Freesurfer

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30132 discussions

asegstats2table in version 4.2.0 error?
by Jesse Bledsoe 24 Jan '11

24 Jan '11

Hello FreeSurfer group, I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant. When I use the following: asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile aseg_stats.txt I get the following error: 'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/ > > asegstats2table", line 4, in ? > import os; > ImportError: No module named os > Thank you for your time, Jesse (Linux-centos4-stable-pub-v4.2.0) On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe <bledsoej(a)msu.edu> wrote: > Hello, > > I am having difficulty generating an aseg_stats.txt table. > > When I use the following: > > asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile > aseg_stats.txt > > I get the following error: > > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? > import os; > ImportError: No module named os > > > I am on Linux-centos4-stable-pub-v4.2.0 > > Any suggestions are much appreciated, > Jesse > -- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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statistical question
by Ilana Hairston 24 Jan '11

24 Jan '11

Hi there, This is a bit outside the pure technical questions. My subject pool has both boys and girls, with the boys having larger intracranial volume. My results when controlling for gender and intracranial volume however are not the same (obviously, one is a dichotomous variable, the other continuous). Looking at the results, i prefer the latter over the former, more consistent with the literature, and more internally consistent (i.e., brain regions associated with intenalizing sub-scales and the internalizing total scale). But it could be argued that I am removing important variance - maybe stressed out kids have smaller heads? Any recommendation? thanks -- ******************************* peligro! flaca pero mala! ******************************

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fixing cortical parcellations
by Kerstin Pannek 23 Jan '11

23 Jan '11

Dear freesurfer experts I am having some trouble with inaccurate cortical parcellation after autorecon3. Cortical regions seem to be "spilling over" into neighbouring regions (for example supramarginal in inferior parietal as seen in the attachment). How can I manually adjust these errors? Thanks! Cheers Kerstin

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Aseg tables
by Ilana Hairston 22 Jan '11

22 Jan '11

Hi there, I have been using QDEC to create data tables, which i then analyze in SPSS. Mainly because I have missing values on some of my variables, and QDEC doesn't seem to like that. and it has limited statistic capabilities. Anyways... I want to do a sanity check to verify that the regions that are labeled as hippocampus or such, is labeled correctly, but i can't seem to find an annotation table that contains aseg.volume. thx ilana -- ******************************* Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** What might have been is an abstraction Remaining a perpetual possibility Only in a world of speculation T.S. Eliot

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Re: [Freesurfer] Beginner Question on registration process
by Gabriele Arnulfo 22 Jan '11

22 Jan '11

Hi again I've finally found the exact transformation which is ... gather from the original nifti the qfrom matrix (say Qf) and then collect with mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras to index in the freesurfer space. I've finally matched the points. Why mri_info -vox2ras 001.mgz is different (signs mismatch and also qoffset values are different) from the original qform matrix ... they do not suppose, as U have said, to share the same space? Thanks for any support and for your hints. g. 2011/1/21 Douglas Greve <greve(a)nmr.mgh.harvard.edu> > yes, 001.mgz and the DICOM share the same space. > > doug > > > On 1/21/11 9:08 AM, Gabriele Arnulfo wrote: > > Hi all, > > MRI, in this context, i was considering the original DICOM T1 MRI space > before the conversion to 001.mgz file. Is your suggestion still the right > way to solve my task? > > > > 2011/1/20 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> >> I don't know of another way to map control points. By MRI space I assume >>> that you mean the scanner RAS space? Eg, the space defined by the nifti >>> qform? I think this matrix will be >>> >>> L = inv(T)*Q >>> >>> where Q is the scanner vox2ras of the orig volume and T is the tkregister >>> vox2ras of the orig volume. >>> You can get both of these matrices using mri_info. >>> >>> doug >>> >>> >>> Martin Reuter wrote: >>> >>>> Hi Gabriele, >>>> >>>> not sure if there is an easy way (probably Doug knows). But if there >>>> isn't, I wrote a tool mri_map_cpdat to map control points from one space >>>> to another. A control points dat file is a txt file containing >>>> coordinates. The tool will be available in 5.1 where it is used to >>>> transfer manual edits in the longitudinal stream. I could send a copy of >>>> it before. >>>> So you can: >>>> - create a control.dat file with your coordinates >>>> - map it using a lta file. >>>> I am not sure how you can get the lta that you need (from native to >>>> freesurfer conform space) but probably someone else can help with that. >>>> This probably has been discussed before. >>>> >>>> Here is the format of the control.dat: >>>> >>>> xcoord1 ycoord1 zcoord2 >>>> xcoord2 ycoord2 zcoord2 >>>> xcoord3 ycoord3 zcoord3 >>>> info >>>> numpoints 3 >>>> useRealRAS 0 >>>> >>>> >>>> So instead of the coords put your numbers, of course you can have more >>>> than three points. >>>> >>>> Best, Martin >>>> >>>> On Thu, 2011-01-20 at 17:26 +0200, Gabriele Arnulfo wrote: >>>> >>>> >>>>> Hi all, >>>>> >>>>> I'm a new freesurfer user and I've a small question for you all. Which >>>>> the faster and reliable way to map a list of points into the >>>>> freesurfer >>>>> geometrical space? >>>>> I've already read the pdf/ppt but there's no suggestion in there about >>>>> which command should be used (if any). I've read about matlab tools >>>>> that >>>>> could be used for this purpose is it right? >>>>> >>>>> My task is really simple but i cannot figure out which is the best >>>>> way. >>>>> I've got a list of points (basically intra-cerebral electrodes >>>>> coordinates segmented from MRI) in the MRI space and I'd like to >>>>> calculate the respective points in the freesurfer space. >>>>> Cheers, >>>>> >>>>> gabriele >>>>> >>>>> -- >>>>> In a world without wall, how needs WINDOWS?? >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >> >> -- >> In a world without wall, how needs WINDOWS?? >> > > > > -- > In a world without wall, how needs WINDOWS?? > > -- In a world without wall, how needs WINDOWS??

