Freesurfer December 2008

freesurfer@nmr.mgh.harvard.edu

65 participants
107 discussions

Re: AW: AW: AW: [Freesurfer] mri_extract_label 4181
by Bruce Fischl 10 Dec '08

10 Dec '08

Hi Markus, I think the problem is that we generate the wmparc.mgz using the Desikan/Killiany atlas, not Christophe's, so the wmparc doesn't have Christophe's labels in it. You could generate a wmparc.a2005s.mgz pretty easily by rerunning mri_aparc2aseg using --a2005s or --annot aparc.a2005s. cheers, Bruce On Wed, 10 Dec 2008, Markus Röhl wrote: > Hi Bruce, > > Thank you for this quick check. Your results confirm my suspicion: > "aparc.a2005s+aseg.mgz" does not have this wm-label. So, after trying every > segmentation file I found in /mri (aparc+aseg.mgz, wmparc.mgz, > aparc.a2005s+aseg.mgz) without success, I asked me > > Where can I find or how can I create the necessary segmentation volume to > extract 3136 or 4181? > > Somebody has an idea? > > kind regards, > > Markus > > > -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Gesendet: Mittwoch, 10. Dezember 2008 19:16 > An: Markus Röhl > Betreff: Re: AW: AW: [Freesurfer] mri_extract_label 4181 > > Hi Markus, > > are you sure there is a 3136 in the data? That is a wm label, and is > probably in the wmparc.mgz, not this one. The 1136 is the ctx label. I > did: > > matlab > >>> [v,M,mr] = load_mgh('aparc.a2005s+aseg.mgz'); >>> find(v(:) == 3136) > ans = > Empty matrix: 0-by-1 >>> find(v(:) == 1136) > ans = > 4607151 > 4672429 > 4672430 > 4672687 > 4672944 > 4737453 > 4737708 > 4737709 > 4737963 > 4737965 > 4737966 > 4737967 > . > . > . > > > > On > Wed, 10 Dec 2008, Markus Röhl wrote: > >> Hi Bruce, >> >> the command line that fails is: >> >> mri_extract_label ./aparc.a2005s+aseg.mgz 3136 ./test.nii.gz >> >> This works fine: >> >> mri_extract_label ./aparc.a2005s+aseg.mgz 1136 ./test2.nii.gz >> >> Best regards, >> >> Markus >> >> -----Ursprüngliche Nachricht----- >> Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Gesendet: Mittwoch, 10. Dezember 2008 18:38 >> An: Markus Röhl >> Betreff: Re: AW: [Freesurfer] mri_extract_label 4181 >> >> Hi Markus >> >> can you email me the aparc.a2005s+aseg.mgz and the exact command line >> that fails? >> Bruce >> On Wed, 10 Dec 2008, Markus Röhl wrote: >> >>> Hi >>> >>> for the purpose of illustration I change to >>> >>> 3136 wm-lh-G_temp_sup-Planum_tempolare >>> >>> The corresponding gray matter part (1136) can seen in cortex.tiff. It is >>> labeled green and can be found quite in the middle of the picture right >> from >>> the red labeled S_temporal_transverse. The successful extraction of the >> 1136 >>> ctx-lh-G_temp_sup-Planum_tempolare is shown in success.png. >>> >>> The corresponding white matter of this landmark (3136 >>> wm-lh-G_temp_sup-Planum_tempolare) can also be seen on the right side of >>> WM.tiff as a green labeled area superior of the pink labeled lateral >> aspect >>> of G_temp_sup. (the 3181 wm-lh-S_temporal_transverse is also present as a >>> very very small red labeled area between the small blue and green areas > in >>> the middle of WM.tiff). >>> >>> I am not able to extract 3136 and I think this seems to hold also for the >>> other 3XXX or 4XXX wm-labels from aparc.a2005s+aseg.mgz. >>> >>> I extracted 2034 ctx-rh-transversetemporal from "aparc+aseg.mgz" and >> analog >>> 4034 wm-lh-transversetemporal from "wmparc.mgz". I assumed that there > must >>> be a corresponding file of "aparc.a2005s+aseg.mgz" like >>> "wmparc.a2005s+aseg.mgz" to extract white matter labels. >>> "aparc.a2005s+aseg.mgz" seems to work only for ctx- but not for > wm-labels, >>> and I don't found something else. The problem is not subject-related. >>> >>> Regards, >>> >>> Markus >>> >>> >>> -----Ursprüngliche Nachricht----- >>> Von: Christophe Destrieux [mailto:destrieux@med.univ-tours.fr] >>> Gesendet: Mittwoch, 10. Dezember 2008 14:24 >>> An: Bruce Fischl >>> Cc: Markus Röhl; freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] mri_extract_label 4181 >>> >>> Hi Bruce and Markus >>> >>> S_temporal_transverse is constant and should be present on the surface ; >>> >>> cheers >>>> HI Markus, >>>> >>>> that's one of Christophe's labels, so would only be in the >>>> aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the >>>> surface to verify that it is present there? There are also some labels >>>> that don't appear on every subject, Christophe would know if this is >>>> one of them. >>>> >>>> cheers, >>>> Bruce >>>> >>>> On Wed, 10 Dec 2008, Markus Röhl wrote: >>>> >>>>> Dear all, >>>>> >>>>> I used mri_extract_label recently to get NIfTI -binary maps for certain >>>>> anatomical landmarks, e.g. the Gyrus temporalis inferior of the left >>>>> hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: >>>>> >>>>> mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz > 1009 >>>>> $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz >>>>> >>>>> This works fine. Now I want to extract the labels of anatomical >>>>> landmarks >>>>> like >>>>> >>>>> 4181 wm-rh-S_temporal_transverse >>>>> >>>>> I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, >>>>> aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I >>>>> can find >>>>> or how can I create the necessary segmentation volume? >>>>> >>>>> Regards, >>>>> >>>>> Markus >>>>> >>>>> >>>>> >>>>> >>> >>> >>> >> > > > >

