Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

FSL/Freesurfer
by Clifford A. Smith, PhD 21 Mar '06

21 Mar '06

I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source SetUpFreeSurfer.csh command. The following is the error output. Any work around besides run separate X11 windows for FSL and Freesurfer? [Clifford-Smiths-Computer:~] Cliff% source SetUpFreeSurfer.csh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Users/Cliff/Imaging/freesurfer FSFAST_HOME /Users/Cliff/Imaging/freesurfer/fsfast SUBJECTS_DIR /Users/Cliff/Imaging/freesurfer/subjects FUNCTIONALS_DIR /Users/Cliff/Imaging/freesurfer/sessions MINC_BIN_DIR /Users/Cliff/Imaging/freesurfer/mni/bin MINC_LIB_DIR /Users/Cliff/Imaging/freesurfer/mni/lib PERL5LIB /Users/Cliff/Imaging/freesurfer/mni/lib/../System/Library/Perl/5 .8.6 GSL_DIR /Users/Cliff/Imaging/freesurfer/lib/gsl QTDIR /Users/Cliff/Imaging/freesurfer/lib/qt TCLLIBPATH /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib MISC_LIB /Users/Cliff/Imaging/freesurfer/lib/misc/lib FSL_DIR /users/cliff/fsl [Clifford-Smiths-Computer:~] Cliff% fsl Error in startup script: no suitable image found. Did find: /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a: unknown file type, first eight bytes: 0 x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A while executing "load /Users/Cliff/Imaging/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix" ("package ifneeded" script) invoked from within "package require Tix" invoked from within "if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] != 0 } { package require Tix tix configure -scheme TixGray option add ..." (file "/users/cliff/fsl/tcl/fslstart.tcl" line 3) invoked from within "source [ file dirname [ info script ] ]/fslstart.tcl" (file "/users/cliff/fsl/tcl/fsl.tcl" line 71) invoked from within "source ${FSLDIR}/tcl/${origname}.tcl" (file "/users/cliff/fsl/bin/fsl" line 19) [Clifford-Smiths-Computer:~] Cliff% ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
by Goldman, Aaron (NIH/NIMH) [C] 21 Mar '06

21 Mar '06

Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the default for lh.aparc.annot). I'm not sure if this is what your 2nd question is asking, but the pial outlines do tend to "cross under" the orig slightly (as shown above). I kind of assumed this was normal though. Anyway, I've looked at some more, and when I look at the orig surface I think most of ours look like the image Greg posted. Were you able to answer his question (if so, I don't think it went to the list)? Thanks, Aaron -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Monday, March 20, 2006 2:20 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: Greg Harris; Freesurfer Mailing List; Karl Helmer Subject: RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Aaron, Which version of Freesurfer and which version of the parc atlas are you using? Also have you checked your surfaces along the midline to see if they are acting in a strange way (i.e. self-intersecting, crossing the midline, etc.)? thanks, Rahul On Mon, 20 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote: > Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here. > > Thanks, > > -Aaron- > > -----Original Message----- > From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] > Sent: Saturday, March 18, 2006 5:51 PM > To: Greg Harris > Cc: Freesurfer Mailing List; Karl Helmer > Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data > > Hi Greg, > > Could you send along jpegs or rgbs detailing what excactly the > parcellation atlas is doing in the cingulate region? Also have you looked > at both the white and pial surfaces in this area? > > Hope you are well othwerwise, > > Rahul > > On Sat, 18 Mar 2006, Greg Harris wrote: > >> Dear Karl, >> >> Has anybody had any success with the midline rois given by the atlas >> curvature.buckner40.filled.desikan_killiany that is automatically applied >> by autorecon3 under the newest stable release, version 3.0? >> >> Our trouble lies in the regions labeled corpuscallosum and >> <anything>cingulate: this >> atlas is giving us a corpus callosum that is exactly the ventral cingulate >> sulcus, and the 4 >> cingulate gyrus segments, which is what we are interested in in this case, >> incorrectly >> exclude their ventral portion. >> >> I presume this has been made to work at mgh, because Rahul Desikan's paper >> contains >> an illustration that is anatomically correctly labeled for these regions. >> >> We are providing an orig/001.mgz image to the autorecon1 step that is >> talairach aligned, >> skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed >> 16-bit >> T1-weighted MRI scan. We have thousands of them, collected over the past 15 >> years. >> We are writing a nifti .nii file, and converting it with >> >> mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 >> /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii >> /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz >> >> We actually mean to numerically measure the extent -- the area and thickness, >> say -- of >> anatomical regions of interest including <anything>cingulate and apply >> statistical tests to >> these data. A line of guff about Type I and Type II errors and what is only >> presumable >> when identifying anatomical rois would be of no interest, and considered >> needlessly >> defensive. After all, the other 29 regions of Desikan's really great atlas >> are in working >> order! >> >> Do we need to convince Rahul Desikan to release the "correct" >> *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 >> that correspond to his paper? >> >> Greg Harris >> The University of Iowa College of Medicine >> Psychiatry NeuroImaging Lab >> >> >> > > --

