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30083 discussions

exporting label/segmented regions in diffusion space
by vin 11 Sep '08

11 Sep '08

Hello Freesurfers ! I have very basic question. I suceesfully completed autorecon first time and now I want to extract the segmentated brain regions/ labels, as a ROI, so that I can use them in diffusion(b0) space. can any one suggest me related wiki page, where I could start for this and understand registeration( diffusion to freesurfer image) and than take the segmented regions and convert them in NIFTI format for example for FSL probtrack. Thank you, vin

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(no subject)
by Al-Radaideh Ali 11 Sep '08

11 Sep '08

Dear FreeSufer Experts, I was running the recon-all autorecon-all -s bert step and I have got the error message below. this is the first time I see this message although I have analysed more than 7 MPRAGEs. Any suggestions please? Note: I usually call my subject as bert. Thanks Ali #@# Talairach Failure Detection Tue Sep 9 16:02:41 BST 2008 /data_local/ali/freesurfer/subjects/MPRAGE/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0090, pval=0.0000 < threshold=0.0050) Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Sep 9 16:02:41 BST 2008 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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LGI question
by j janssen 11 Sep '08

11 Sep '08

Hi, i´m using stable v4.0.5 (for Cent OS 4 x86_64). i have matlab version 7.5. for a brain i have ?h.pial surfaces which give "total defect index = 0" when doing: mris_euler_number ?h.pial for this brain i ran: recon-all -s <subj> -localGI the log tells me that: "recon-all finished without error at Thu Sep 11 00:18:56 CEST 2008" ** however, when i overlay lh.pial_lgi (attached lgi_2.jpg) it does not seem correct. my question: have i done something wrong? thanks! -joost **

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Recon-all -long
by Juergen Haenggi 11 Sep '08

11 Sep '08

Dear FS experts Thanks a lot for the beta version of recon-all -long. It works fine. Is it possible to use more than two time points in the recon-all -long pipeline. If yes, can I add the third and forth time point of each subject with additional -i options (-i tp3.nii -i tp4.nii)? If no, is there a possibility to build a loop with the command foreach? We tested some MR sequences and recognized that the MR images of some sequences produced a very low number of topological defects (10-20 per hemisphere). Can we interpret the number of topological defects as a quality measure for our MR sequences? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Historical Freesurfer Question
by Pedro Paulo de Magalhães Oliveira Junior 10 Sep '08

10 Sep '08

Hi, I don't know if someone know the answer, however I found this question an interesting one: In Dale99 paper, Neuroimage, the authors stats that all recon process would take 90 minutes. Is there a way, using recon-all script to follow the same steps they used in that paper? -- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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3 fast questions on freesurfer
by dfwang 10 Sep '08

10 Sep '08

Dear Freesurfer Users, I have 3 fast questions on freesurfer. Any comments are welcome! 1. how to calculate the GM/WM/CSF volume in freesurfer? 2. how to calculat the volume of the frontal lobe? 3. how to convert the file format from .mgz to .mnc or analyze? Thanks in advance. Vincent

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What is included in the ICV value
by Jeff Sadino 09 Sep '08

09 Sep '08

Hello, I am measuring the shrinkage of the limbic system over time for several subjects and need to know what is included in the ICV value in aseg.stats to do this. We are putting our raw scans into freesurfer without any manual edits until after QA at the end. My understanding is that the brain gets registered to the talairach template, the skull gets stripped, and then everything inside the skull - wm, gm, csf, cerebellum - gets included in the ICV (via scaling of the determinant of talairach_with_skull.lta)? Can someone confirm this work flow for us? Thank you very much, Jeff _________________________________________________________________ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/

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Re: [Freesurfer] annotation file and labels for fsaverage
by Bruce Fischl 09 Sep '08