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AW: AW: AW: [Freesurfer] mri_extract_label 4181
by Markus Röhl 10 Dec '08

10 Dec '08

Hi Bruce, Thank you for this quick check. Your results confirm my suspicion: "aparc.a2005s+aseg.mgz" does not have this wm-label. So, after trying every segmentation file I found in /mri (aparc+aseg.mgz, wmparc.mgz, aparc.a2005s+aseg.mgz) without success, I asked me Where can I find or how can I create the necessary segmentation volume to extract 3136 or 4181? Somebody has an idea? kind regards, Markus -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 10. Dezember 2008 19:16 An: Markus Röhl Betreff: Re: AW: AW: [Freesurfer] mri_extract_label 4181 Hi Markus, are you sure there is a 3136 in the data? That is a wm label, and is probably in the wmparc.mgz, not this one. The 1136 is the ctx label. I did: matlab >> [v,M,mr] = load_mgh('aparc.a2005s+aseg.mgz'); >> find(v(:) == 3136) ans = Empty matrix: 0-by-1 >> find(v(:) == 1136) ans = 4607151 4672429 4672430 4672687 4672944 4737453 4737708 4737709 4737963 4737965 4737966 4737967 . . . On Wed, 10 Dec 2008, Markus Röhl wrote: > Hi Bruce, > > the command line that fails is: > > mri_extract_label ./aparc.a2005s+aseg.mgz 3136 ./test.nii.gz > > This works fine: > > mri_extract_label ./aparc.a2005s+aseg.mgz 1136 ./test2.nii.gz > > Best regards, > > Markus > > -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Gesendet: Mittwoch, 10. Dezember 2008 18:38 > An: Markus Röhl > Betreff: Re: AW: [Freesurfer] mri_extract_label 4181 > > Hi Markus > > can you email me the aparc.a2005s+aseg.mgz and the exact command line > that fails? > Bruce > On Wed, 10 Dec 2008, Markus Röhl wrote: > >> Hi >> >> for the purpose of illustration I change to >> >> 3136 wm-lh-G_temp_sup-Planum_tempolare >> >> The corresponding gray matter part (1136) can seen in cortex.tiff. It is >> labeled green and can be found quite in the middle of the picture right > from >> the red labeled S_temporal_transverse. The successful extraction of the > 1136 >> ctx-lh-G_temp_sup-Planum_tempolare is shown in success.png. >> >> The corresponding white matter of this landmark (3136 >> wm-lh-G_temp_sup-Planum_tempolare) can also be seen on the right side of >> WM.tiff as a green labeled area superior of the pink labeled lateral > aspect >> of G_temp_sup. (the 3181 wm-lh-S_temporal_transverse is also present as a >> very very small red labeled area between the small blue and green areas in >> the middle of WM.tiff). >> >> I am not able to extract 3136 and I think this seems to hold also for the >> other 3XXX or 4XXX wm-labels from aparc.a2005s+aseg.mgz. >> >> I extracted 2034 ctx-rh-transversetemporal from "aparc+aseg.mgz" and > analog >> 4034 wm-lh-transversetemporal from "wmparc.mgz". I assumed that there must >> be a corresponding file of "aparc.a2005s+aseg.mgz" like >> "wmparc.a2005s+aseg.mgz" to extract white matter labels. >> "aparc.a2005s+aseg.mgz" seems to work only for ctx- but not for wm-labels, >> and I don't found something else. The problem is not subject-related. >> >> Regards, >> >> Markus >> >> >> -----Ursprüngliche Nachricht----- >> Von: Christophe Destrieux [mailto:destrieux@med.univ-tours.fr] >> Gesendet: Mittwoch, 10. Dezember 2008 14:24 >> An: Bruce Fischl >> Cc: Markus Röhl; freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] mri_extract_label 4181 >> >> Hi Bruce and Markus >> >> S_temporal_transverse is constant and should be present on the surface ; >> >> cheers >>> HI Markus, >>> >>> that's one of Christophe's labels, so would only be in the >>> aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the >>> surface to verify that it is present there? There are also some labels >>> that don't appear on every subject, Christophe would know if this is >>> one of them. >>> >>> cheers, >>> Bruce >>> >>> On Wed, 10 Dec 2008, Markus Röhl wrote: >>> >>>> Dear all, >>>> >>>> I used mri_extract_label recently to get NIfTI -binary maps for certain >>>> anatomical landmarks, e.g. the Gyrus temporalis inferior of the left >>>> hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: >>>> >>>> mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 >>>> $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz >>>> >>>> This works fine. Now I want to extract the labels of anatomical >>>> landmarks >>>> like >>>> >>>> 4181 wm-rh-S_temporal_transverse >>>> >>>> I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, >>>> aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I >>>> can find >>>> or how can I create the necessary segmentation volume? >>>> >>>> Regards, >>>> >>>> Markus >>>> >>>> >>>> >>>> >> >> >> >

