >> tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, >> l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 >> using quadratic fit line minimization >> complete_dist_mat 0 >> rms 0 >> smooth_averages 0 >> remove_neg 0 >> ico_order 0 >> which_surface 0 >> target_radius 0.00 >> nfields 0 >> scale 0.00 >> desired_rms_height -1.00 >> momentum 0.95 >> nbhd_size -10 >> max_nbrs 10 >> niterations 25 >> nsurfaces 0 >> SURFACES 3 >> flags 16 (10) >> use curv 16 >> no sulc 0 >> no rigid align 0 >> mris->nsize 1 >> mris->hemisphere 0 >> randomSeed 0 >> >> tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, >> l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 >> using quadratic fit line minimization >> >> 1 Reading lh.sulc >> curvature mean = -0.000, std = 0.575 >> curvature mean = 0.028, std = 0.935 >> curvature mean = -0.002, std = 0.850 >> Starting MRISrigidBodyAlignGlobal() >> d=64.00 min @ (16.00, 32.00, -64.00) sse = 463438.8, tmin=0.7880 >> d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, tmin=2.3467 >> d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, tmin=3.1967 >> d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8, tmin=4.0376 >> d=2.00 min @ (-0.50, -0.50, 0.00) sse = 459815.2, tmin=4.8841 >> d=1.00 min @ (0.00, -0.25, 0.25) sse = 459808.6, tmin=5.7246 >> d=0.50 min @ (0.12, 0.38, -0.38) sse = 459786.2, tmin=6.5623 >> mrisComputeCorrelationTerm: delta is not finite at vno 0 >> MRISrigidBodyAlignGlobal() done 6.56 min >> No such file or directory >> Linux 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 1398979 exited with ERRORS at Sun Aug 2 01:00:20 BST 2015 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> Thanks in advance. >> >> >> > ___ > 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 &
[Freesurfer] mris_make_surfaces .out output
Hi all, Is there an explicit way to change the directory of the output file that mris_make_surfaces creates? This command creates a .out file in the directory from which the command was run and the -output flags just allows the user to modify a part in the middle of the name of that file. Cheers. ___ 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] mris_register problem: "No such file or directory"
Hi, I've had time to come back to this problem. It was not solved after recreating the sphere. And plus, it happens in 30% of my subjects (Approximately). I have opened the sphere and I can see no problem there (nor there is any kind of error message after opening it. Could you tell me what files are used in the "mris_register -curv" command (appart from the obvious lh.sphere and lh.average.curvature.filled.buckner40.tif) in order to check if there is any problem with them. The fact that the original error message is "No such file or directory" is intriguing. Cheers. 2015-08-02 18:57 GMT+01:00 Bruce Fischl : > try opening it in tksurfer and see if it complains > > On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: > > Hi, >> >> Thanks for the quick answer. >> >> There was no error message in the previous steps. >> >> I started it with : mris_sphere -seed 1234 ../surf/lh.inflated >> ../surf/lh.sphere >> >> Although if the seed is the same, I am guessing that any non-deterministic >> process would have the same output. >> >> Is there a a way to automatically know if there was a problem in the >> sphere >> creation? >> >> Cheers. >> >> >> 2015-08-02 16:27 GMT+01:00 Bruce Fischl : >> hmm, something seems to be wrong maybe the the ?h.sphere. Can >> you try recreating it >> cheers >> Bruce >> On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: >> >> Hi all, >> >> I received an error in one of the steps of >> recon-all. The error is "No such >> file or directory" at the end of one of the >> registration processes. >> >> The step was mris_register -curv. The command was: >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> I already checked that ../surf/lh.sphere and >> /average/lh.average.curvature.filled.buckner40.tif >> exist (and are >> readable). I also checked that the output directorry >> (../surf/ ) has the >> proper permisons to write. >> >> The version of mris_register is "stable5". >> >> Finally, the complete output message is (Please, >> note that the parts with <> >> have been edited by me for privacy reasons: >> >> # >> #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 >> /scripts >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> using smoothwm curvature for final alignment >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 >> nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 >> nicks Exp $ >> reading surface from ../surf/lh.sphere... >> reading template parameterization from >> /average/lh.average.curvature.filled.buckner40.tif... >> MRISregister() --- >> max_passes = 4 >> min_degrees = 0.50 >> max_degrees = 64.00 >> nangles = 8 >> tol=5.0e-01, sigma=0.0, host=., nav=1024, >> nbrs=1, l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, >> l_dist=5.000 >> using quadratic fit line minimization >> complete_dist_mat 0 >> rms 0 >> smooth_averages 0 >> remove_neg 0 >> ico_order 0 >> which_surface 0 >> target_radius 0.00 >> nfields 0 >> scale 0.00 >> desired_rms_height -1.00 >> momentum 0.95 >> nbhd_size -10 >> max_nbrs 10 >> niterations 25 >> nsurfaces 0 >> SURFACES 3 >> flags 16 (10) >> use curv 16 >> no sulc 0 >> no rigid align 0 >> mris->nsize 1 >> mris->hemisphere 0 >> randomSeed 0 >> >> tol=5.0e-01, sigma=0.0, host=., nav=1024, >> nbrs=1, l
[Freesurfer] Sulci segmentation
Hi, I am pretty new in freesurfer and I do not know if this question has been answered before (It is difficult to search for 1 basic question), so I will post it anyways: - Is there any segmentation/labeling in freesurfer that allows the user to identify all the sulci of an MR image? I have done the recon-all, correctly, but I am not able to see any sulcus using tkmedit with the generated segmentations. Thanks in advance. ___ 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] Sulci segmentation
Thanks mr Fischl, but these surfaces are a deformation of the original brain (According to what I have read in the wiki). My intention is to write an algorithm to do some operations on the original images, using the sulci information from freesurfer. In order to do that, I would need the sulci information IN a segmentation of the brain with the same size as the original. Is there any transformation I can apply to have this information? Thanks again. > the gyral/sulcal segmentations are generated on the surfaces and viewable > in tksurfer. For example: > > tksurfer lh inflated -aparc > > will bring up and show the lh.aparc.annot on top of the inflated > surface. You can also load them from the tksurfer interface using > file->label->import annotation > > cheers > Bruce > > On Mon, 20 Dec 2010, FIDEL ALFARO ALMAGRO wrote: > >> >> Hi, >> >> I am pretty new in freesurfer and I do not know if this question has >> been >> answered before (It is difficult to search for 1 basic question), so I >> will post it anyways: >> >> - Is there any segmentation/labeling in freesurfer that allows the user >> to >> identify all the sulci of an MR image? I have done the recon-all, >> correctly, but I am not able to see any sulcus using tkmedit with the >> generated segmentations. >> >> Thanks in advance. >> >> >> ___ >> 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] Sulci segmentation
Then I am not doing the question propperly, and I obviously did not understand the basis of tksurfer :) I am going to work in Matlab, and I just wanted to use the output of Freesurfer to help me with my algorithm, so I am not going to use neither tkmedit nor tksurfer. Hence, I do not exactly need to know how to visualize these data correctly in tksurfer :). My needs are in a lower level. So, the question now is: having a pixel of one of the slices of the original image, how can I know if it is a sulcus, a gyrus or none of those? From what file(s) can I read that information? Cheers. > Hi Fidel > > the surfaces of the same hemi for a given subject area all topologically > equivalent and share an index structure. what that means is that the > vertex label/annotation can be shown/used on any surface, including the > ?h.white and ?h.pial surfaces (which is probably what you want). Or you > can > look at the aparc+aseg.mgz, which combines the subcortical and cortical > labelings into a single volume. > > cheers > Bruce > > > > On Mon, 20 Dec 2010, FIDEL ALFARO ALMAGRO wrote: > >> Thanks mr Fischl, but these surfaces are a deformation of the original >> brain (According to what I have read in the wiki). My intention is to >> write an algorithm to do some operations on the original images, using >> the >> sulci information from freesurfer. In order to do that, I would need the >> sulci information IN a segmentation of the brain with the same size as >> the >> original. Is there any transformation I can apply to have this >> information? >> >> Thanks again. >> >>> the gyral/sulcal segmentations are generated on the surfaces and >>> viewable >>> in tksurfer. For example: >>> >>> tksurfer lh inflated -aparc >>> >>> will bring up and show the lh.aparc.annot on top of the >>> inflated >>> surface. You can also load them from the tksurfer interface