Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

aseg, aparc regions reference table (aka "data dictionary")?
by Graham Wideman 22 Dec '06

22 Dec '06

Folks: It would be *really* great if there was a page somewhere (or just a file) giving some info on the various measures that are captured in the aseg and aparc files. For each measure (in the table or the "comments" above the table): -- Description of what it includes -- some are obvious from the name, others not. -- Whether it's deprecated. -- Whether FS V-whatever actually produces this value, or just zero. (Very useful, and probably not too much work? Plus I'd like to adapt this info so as to pull only the non-inert rows from the data file). (Or is there some other way to determine this?) -- Some suggestions on what numbers need to be added to get popular subtotals. I've just read through the last six months of freesurfer list traffic, and I see numerous questions along these lines... and replies with some clues here and there. Also references to papers, but these don't detail the nitty gritty of what FS V-something actually does. Probably numerous users would get a lot of use out of having this info in one place. Thanks, Graham

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maybe a problem of tcl
by lv bin 21 Dec '06

21 Dec '06

hi, I am a newcomer of freesurfer.Sereral days ago,I installed the freesurfer(its version is freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4),and practiced the data "bert"with tkmedit,tksurfer,it works ok. These days ,I meet a problem about tksurfer.At first,I run the command %tksurfer bert lh white it's good to show the surface ,and then when I try to load the Curvature " lh.curv",the tksurfer interface is closed suddenly,and the wrong information that appears on the termial is that %alloc:invalid block: 0xb1ea60: 0 0 75 Abort I googled this with"alloc:invalid block",maybe it is a problem of "tcl",but I don't know how to slove it,any suggestion would be appreciated! Best wishes! lvbin

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GLM - Multiple Comparisons
by David Zai 21 Dec '06

21 Dec '06

In running a glm analysis with multiple classes (A, B, C, D, E, F) and no variables, is it better to: (1) have one fsgd with a contrast vector of (1 -1 0 0 0 0) to compare Group A thickness to Group B thickness, or (2) should I make an fsgd with just my Group A and B subjects and have my contrast vector (1 -1)? We ran both options to compare Group A and B as an example and the results of each are extremely similar but there are some very minor differences in the significance maps. We're wondering about the two methods because we eventually want to compare every two-group pairing (A vs C, A vs D, E vs F, etc.), and was wondering whether one method is more accurate or preferred over the other when we try multiple group comparisons. Also, could there be a randomizing effect that causes the slightly different maps for our example? Thanks. David

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unpacksdcmdir & multiple volume protocols
by Sebastian Moeller 21 Dec '06

21 Dec '06

Hi Doug, hi List, I ran into slight problems with unpacksdcmdir. I acquired some combined proton density and T2 volumes with one sequence (plus a bunch of additional slices from Inline/generic tab on out allegra menue), which resulted in mri_convert choling at the import of the second part of the series. In other words the proton density volume was imported fine, but the T2 and the MIP images did not make it into the target directory. Now I sit on a bunch of these things, where I am really interested in the T2s, but all freesurfer imports are the PDs (whichg are nice to have). So is this a known prblem with work arounds or is this a case of "don't do that then"? On a related note, I tried mri_convert to convert bfloat stacks into 3d analyze (from 1 stack per slice containing all time points, to one stack per timepoint containing all slices) while using --in_orientation (to correct for our inability to select the proper patient orientation); and lo, all that was converted was the first timepoint (I did not specify any specific frame, and was therefore expecting all time points to appear). Interestingly, doing the format conversion first and the "--in_orientation" thing later on the .img works like a charm, I am now puzzled whether this is the right behaviour. I am more than willing to test anything out or send test images if that helps... Anyway, thanks for the nice tools and the great support Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_annotation2label
by Ran Tao 20 Dec '06

20 Dec '06

Hi All, When I ran mri_annotation2label --subject UNC_4 --hemi rh --labelbase ./labels/aparc-rh --table $FREESURFER_HOME/surface_labels.txt Some labels are always skipped such as 6,7... I also tried on tutorial data, the same thing happened. Any ideas? Is surface_labels.txt a complete label list I should use? I also want to add some own labels(not extract them from annot), and cannot figure it out. How can I do this? Thanks in advance, Ran

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surfaces
by Daniel G. Wakeman 20 Dec '06