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Re: AW: [Freesurfer] mri_extract_label 4181
by Christophe Destrieux 10 Dec '08

10 Dec '08

Hi Markus I'mm not very familiar with the labels extraction , I can just answer you in anatomical terms ; the anatomical labelling sounds correct to me. Soory not to be more helpfull cheers > Hi > > for the purpose of illustration I change to > > 3136 wm-lh-G_temp_sup-Planum_tempolare > > The corresponding gray matter part (1136) can seen in cortex.tiff. It is > labeled green and can be found quite in the middle of the picture right from > the red labeled S_temporal_transverse. The successful extraction of the 1136 > ctx-lh-G_temp_sup-Planum_tempolare is shown in success.png. > > The corresponding white matter of this landmark (3136 > wm-lh-G_temp_sup-Planum_tempolare) can also be seen on the right side of > WM.tiff as a green labeled area superior of the pink labeled lateral aspect > of G_temp_sup. (the 3181 wm-lh-S_temporal_transverse is also present as a > very very small red labeled area between the small blue and green areas in > the middle of WM.tiff). > > I am not able to extract 3136 and I think this seems to hold also for the > other 3XXX or 4XXX wm-labels from aparc.a2005s+aseg.mgz. > > I extracted 2034 ctx-rh-transversetemporal from "aparc+aseg.mgz" and analog > 4034 wm-lh-transversetemporal from "wmparc.mgz". I assumed that there must > be a corresponding file of "aparc.a2005s+aseg.mgz" like > "wmparc.a2005s+aseg.mgz" to extract white matter labels. > "aparc.a2005s+aseg.mgz" seems to work only for ctx- but not for wm-labels, > and I don't found something else. The problem is not subject-related. > > Regards, > > Markus > > > -----Ursprüngliche Nachricht----- > Von: Christophe Destrieux [mailto:destrieux@med.univ-tours.fr] > Gesendet: Mittwoch, 10. Dezember 2008 14:24 > An: Bruce Fischl > Cc: Markus Röhl; freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] mri_extract_label 4181 > > Hi Bruce and Markus > > S_temporal_transverse is constant and should be present on the surface ; > > cheers > >> HI Markus, >> >> that's one of Christophe's labels, so would only be in the >> aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the >> surface to verify that it is present there? There are also some labels >> that don't appear on every subject, Christophe would know if this is >> one of them. >> >> cheers, >> Bruce >> >> On Wed, 10 Dec 2008, Markus Röhl wrote: >> >> >>> Dear all, >>> >>> I used mri_extract_label recently to get NIfTI -binary maps for certain >>> anatomical landmarks, e.g. the Gyrus temporalis inferior of the left >>> hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: >>> >>> mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 >>> $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz >>> >>> This works fine. Now I want to extract the labels of anatomical >>> landmarks >>> like >>> >>> 4181 wm-rh-S_temporal_transverse >>> >>> I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, >>> aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I >>> can find >>> or how can I create the necessary segmentation volume? >>> >>> Regards, >>> >>> Markus >>> >>> >>> >>> >>> > > > -- Christophe Destrieux 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

