Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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Using peak activation voxels to determine structural areas of interest
by Nathan Dankner 01 Jun '10

01 Jun '10

Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks, Nathan

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(no subject)
by Guang Zeng 28 Jan '10

28 Jan '10

Hi, there, I want to know how the FS GCA atlas looks like, is there a way to load the FS GCA Atlas and view it using tkmedit or matlab? Is it possible to replace FS Atlas with our own Atlas and use it for analysis? Thanks a lot! Guang _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://www.microsoft.com/windows/pc-scout/default.aspx?CBID=wl&ocid=PID2472…

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Re: [Freesurfer] images with poor resolution
by Nick Schmansky 25 Jan '10

25 Jan '10

Dana, First I would run: recon-all -s subid -clean to remove any prior control points and edits. Then I would open nu.mgz: tkmedit subjid nu.mgz and *sparingly* put control points well into white matter areas on a few different slices. you only need a half dozen or so. to add control points, see: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints except you will add them to nu.mgz, to make sure that T1.mgz gets created properly. Then create a file name xopts.txt containing these lines: mri_normalize -gentle Then run: recon-all -s subjid -autorecon1 -expert <path_to>/xopts.txt and when done, open brainmask.mgz tkmedit subjid brainmask.mgz and check again to get a sense of the low value for white matter and high value for gray matter, then run: recon-all -s subjid -autorecon2 -seg-wlo wlo -seg-ghi ghi replacing wlo and ghi with those values. if the surfaces still look bad, you can add a line to the xopts.txt file : mris_make_surfaces -max_gray val -min_gray_at_white_border val replacing the two 'val's with something you find appropriate, then run: recon-all -s subjid -autorecon2-pial -autorecon3 \ -expert <path_to>/xopts.txt good luck! Nick On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > Hi Nick, > > Below is Bruce's response to a problem I'm having with the gray/white > segmentation. (Pasted below, you can see the brainmask.mgz volume and > surfaces--the entire brain is labeled as white matter). I could use > some guidance in carrying out his advice. He says to adjust the > intensity normalization using control points and then use expert opts > for mri_segment and mris_make_surfaces. > > When I look at the brain.mgz volume, the white matter tends to have an > intensity of 110, as it should, but the gray matter at times goes as > high as 115. I was thinking, I could set ghi to 115 and wlo to 110. > Then, I am not sure how to actually run the corrections and what > language to use to implement the control points and mri_segment > adjustments. I will save control points and then run: recon-all > -autorecon2-cp -autorecon3 -subjed <subject>. Can I somehow include > the mri_segment adjustments into this command, or do I have to run > that separately? > > I am also not sure how options for mris_make_surfaces might help. > > I appreciate your help with this! > > Thanks, > dana > > > > > [] > > At 04:40 PM 10/2/2009, Bruce Fischl wrote: > > Hi Dana, > > > > it looks like the gray/white density estimation failed. Try setting > > them with the expert opts for mri_segment and mris_make_surfaces > > (Nick can point you in the right direction if you can't figure it > > out). Things like max gm at white border and such. > > > > cheers, > > Bruce > > > p.s. it also looks like the intensity normalization went too far due > to the low contrast. You'll probably need to add some control points > and run it with the -gentle option > > > > > On Fri, 2 Oct 2009, Dana W. Moore wrote: > > > > > Hi everyone, > > > > > > I am trying to salvage some images that were done with poor > > > gray/white boundary contrasts. First, FreeSurfer includes an area > > > of dura in the skull strip. I tried adjusting the watershed but > > > it made no differences. FreeSurfer is subsequently unable to > > > detect the gray/white boundary and labels the dura as cortex: > > > > > > [] > > > > > > > > > > > > Looking at the raw images, the gray/white boundaries are faint but > > > visible. Is there anything I can adjust to try to make this work > > > with FreeSurfer? > > > > > > Thanks, > > > Dana > > > > > > > > > Dana W. Moore, Ph.D. > > > Neuropsychology Fellow > > > Cornell Neuropsychology Service > > > Weill Medical College of Cornell University > > > New York Presbyterian Hospital > > > Department of Neurology & Neuroscience > > > 428 East 72nd Street, Suite 500 > > > New York, NY 10021 > > > Phone: 212-746-2823 > > > Fax: 212-746-5584 > > > Email: dwm2003(a)med.cornell.edu > > Dana W. Moore, Ph.D. > Neuropsychology Fellow > Cornell Neuropsychology Service > Weill Medical College of Cornell University > New York Presbyterian Hospital > Department of Neurology & Neuroscience > 428 East 72nd Street, Suite 500 > New York, NY 10021 > Phone: 212-746-2823 > Fax: 212-746-5584 > Email: dwm2003(a)med.cornell.edu > >