20 Dec '06

Hi freesurfers, I have a question. I deleted some of the optic nerve on a participant and ran source /usr/local/freesurfer/nmr-std-env cd /space/doodles/3/users/dwakeman/pilot/again setenv SUBJECTS_DIR `pwd` recon-all -autorecon2-wm -autorecon3 -subjid p001 -mail dwakeman When the surfaces were regenerated the optic nerve was still present in the surfaces. Can someone please take a look at this and tell me what I'm doing wrong? This has repeated on several other participants; however, I need a couple more edits on those participants. Thanks, Dan

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Can Tkmedit use a certain parcellated cortical area?
by Bum Seok Jeong 20 Dec '06

20 Dec '06

Hi! I'd like to see a certain parcellated cortical area, for example, right inferior frontal gyrus (Rt IFG).., using Tkmedit. After that, I'd like to use a certain cortical area, Rt IFG, as ROI which could be used in measuring functional activity, fa value so on. Is it possible? Thank you for advance. bsjeong

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faster mri_parse_sdcmdir?
by Keith Schneider 20 Dec '06

20 Dec '06

I've been using mri_parse_sdcmdir for a long time to convert my dicom files to nifti or analyze. It takes 10 minutes or more on my G5 Mac for an entire data session. Some other Mac tools like Osirix and Neurolens can read in all of the dicom files and parse them in a few seconds. It seems like mri_parse_sdcmdir spends most of its time parsing the dicom files and reading the headers. Is there some way to speed this up? I'm not complaining, just inquiring. There are some programmers here that may be able to help. The source for Neurolens is available, for instance. I found another program on the web, dinifti that seemed like it was going to be pretty fast, but then it died with a segmentation fault. keith

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NIfTI format conversion
by Kirk, Gregory 19 Dec '06

19 Dec '06

Hi All , I am using mri_convert to convert Siemens 30 direction diffusion data into NIfTII for proc. with fsl. mri_convert does it well except that it is a bit problematic that it comes out in neurological convention. Also the tools is fsl do not seem capable to change the orientation to radiological convention. I want to use a structural cooregistered to the diffusion b0 to navigate for placing seeds for stochastic tract processing. mri_convert takes my Siemens structurals and puts them in NIfTI files that are oriented completely wrong, upside down etcetera. Obviously mri_convert knows how to read Siemens structurals ... it's does it all the time for freefurfer processing. So I take analyze 7.5 format structurals and it comes out in radiological convention and fsl tools are incapable to change these into neurological convention ! so a bit of a sticky wicket, of course it would be nice if fsl would support it's own tools for data inport, but as far as I know they do not. NIfTI code from COX et. al. is well.... as he puts it himself Klingon software, Klingon's that fell on their head anyway. it is not organized well enough to spend the time to see if anything usable is there. I guess the q-form or s-form are not set such that the fsl tools can work with 7.5 or mri_convert produced files. any way to get correctly oriented NIfTI structurals or to reorient the diffusion data to radiological. cheerio Greg.

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MRInormalize: could not find any valid peaks
by Juergen Haenggi, Psychiatrische Uni-Klinik 19 Dec '06

19 Dec '06

Dear Freesurfer users While running recon-all, the following error occured: #-------------------------------------------- #@# Intensity Normalization Sat Dec 16 13:10:39 CET 2006 /scratch/bli/AN1792/subjects/Patient02_2002/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.796 -0.256 -0.057 -8195.100; 0.086 0.398 -0.583 12578.642; 0.224 0.596 0.440 21656.441; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux node0214 2.6.15.6-id-x86_64-k8-smp #1 SMP Wed Mar 22 12:35:20 CET 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Dec 16 13:10:41 CET 2006 If I try to check the talairach.xfm with tkregister2, I see only a little part of the brain in the left upper corner of the graphic window. Because the DICOM files used were converted from ANALYSE files, I guess that there is a problem with the coordinate origin of the DICOMs. Could it be that this is the cause of my problem? The transformation matrix seems also not OK. Because I have about 250 brains which is the fastest way to fix that problem? Thanks in advance Best regards Juergen ----------------------------------------------- Juergen Haenggi, Ph.D. student Psychiatric University Hospital Division of Psychiatry Research University of Zurich, Switzerland PO Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------

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