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RE: [Freesurfer] Statistic analysing for a mask
by Alexandru Hanganu 10 Dec '08

10 Dec '08

Thank you Doug, I have found the summary file. So the final results that I have are the thickness data of the Mask. What we wanted to find out was more how can we run the statistics not on the whole brain or one hemisphere, but only on one Mask (for i.e. a 3D Mask from FSL). the transformation of 3D to surface ? Thank you for your help, Alex. ________________________________ Von: Doug Greve <greve(a)nmr.mgh.harvard.edu> An: Alexandru Hanganu <hanganu.alexandru(a)yahoo.de> CC: FS Mailing List <Freesurfer(a)nmr.mgh.harvard.edu> Gesendet: Montag, den 8. Dezember 2008, 19:41:52 Uhr Betreff: Re: [Freesurfer] Statistic analysing for a mask what's your cmd? You need to make sure to add --in lh.thickness to get thickness in the summary file Alexandru Hanganu wrote: Thank you Nick, and Doug for your answers. I used both "--reshape" flag and "--noreshape" flag and the results after "mri_segstats" were in both cases: . . . Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation 0 0 134504 134504 1 1 29338 29338 Reporting on 2 segmentations So I understand that these are the thickness data of the mask I used. Are these data in mm ? Because when using "mris_anatomical_stats" command line to see the thickness - the data is in mm, and is very different. Sincerely, Alex. ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] mri_extract_label 4181
by Bruce Fischl 10 Dec '08

10 Dec '08

HI Markus, that's one of Christophe's labels, so would only be in the aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the surface to verify that it is present there? There are also some labels that don't appear on every subject, Christophe would know if this is one of them. cheers, Bruce On Wed, 10 Dec 2008, Markus Röhl wrote: > Dear all, > > I used mri_extract_label recently to get NIfTI -binary maps for certain > anatomical landmarks, e.g. the Gyrus temporalis inferior of the left > hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: > > mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 > $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz > > This works fine. Now I want to extract the labels of anatomical landmarks > like > > 4181 wm-rh-S_temporal_transverse > > I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, > aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I can find > or how can I create the necessary segmentation volume? > > Regards, > > Markus > > > >

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mri_extract_label 4181
by Markus Röhl 10 Dec '08

10 Dec '08

Dear all, I used mri_extract_label recently to get NIfTI -binary maps for certain anatomical landmarks, e.g. the Gyrus temporalis inferior of the left hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz This works fine. Now I want to extract the labels of anatomical landmarks like 4181 wm-rh-S_temporal_transverse I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I can find or how can I create the necessary segmentation volume? Regards, Markus

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Docs for FSGD Files
by Doug Greve 09 Dec '08

09 Dec '08

Hi Y'all, I've completed some new documentation on the FreeSurfer Group Descriptor (FSGD) files. They can be found in these locations: https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdFormat https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss Please let me know if you have questions (or find typos:). doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Hi and for clustering and tksurfer showing
by Zhang, Xiaochu (NIH/NIDA) [F] 09 Dec '08

09 Dec '08

Hi Freesurfer Experts, Thank you very much for your previous help! Thank you Nick so much for your really nice help! Everything is going on, now. The old problem has been resolved. However, the new problem was coming. I did a group analysis following the instruction in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. Everything was good only except the last step. In the surfcluster summary file I found there are two clusters's CWP were lower than 0.05 (one is 0.005, the other is 0.03). However, when I used tksurfer to see my result (the overlay is sig.cluster.mgh). I only can see one (the 0.005 one) but I can not see the other. But I want to see both. I went over the tksurfer's manual and try to change the threshold in view/configure/overlay but it was not worked. I also went over the mri_surfcluster's manual and did not find related information. Could you please do me a favor and tell me how to show another clusters? BTW, I want to do some ROI analysis for these two clusters (for example, I want to get the thickness of these two clusters in all subjects), is there some manuals I can read in the wiki. I think it should be have and looked for it but I can not find it. Thanks, again! All the best, Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619

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09 Dec '08

Hi I need one piece of info that I can't seem to find anywhere (after 1h of searching). What exactly do the numbers in register.dat correspond to (I know for the first four rows, but the last four rows are still a "mystery")? Can I manually temper with that info (if I know I translated an image by hand before coregistration, for example)? Thank you very much in advance - Julien Dubois

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Announcement: Freesurfer Tutorial and Workshop, January 20 & 21, 2009
by Nick Schmansky 09 Dec '08

09 Dec '08

Announcement: A Freesurfer Tutorial and Workshop will be held this January 20 & 21st, 2009 at the Martinos Center for Biomedical Imaging in Boston. A course description and link to the registration form is found here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription The Freesurfer Team

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Freesurfer December 2008