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fsaverage to mni152
by Yigal Agam 17 Dec '09

17 Dec '09

Hi, What's the best way to convert an fsaverage volume into an MNI152 volume that can be viewed on top of a standard brain (MNI152_T1_2mm_brain.nii.gz) in fslview? Thanks, Yigal

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4.5 and 4.4 longitudinal base creation error from mri_concatenate_lta
by Matt Erhart 09 Nov '09

09 Nov '09

Hello everyone, %% After running this command with v4.5 and v4.4: recon-all -base FREESURFERRECON_TEST_005_S_ 0221BASE45 -tp FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1 -tp FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1 -all -force %% I get this error: %%%%%%%%%% mri_concatenate_lta -invert1 FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta identity.nofile FREESURFERRECON_TEST_005_S_0221BASE45_to_FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs %%%%%%%%%% Any ideas on how to solve this? A side note for other troubleshooters: getting to this stage takes around 5 minutes with 2 subjects and around 90 minutes with 3. thanks! Matt

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masking out ROIs on the surface
by Mishkin Derakhshan 07 Nov '09

07 Nov '09

Hello list, I would like to create a mask on fsaverage/surf/?h.pial that masks out the areas where the surface does not follow the cortex, but is just cutting across the mid line or across the brain stem. I know Freesurfer does this to maintain the surface toplogy, and I think it only does this in these two areas. Does a simple txt file with n vertices and a 0 or 1 value at each vertex exist somewhere? Has anyone on the list bothered to label this area manually and would be willing to share? thanks, mishkin

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comparison of mean thickness of gyri in two groups
by Mehul Sampat 02 Nov '09

02 Nov '09

Hi Folks, If am comparing the mean thickness for certain gyri (pre-central, post-central) in a controls versus patients. I obtain the thickness measurements from lh.aparc.a2009s.stats and rh.aparc.a2009s.stats I was wondering if I need to normalize these thickness measurement with the estimated total intracranial volume (eTIV) ? Or has anyone reported that the these are independent of eTIV ? If so then as I understand I would only need to account for age and gender in any subsequent analysis using GLM. Thanks Mehul

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editing grey matter or white matter
by karlkarl 30 Oct '09

30 Oct '09

Hello, freesurfer experts: I attached one sample picture of the results from autorecon2. In the bottom of right hemisphere, both the red and yellow line shrink, leaving some tissue outside. How should I fix these since it involves both grey matter and white matter editing? thanks Karl _________________________________________________________________ 全新 Windows 7：寻找最适合您的 PC。了解详情。 http://www.microsoft.com/china/windows/buy/

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Re: [Freesurfer] transverse gyrus and intermediate sulcus
by Narly A Golestani 30 Oct '09