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RE: [Freesurfer] want to view one segmented subcortical object at a time...
by Goradia, Dhruman D 21 Mar '06

21 Mar '06

Hello Bruce and all, Is it possible to perform group analysis based only on a particular subcortical region of interest and visualize it? -Dhruman -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday 20 March 2006 16:20 To: Shahabuddin Ansari Cc: freesurfer(a)nmr.mgh.harvard.edu; Steve Pieper Subject: Re: [Freesurfer] want to view one segmented subcortical object ata time... Hi Shahab, we don't have anything to do that, although I think slicer probably can do it with our data. Bruce On Mon, 20 Mar 2006, Shahabuddin Ansari wrote: > Hello, > > I have segmented subcortical regions of the whole > brain from Freesurfer. Can somebody help me how to > view one object (say right hippocampus) at a time. > > Thanks > Shahab > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > _______________________________________________ > 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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want to view one segmented subcortical object at a time...
by Shahabuddin Ansari 20 Mar '06

20 Mar '06

Hello, I have segmented subcortical regions of the whole brain from Freesurfer. Can somebody help me how to view one object (say right hippocampus) at a time. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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'zero distance at v' printing associated with missing hemi.smoothwm files.
by Greg Harris 20 Mar '06

20 Mar '06

In a sample of 50 brains, I found two hemispheres that fail at autorecon3, printing a whole lot of this: zero distance at v 91420, n 0 (vn = 89897) zero distance at v 91420, n 1 (vn = 91419) zero distance at v 91420, n 2 (vn = 91421) zero distance at v 91420, n 3 (vn = 91402) zero distance at v 91420, n 4 (vn = 88463) zero distance at v 91420, n 5 (vn = 89896) zero distance at v 91420, n 6 (vn = 88475) zero distance at v 91420, n 7 (vn = 89912) zero distance at v 91420, n 8 (vn = 91401) zero distance at v 91420, n 9 (vn = 89913) zero distance at v 91420, n 10 (vn = 91438) zero distance at v 91420, n 11 (vn = 91404) zero distance at v 91420, n 12 (vn = 91422) zero distance at v 91420, n 13 (vn = 92898) zero distance at v 91420, n 14 (vn = 92899) zero distance at v 91420, n 15 (vn = 91384) zero distance at v 91420, n 16 (vn = 91385) zero distance at v 91420, n 17 (vn = 92900) zero distance at v 91420, n 18 (vn = 92900) zero distance at v 91420, n 19 (vn = 92900) zero distance at v 91420, n 20 (vn = 92898) zero distance at v 91420, n 21 (vn = 91439) zero distance at v 91420, n 22 (vn = 91384) zero distance at v 91420, n 23 (vn = 92881) zero distance at v 91420, n 24 (vn = 91404) zero distance at v 91420, n 25 (vn = 89899) zero distance at v 91420, n 26 (vn = 91400) zero distance at v 91420, n 27 (vn = 88462) zero distance at v 91420, n 28 (vn = 89882) zero distance at v 91420, n 29 (vn = 91440) zero distance at v 91420, n 30 (vn = 88485) zero distance at v 91420, n 31 (vn = 91385) zero distance at v 91420, n 32 (vn = 89884) zero distance at v 91420, n 33 (vn = 88474) zero distance at v 91420, n 34 (vn = 89928) zero distance at v 91420, n 35 (vn = 88449) zero distance at v 91420, n 36 (vn = 88496) zero distance at v 91420, n 37 (vn = 88486) zero distance at v 91420, n 38 (vn = 89885) zero distance at v 91420, n 39 (vn = 88450) zero distance at v 91420, n 40 (vn = 89869) zero distance at v 91420, n 41 (vn = 91474) zero distance at v 91420, n 42 (vn = 91441) zero distance at v 91420, n 43 (vn = 86953) zero distance at v 91420, n 44 (vn = 89852) zero distance at v 91420, n 45 (vn = 88451) zero distance at v 91420, n 46 (vn = 86952) zero distance at v 91420, n 47 (vn = 92853) zero distance at v 91420, n 48 (vn = 89942) zero distance at v 91420, n 49 (vn = 88414) zero distance at v 91420, n 50 (vn = 86929) zero distance at v 91420, n 51 (vn = 91473) zero distance at v 91420, n 52 (vn = 89867) zero distance at v 91420, n 53 (vn = 92928) zero distance at v 91420, n 54 (vn = 89939) zero distance at v 91420, n 55 (vn = 91443) zero distance at v 91420, n 56 (vn = 91476) zero distance at v 91420, n 57 (vn = 86928) zero distance at v 91420, n 58 (vn = 88494) zero distance at v 91420, n 59 (vn = 86973) zero distance at v 91421, n 0 (vn = 89898) zero distance at v 91421, n 1 (vn = 91420) etc. etc. Any idea where to look for the cause of this bug? I discovered it because these hemispheres are missing their [lr]h.smoothwm, although they have [lr]h.smoothwm.nofix files. ( for my reference, they are the left hemisphere of scan 0182497 and the right hemisphere of scan 0193095.) Greg Harris