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two issues with the processing stream
by Ilana Hairston 22 Jan '11

22 Jan '11

Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: could not find path! *We looked it up on the freesurfer wiki and there is an entry about this error, but the answer perhaps was not posted. thanks ilana -- ******************************* peligro! flaca pero mala! ******************************

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corpus intrudes into other structures
by Keefe, Helen L 21 Jan '11

21 Jan '11

Hi Everyone, I have frequent cases of the corpus callosum intruding into other structures. I followed directions for "Expand the boundary of an existing region" at https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit#Alternateediti… without success, Then I heard that version 5.0 might solve the problem of structures intruding into others. However, when I used the new version, the entire corpus area was labeled as "none" I returned to the previous version and to "Expand the boundary of an existing region" but am still not able to make it work. I got the path drawn between the two structures, but when I choose "remove from label" on the "Custom Fill" box, the entire brain is labeled as the structure I want to expand. I simply want to relabel the part of the caudalantriorcingulate that has been labeled corpus. Thanks, Helen

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Errors with the "Cut Plane" feature in tksurfer
by Iris.steinmann 21 Jan '11

21 Jan '11

Hello freesurfers, I installed 'freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz' on my ubuntu 10.10 mashine. First I had a little trouble but now it works (thank you Doug!!!), except one little problem: I tried to cut a plane in tksurfer to get a patch. I marked a closed area, pressed the 'cut closed line' button, than click into my area and press the 'fill uncut area' button ….than tksurfer crashed and the following error appears tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Abort I found the same question in the mailing list , but no answer. Is there a solution? Did i made something wrong? Kind regards Iris

1 0

Different sequences in one evaluation
by Gergely Orsi 21 Jan '11

21 Jan '11

Hi Freesurfers, I have a quick question: I have two groups, both measured on the same scanner, with the same sequence (3D MPRAGE), and with almost the same parameters. TR/TE/TI/BW/MATRIX/FOV/FOV-phase/Flip angle/Slice thickness/in-plane resolution... everything is the same, but the number of slices. Total measurement time was also the same. One group was measured with 160 slices, the other with 176. Can I compare the two groups in freesurfer? Thanx, -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi(a)gmail.com

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Sig.mgh to annotation
by Jürgen Hänggi 20 Jan '11

20 Jan '11

Dear FS experts We would like to transform the sig.mgh file to an annotation file in order to extract the thickness value in each individual brain. The problem is that we have 3 clusters in the sig.mgh file and we would like to split these 3 clusters into annotations in order to compute cortical thickness within each single cluster. How to do it? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division 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[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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