09 Sep '08

great, thanks Ron. Bruce On Tue, 9 Sep 2008, Ron Killiany wrote: > I believe Sarah will be over at MGH on friday to begin finalizing this. > > --ron > > On Mon, Sep 8, 2008 at 9:31 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Dara, >> >> there is an insula label in the works (*lots* of people have asked this >> question). Ron: any updates on the insula label? >> >> thanks >> Bruce >> >> On Mon, 8 Sep 2008, Dara Manoach wrote: >> >> Thanks very much for the detailed info Karl (and Doug and Bruce)! >>> >>> My primary ROI is ACC, so we'll probably use Aparc with the cingulate >>> divisions. I'll have to review the paper to see if the anatomic bases of >>> the divisions are described. I'm surprised, though, that there is not an >>> insula label, and I'm wondering why it would not be possible to use ROI >>> labels from the two annotation schemes to examine activation in group data >>> (i.e., ACC labels from aparc and insula from aparc2005). >>> >>> best, >>> dara >>> >>> On Sep 8, 2008, at 8:18 PM, Bruce Fischl wrote: >>> >>> for what it's worth we label the cc now explicitly in the aseg, which is >>>> certainly more accurate than the aparc used to be. >>>> >>>> Thanks for the detailed answer though Carl! >>>> >>>> Bruce >>>> On Mon, 8 Sep 2008 carl(a)nmr.mgh.harvard.edu wrote: >>>> >>>> >>>>> Hi Dara, >>>>> >>>>> You can certainly use either one as Doug says, but depending on your >>>>> purposes, one or the other may have some virtues. 2005 consists of >>>>> discrete sulcal and gyral labels with traditional anatomical names so >>>>> there are a lot more labels (which is why Doug describes it as very >>>>> detailed), whereas aparc in general collapses these into summary >>>>> regions. >>>>> >>>>> But it is not a a simple case of lumper vs splitter....For instance it >>>>> seems that >>>>> >>>>> Aparc divides the cingulate into rostral anterior, caudal anterior, >>>>> posterior cingulate whereas in aparc 2005 it is lumped into one >>>>> cingulate >>>>> label >>>>> >>>>> Aparc shows the corpus c. nicely (I think there may even be a >>>>> subparcellation available in development) whereas the cc is lost in the >>>>> medial wall in 2005. >>>>> >>>>> Aparc differentiates the pars orbitalis nicely on the orbital surface >>>>> from >>>>> the rest of the ofc, aparc 2005 does not ? possibly of interest to >>>>> someone >>>>> who is looking at ventrolateral pfc and its neighbors >>>>> >>>>> Aparc includes in its lateral ofc label everything lateral to the rectus >>>>> gyrus, including the central ofc and the (unlabeled) transverse sulcus >>>>> neither of which would be understood as being in the lateral ofc as that >>>>> term is typically used today. >>>>> >>>>> Aparc 2005 shows a view that nicely differentiates the rectus gyrus on >>>>> sagital section from the adjoining, whereas aparc lumps a broad >>>>> territory >>>>> into ?medial OFC? >>>>> >>>>> Aparc 2005 includes parcellation of the Insula, aparc does not and it is >>>>> lost in the unknown medial wall (there has been talk of fixing this but >>>>> is >>>>> this real, Bruce or Doug?) >>>>> >>>>> Perhaps what we need is a ?best of aparc and aparc 2005?. >>>>> >>>>> For surfing purposes you can also ?fool? tksurfer into showing you the >>>>> names of the (typically more more detailed) 2005 parcellations while >>>>> viewing the brain labeled with the aparc labels which at times have more >>>>> detail ? though I have never asked Doug if this will always work >>>>> correctly. >>>>> >>>>> If others have discovered pros and cons in other regions, please share. >>>>> >>>>> Best, >>>>> >>>>> >>>>> Carl >>>>> >>>>> >>>>> >>>>> Carl E. Schwartz, M.D. >>>>> Harvard Medical School >>>>> Director, Developmental Neuroimaging & Psychopathology Laboratory >>>>> Psychiatric Neuroscience Program >>>>> Massachusetts General Hospital >>>>> tel 617-726-8965 >>>>> fax 617-726-4078 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> > > >

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Re: [Freesurfer] annotation file and labels for fsaverage
by carl＠nmr.mgh.harvard.edu 08 Sep '08

08 Sep '08

Hi Dara, You can certainly use either one as Doug says, but depending on your purposes, one or the other may have some virtues. 2005 consists of discrete sulcal and gyral labels with traditional anatomical names so there are a lot more labels (which is why Doug describes it as very detailed), whereas aparc in general collapses these into summary regions. But it is not a a simple case of lumper vs splitter....For instance it seems that Aparc divides the cingulate into rostral anterior, caudal anterior, posterior cingulate whereas in aparc 2005 it is lumped into one cingulate label Aparc shows the corpus c. nicely (I think there may even be a subparcellation available in development) whereas the cc is lost in the medial wall in 2005. Aparc differentiates the pars orbitalis nicely on the orbital surface from the rest of the ofc, aparc 2005 does not possibly of interest to someone who is looking at ventrolateral pfc and its neighbors Aparc includes in its lateral ofc label everything lateral to the rectus gyrus, including the central ofc and the (unlabeled) transverse sulcus neither of which would be understood as being in the lateral ofc as that term is typically used today. Aparc 2005 shows a view that nicely differentiates the rectus gyrus on sagital section from the adjoining, whereas aparc lumps a broad territory into medial OFC Aparc 2005 includes parcellation of the Insula, aparc does not and it is lost in the unknown medial wall (there has been talk of fixing this but is this real, Bruce or Doug?) Perhaps what we need is a best of aparc and aparc 2005. For surfing purposes you can also fool tksurfer into showing you the names of the (typically more more detailed) 2005 parcellations while viewing the brain labeled with the aparc labels which at times have more detail though I have never asked Doug if this will always work correctly. If others have discovered pros and cons in other regions, please share. Best, Carl Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078

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Re: [Freesurfer] Problem to run FreeSurfer for under one year old baby subject
by Yuan Xu 08 Sep '08

08 Sep '08

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