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RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
by Goldman, Aaron (NIH/NIMH) [C] 20 Mar '06

20 Mar '06

Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here. Thanks, -Aaron- -----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Saturday, March 18, 2006 5:51 PM To: Greg Harris Cc: Freesurfer Mailing List; Karl Helmer Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data Hi Greg, Could you send along jpegs or rgbs detailing what excactly the parcellation atlas is doing in the cingulate region? Also have you looked at both the white and pial surfaces in this area? Hope you are well othwerwise, Rahul On Sat, 18 Mar 2006, Greg Harris wrote: > Dear Karl, > > Has anybody had any success with the midline rois given by the atlas > curvature.buckner40.filled.desikan_killiany that is automatically applied > by autorecon3 under the newest stable release, version 3.0? > > Our trouble lies in the regions labeled corpuscallosum and > <anything>cingulate: this > atlas is giving us a corpus callosum that is exactly the ventral cingulate > sulcus, and the 4 > cingulate gyrus segments, which is what we are interested in in this case, > incorrectly > exclude their ventral portion. > > I presume this has been made to work at mgh, because Rahul Desikan's paper > contains > an illustration that is anatomically correctly labeled for these regions. > > We are providing an orig/001.mgz image to the autorecon1 step that is > talairach aligned, > skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed > 16-bit > T1-weighted MRI scan. We have thousands of them, collected over the past 15 > years. > We are writing a nifti .nii file, and converting it with > > mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 > /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii > /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz > > We actually mean to numerically measure the extent -- the area and thickness, > say -- of > anatomical regions of interest including <anything>cingulate and apply > statistical tests to > these data. A line of guff about Type I and Type II errors and what is only > presumable > when identifying anatomical rois would be of no interest, and considered > needlessly > defensive. After all, the other 29 regions of Desikan's really great atlas > are in working > order! > > Do we need to convince Rahul Desikan to release the "correct" > *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 > that correspond to his paper? > > Greg Harris > The University of Iowa College of Medicine > Psychiatry NeuroImaging Lab > > > -- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesufer] Problems with control points
by Martin Ystad 20 Mar '06

20 Mar '06

Hi, I have some problems with the white matter segmentation on some of my brains. the Main-surface cuts into the white matter in certain bright areas. I tried to fix this by adding control points to the area. Then I ran recon-all -autorecon2-cp again, but this didn't resolve the problem. Any Ideas ? I've attached a picture of the problem. Thanks, Martin Ystad University of Bergen, Norway.

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lh.curv versus lh.curv.pial
by Yuhong Jiang 19 Mar '06

19 Mar '06

Dear Bruce and others, We recently started using the newly released freesurfer stable version 3.0.1. After auto-recon2 a few files are saved, including lh.curv and lh.curv.pial. When lh.curv is loaded as the curvature, the output looks awful. But lh.curv.pial looks great. What's the difference between these two files? Which one should be used for curvature overlay? Thanks. --Yuhong ============================================================================= Yuhong Jiang yuhong(a)MIT.EDU 617-876-2054 http://web.mit.edu/yuhong/www =============================================================================

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How to display isolated segmented object in Freesurfer viewer
by Shahabuddin Ansari 19 Mar '06

19 Mar '06

Hello, Thanks for answering my previous querry. I have successfully segmented the subcortical regions of the brain. Now, my next simple question is how to display each segmented object separately? I think it is to do with masking, but not sure how to apply that in 3D. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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question about subcortical brain segmentation using Freesurfer...
by Shahabuddin Ansari 18 Mar '06

18 Mar '06

Hello, I am new Freesurfer user. I need to segment subcortical regions of brain and wondering that if there is any doc or tutorial on the subject. I appreciate your comments. Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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