using >>> file->label->import annotation >>> >>> cheers >>> Bruce >>> >>> On Mon, 20 Dec 2010, FIDEL ALFARO ALMAGRO wrote: >>> >>>> >>>> Hi, >>>> >>>> I am pretty new in freesurfer and I do not know if this question has >>>> been >>>> answered before (It is difficult to search for 1 basic question), so I >>>> will post it anyways: >>>> >>>> - Is there any segmentation/labeling in freesurfer that allows the >>>> user >>>> to >>>> identify all the sulci of an MR image? I have done the recon-all, >>>> correctly, but I am not able to see any sulcus using tkmedit with the >>>> generated segmentations. >>>> >>>> Thanks in advance. >>>> >>>> >>>> ___ >>>> 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] (no subject)
Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance. ___ 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_mark_temporal_lobe
Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance. ___ 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] (no subject)
Hello, I am trying to obtain a segmentation of the cortex to get the different lobes (specifically, the temporal lobe). I have read (via google) that someone asked that before in this mailing list, but the answer was old and not very clear, so I guessed this program was the solution. So... Is there any tool in the freesurfer suite to allow me to get a segmentation of the different lobes of the brain? Thanks. > Hi Fidel, > > that is deprecated code. What are you trying to do? > > cheers (and happy holidays) > > Bruce > On Fri, 24 Dec 2010, > FIDEL ALFARO ALMAGRO wrote: > >> Happy holidays for those who celebrate it today, >> >> Hi. Is there any documentation on how to use mri_mark_temporal_lobe >> application and what is its output? I cannot find any. >> >> Thanks in advance. >> >> ___ >> 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] (no subject)
Thank you very much for the quick answer and happy holidays. > Forwarding a previous answer from doug. I tried it before (and > recently). It does seem to work. > >>>> >>>> Try running mri_annotation2label with --lobes lh.lobes.annot >>>> >>>> doug >>>> >>>> >>>> On Thu, 20 May 2010, Rudolph Pienaar wrote: >>>> >>>>> Hi all -- >>>>> >>>>> Is there a simple way to create an annotation for >>>>> frontal/temporal/occipital/parietal lobes based off the ? >>>>> h.aparc.annot >>>>> files in a FS 'label' dir? Ideally speaking, I'd like to have a >>>>> ?h.lobar.annot with corresponding lobar.annot.ctab. >>>>> >>>>> Apologies if this question has come up before... a quick google >>>>> didn't >>>>> reveal anything. >>>>> >>>>> Many thanks >>>>> -=R >>>>> >>>>> >>>> >>> >> > > On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote: > >> Hello, >> >> I am trying to obtain a segmentation of the cortex to get the >> different >> lobes (specifically, the temporal lobe). I have read (via google) that >> someone asked that before in this mailing list, but the answer was >> old and >> not very clear, so I guessed this program was the solution. >> >> So... Is there any tool in the freesurfer suite to allow me to get a >> segmentation of the different lobes of the brain? >> >> Thanks. >> >>> Hi Fidel, >>> >>> that is deprecated code. What are you trying to do? >>> >>> cheers (and happy holidays) >>> >>> Bruce >>> On Fri, 24 Dec 2010, >>> FIDEL ALFARO ALMAGRO wrote: >>> >>>> Happy holidays for those who celebrate it today, >>>> >>>> Hi. Is there any documentation on how to use mri_mark_temporal_lobe >>>> application and what is its output? I cannot find any. >>>> >>>> Thanks in advance. >>>> >>>> ___ >>>> 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] (no subject)
Hello experts, After several days of trying, I have accomplished to get what you thought I was asking for. Unfortunately I was not asking for that. First, I have to say that there is no --lobes option in mri_annotation2label (It is not documented, and if you try it, nothing happens). Then I ran these commands: [1] mri_annotation2label --subject XXX --hemi rh --outdir ../subjects/XXX/tmp/ --annotation lobes [2] mri_label2vol --label ../subjects/XXX/rh.temporal.label --subject XXX --o test.nii --temp ../subjects/XXX/mri/orig.mgz --identity I have seen that what I get in test.nii is a volume with the segmentation of the border between the white matter and grey matter in the temporal lobe. I am afraid I was not clear enough, as I was looking for a volume with the segmentation of the grey matter of the temporal lobe. I have tried changing the parameters in the first command, but it does not seem to work. Does anybody know how can I do this? Thanks in advance. Fidel. > Thank