30 Oct '09

Hi Chrisophe, Thanks very much for your answer but I'm not sure I understand. I see the below labels in the '?h.aparc.a2005s.annot' label files generated by freesurfer version 4.4 as well as in those generated by freesurfer version 3.0.5: 'S_temporal_transverse' 'G_temp_sup-G_temp_transv_and_interm_S' In the 'default' label file (ie; 'lh.cortex.label' and 'rh.aparc.annot') of the output generated by both of these versions of freesurfer, I see the following labels only: '?h_transversetemporal'. In sum, I'm not sure how the atlases that you've mentioned below relate to the 'default' versus '2005a' versions of the label files, and also how they relate to different version of freesurfer. If the 'atlas2002_simple.gcs' atlas is used to generate the 'default' labels (ie; '?h.cortex.label'), then I'm not sure why I don't see the 'G_temp_sup-G_temp_transv_and_interm_S' amongst the labels generated by freesurfer version 3.0.5. I'm also not clear on how this changed between versions 3.0.5 and 4.4 - I would expect to see different labels between the 2 versions, but I don't. I have another, related question: I would also like to know if there is a way of seeing whether an intermediate sulcus was detected at all or not for a particular brain/hemisphere (eg; there should not be any detected if there is only one transverse temporal gyrus). In other words, I would like to know when freesurfer detected multiple transverse gyri and when it did not. thanks very much in advance, and all the best, Narly. On Thu, 15 Oct 2009, Christophe Destrieux wrote: > Hi Narly > > Hello Christophe, hello all, > > > > I would like to know if the way that the transverse gyrus is labelled in > > freesurfer, and specifically the fact that in the case of multiple > > transverse gyri only the more anterior transverse temporal gyrus (ie; > > Heschl's gyrus) is included, has changed across different releases of > > freesurfer, or if it differs between the different atlases used by > > freesurfer. I ask this because I see a somewhat different pattern of > > results in this part of the brain when comparing output generated by > > freesurfer version 3.0.5 and version 4.4. > > > the changed occured in 2005; but both atalases (atlas2002_simple.gcs and > atlas2005_simple.gcs) were distributed for a while) > > In the 2002 version the parcellation was indeed different : > > * When several transverse temporal gyri were present they were > grouped together in a common label with the sulcus limiting them > (G_temp_sup-G_temp_transv_and_interm_S) > * The sulcus posterior to this label was then labeled > "S_temporal_transverse" > > I hope that it helped > > More generally, I would like to know if there is any version of > > freesurfer, or any atlas, that includes multiple transverse gyri when they > > exist (ie; that does NOT exclude the more posterior one in cases of > > multiple transverse gyri). > > > > > thanks in advance and best wishes, > > Narly. > > > > > >> On Thu, 2009-08-06 at 20:57 +0200, Christophe Destrieux wrote: > >> > >> > >>> Hi Narly > >>> > >>> below are a few explanations on the transverse temporal gyrus in the > >>> a2005 parcellation > >>> > >>> At the superior aspect of the superior temporal gyrus: > >>> > >>> * the transverse temporal *sulcus* limits the planum temporale > >>> (posteriorly) from the transverse temporal gyrus (anteriorly); it > >>> originates at the posterior segment of the lateral sulcus, runs > >>> anterior and lateral and joins the lateral aspect of the temporal > >>> lobe. > >>> > >>> * The transverse temporal gyrus (or Heschl's gyrus) is just anterior > >>> and parallel to the transverse temporal sulcus. Instead of a > >>> single transverse temporal gyrus, several �transverse� temporal > >>> gyri bordered by intermediate sulci may be present. Only the more > >>> anterior transverse temporal gyrus is labeled in Freesurfer, the > >>> posterior ones being included in the planum temporale since they > >>> where shown not to correspond to primary, but to secondary > >>> auditory cortex > >>> > >>> I hope that it helped > >>> > >>> cheers > >>> > >>> -- > >>> Christophe Destrieux > >>> Laboratoire d'Anatomie - Facult� de M�decine - 10 Bd Tonnell� > >>> 37032 Tours - France > >>> tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > >>> > >>> > >>>> Narly, > >>>> > >>>> I'm forwarding this to Christophe Destrieux, cc'd, who I think can > >>>> answer your question about how that region is labelled. > >>>> > >>>> It is not possible to do translucent viewing in tksurfer. However, it > >>>> is possible in qdec. Just use the load surface and load annotation menu > >>>> options. > >>>> > >>>> Nick > >>>> > >>>> > >>>> On Thu, 2009-08-06 at 16:26 +0100, Narly A Golestani wrote: > >>>> > >>>> > >>>>> Hello, > >>>>> > >>>>> I would like to know more about the automatic labelling of the transverse > >>>>> temporal gyrus is done. I looked at the below article but don't see any > >>>>> details about this structure. > >>>>> > >>>>> https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf > >>>>> > >>>>> I would for example like to know how the boundaries of this structure are > >>>>> defined/determined. > >>>>> > >>>>> Also, when using tksurfer to view labels ('import annotation'), is it > >>>>> possible to make the 3D brain surface (and labels) translucent so that one > >>>>> can more carefully view where this (medial-spanning) gyrus was identified? > >>>>> > >>>>> thanks in advance, > >>>>> Narly. > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>> > >> > > > > ==================================== > > Narly Golestani > > Institute of Cognitive Neuroscience > > 17 Queen Square > > London WC1N 3AR > > United Kingdom > > Tel: +44 (0)20 7679 7529 > > ==================================== > > > > > > > -- > Christophe Destrieux > Laboratoire d'Anatomie - Facult� de M�decine - 10 Bd Tonnell� > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > ==================================== Narly Golestani Institute of Cognitive Neuroscience 17 Queen Square London WC1N 3AR United Kingdom Tel: +44 (0)20 7679 7529 ====================================

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Freesurfer October 2009