Freesurfer

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30132 discussions

averaging DTI sequences
by Jose Luis Cantero Lorente 16 Oct '09

16 Oct '09

Dear Freesurfers, I have 2 identical DTI sequences for each patient (adquired within the same session), but would like to work with the average DTI sequence in all my subsequent analysis. How to obtain the average of both DTI sequences with Freesurfer, and convert the resulting file into .nii? Does the resulting nii file change the brain hemispheries? Thanks in advance. Best regards, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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test message
by Christophe Destrieux 15 Oct '09

15 Oct '09

-- 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] images with poor resolution
by Dana W. Moore 15 Oct '09

15 Oct '09

Hi Nick, After trying all of the steps below, the surfaces are much improved, but the pial surface still has problems, particularly in the temporal lobes (see below). So, maybe this is the best we can do with this image. Thank you for helping out with this. Thanks, Dana [] At 06:58 PM 10/5/2009, Nick Schmansky wrote: >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 > > > > 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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Re: [Freesurfer] transverse gyrus and translucent brain renderings (fwd)
by Bruce Fischl 15 Oct '09

15 Oct '09

>From Christophe.... ------------------------ 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. -- 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] isxconcat-sess
by Maximilien Chaumon 15 Oct '09

15 Oct '09

Hi freesurfers, I've been running isxconcat-sess with this line chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf subjlist.txt -analysis Analyse_Simple_Confidence -c High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 I was expecting to find a directory called osgm in the specified analysis directory with which I could feed data to mri_glmfit, but I can't find it. /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor The log file is attached. I don't find "error" in the text. Where am I wrong? Is there any mri_glmfit-sess like script somewhere? It's going to be pretty tough to find each parameter to feed to mri_glmfit... Thanks, Max

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process dying during longitudinal reconstruction
by Dana W. Moore 15 Oct '09

15 Oct '09

Hi everyone, I am trying to run the longitudinal stream on some images. I have 3 timepoints, and 2 of them finished the stream just fine, but a third quits during autorecon1 during the 3rd and final longitudinal step. There is no error message or anything, it just stops. The log file is attached--any insight into what is going wrong will be appreciated. Thanks, Dana

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Inflation Transformation
by Tina Jeon 15 Oct '09

15 Oct '09

Hello FreeSurfers, I have inflated a couple surfaces less so that the gyri and sulci are more prominent on the surface using the parameters: mris_smooth -a 70 -n 70 -nw ./subj/surf/lh.white ./subj/surf/lh.smoothwm mris_inflate -n 5 ./subj/surf/lh.smoothwm ./subj/surf/lh.inflated mris_curvature -w -a 70 -thresh .999 -distances 10 10 ./subj/surf/lh.inflated Which seemed to do the trick, however, when I viewed the surfaces on the 3D surface generator Amira, I realized that inflating less caused the left and right surfaces to shift toward each other when viewed on the same coordinate system. The left and right surfaces must have been translated somewhere in the inflation process. How do I put them back into the correct coordinate space that the pial and white surfaces are? Thank you. Tina Jeon, M.S. Project Supervisor UT Southwestern Medical Center Advanced Imaging Research Center 2201 Inwood Road, NE 3.2 Dallas, Texas 75390-8568 Office (214) 645-2766 Fax (214) 645-2744 Cell (310) 592-1853 tina.jeon(a)utsouthwestern.edu

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Edits in the longitudinal stream
by hakon.grydeland＠psykologi.uio.no 15 Oct '09

15 Oct '09

Hi, I have a couple of questions regarding manual edits such as deleting non-brain tissue included in the pial surface in the longitudinal stream (v4.5): 1. Where in the longitudinal stream would you recommend doing edits? On the brainmask.mgz of the base? 2. If so, would you then re-run the base as a cross-sectional (recon-all -s baseid -autorecon2-pial -autorecon3)? Thanks, Håkon

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Re: [Freesurfer] transverse gyrus and translucent brain renderings
by Nick Schmansky 15 Oct '09

15 Oct '09

forwarding to the list.... 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 - Faculté de Médecine - 10 Bd Tonnellé > 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 > >> > >> > >> > > > > > >

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a question about mri_label_volume -eTIV
by Guang Zeng 14 Oct '09

14 Oct '09

Hi, there, >From FS Wiki, eTIV - estimated Total Intracranial Volume, aka ICV, I read mri_label_volume requires specifying the transform file to use, and the scale factor: mri_label_volume -eTIV \ $sdir/transforms/talairach.xfm 1948 \ $sdir/aseg.mgz 17 53where $sdir is the path to the subject's mri directory (ie, $SUBJECTS_DIR/<subjid>/mri). The '17' and '53' are label ID's, in this case left and right hippocampus (see the subjects /stats/aseg.stats file for IDs). The output will look like: using eTIV from atlas transform of 1528 cm^3 processing label 17... 3822 voxels (3822.0 mm^3) in label 17, %0.250119 of eTIV volume (1528075) processing label 53... 4410 voxels (4410.0 mm^3) in label 53, %0.288598 of eTIV volume (1528075)>From a previous post at FS mailing list, I also read something similar, Just as an aside, once you have a talairach_with_skull.lta file (whether from v3 or v4), you can calculate eTIV as scale_factor/determinant(lta), where the scale_factor employed is 2150. Just want to know where dose this scale factor number 1948 and 2150 come from? Thanks a lot! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/

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