you very much for the quick answer and happy holidays. > >> Forwarding a previous answer from doug. I tried it before (and >> recently). It does seem to work. >> >>>>> >>>>> Try running mri_annotation2label with --lobes lh.lobes.annot >>>>> >>>>> doug >>>>> >>>>> >>>>> On Thu, 20 May 2010, Rudolph Pienaar wrote: >>>>> >>>>>> Hi all -- >>>>>> >>>>>> Is there a simple way to create an annotation for >>>>>> frontal/temporal/occipital/parietal lobes based off the ? >>>>>> h.aparc.annot >>>>>> files in a FS 'label' dir? Ideally speaking, I'd like to have a >>>>>> ?h.lobar.annot with corresponding lobar.annot.ctab. >>>>>> >>>>>> Apologies if this question has come up before... a quick google >>>>>> didn't >>>>>> reveal anything. >>>>>> >>>>>> Many thanks >>>>>> -=R >>>>>> >>>>>> >>>>> >>>> >>> >> >> On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote: >> >>> Hello, >>> >>> I am trying to obtain a segmentation of the cortex to get the >>> different >>> lobes (specifically, the temporal lobe). I have read (via google) that >>> someone asked that before in this mailing list, but the answer was >>> old and >>> not very clear, so I guessed this program was the solution. >>> >>> So... Is there any tool in the freesurfer suite to allow me to get a >>> segmentation of the different lobes of the brain? >>> >>> Thanks. >>> >>>> Hi Fidel, >>>> >>>> that is deprecated code. What are you trying to do? >>>> >>>> cheers (and happy holidays) >>>> >>>> Bruce >>>> On Fri, 24 Dec 2010, >>>> FIDEL ALFARO ALMAGRO wrote: >>>> >>>>> Happy holidays for those who celebrate it today, >>>>> >>>>> Hi. Is there any documentation on how to use mri_mark_temporal_lobe >>>>> application and what is its output? I cannot find any. >>>>> >>>>> Thanks in advance. >>>>> >>>>> ___ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and >>>> the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>> you in >>>> error >>>> but does not contain patient information, please contact the sender >>>> and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Equivalent labels
Hi Freesurfer experts, I would like to know what are the equivalent labels to - Gyrus Intralmibic - Sulcus semmi annularis In the label file FreeSurferColorLUT.txt. I have checked the paper "Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature" but the information there is not useful (e.g. indusium griseum does not appear in that file). Thanks and best regards. Fidel. ___ 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] Equivalent labels
Hi mr Destrieux, Does this mean that those structures cannot be found in ANY segmentation or labelling made by freesurfer? Thanks again for your quick answer, Fidel. > Hi Fidel > > as stated in the paper you cited, the intralimbic gyrus is made of : > prehippocampal rudiment, indusium griseum and hippocampus. Only the latter > vas clearly visible on the MR scans used to build the atlas, but was not > correctly unfolded. For this reason the intralimbic gyrus can not be > automatically labelled on the surface. Nevertheless, Hippocampus is > segmented by the volume autoparcellation. > > Similarly, Sulcus semi annularis was not correctly unfolded and was not > labelled. > > Sorry about that > > > > > > -- > Christophe Destrieux, > > Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, > Université François Rabelais de Tours > http://www.u930.tours.inserm.fr/ > > Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > - Mail original - > De: "FIDEL ALFARO ALMAGRO" > Ã: freesurfer@nmr.mgh.harvard.edu > Envoyé: Mercredi 12 Janvier 2011 16:20:10 > Objet: [Freesurfer] Equivalent labels > > > Hi Freesurfer experts, > > I would like to know what are the equivalent labels to > > - Gyrus Intralmibic > - Sulcus semmi annularis > > In the label file FreeSurferColorLUT.txt. I have checked the paper > "Automatic parcellation of human cortical gyri and sulci using standard > anatomical nomenclature" but the information there is not useful (e.g. > indusium griseum does not appear in that file). > > Thanks and best regards. > > Fidel. > > ___ > 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] Equivalent labels
Thanks to both of you. Cheers. > no we haven't done them > On Wed, 12 Jan 2011, Christophe Destrieux wrote: > >> I meant : am i right to think that we don't have any other parcellation >> available showing the other labels Fidel would like to use ? >> (I thought that maybe somebody localized these structures in a way >> similar to what you did for the entorhinal cortex in your exvivo/invivo >> 2008 paper) >> >> cheers >> >> > > > 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
