Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

tksurfer display
by Peter Glynn 22 Sep '11

22 Sep '11

Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn

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mri_watershed for inner_skull_surface question
by Roderick McColl 22 Sep '11

22 Sep '11

Hi all, Trying to get mri_watershed to give me a good inner_skull_surface, which I want to combine with the pial surface to estimate sulcal CSF, as I don't see any other way. Unfortunately the data I have tested on all generate unreliable inner_skull surfaces. Can anyone provide a tip for optimizing the result? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 2

Discrete and Continuous factors in QDEC
by Antonella Kis 22 Sep '11

22 Sep '11

Hi Doug, One more question please: if I want to do a cortical thickness study between two groups (patients and controls) and I want to eliminate the age and gender what should be my Discrete and Continuous factors in QDEC? Thank you. AK

2 1

Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 22 Sep '11

22 Sep '11

Hi, I am running FreeSurfer on ADNI data and get an error when mri_ca_register attempts to write to transforms/talairach.m3z using gzip. I run the full FreeSurfer pipeline using a bash script containing the following: #!/bin/bash export FREESURFER_HOME=/usr/local/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=/home/lauges/storage /usr/local/freesurfer/bin/recon-all -i /image/data2/ADNI/009_S_0751/MP_RAGE/2006-07-25_12_31_19.0/S17487/ ADNI_009_S_0751_MR_MP_RAGE__br_raw_20060801143246276_1_S17487_I20013.dcm -s 009_S_0751 -all The error appears to happen when mri_ca_register writes using gzip through a pipe and the popen error code is 38. This is not a memory nor a space issue since there is plenty of both available. As far as I now, error code 38 may be related to too many pipes being open at once, but I am not sure of this. Excerpt from 009_S_0751/scripts/recon-all.log: ... GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 38 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Thu Sep 15 23:43:42 CEST 2011 /storage/lauges/009_S_0751/mri mri_ca_register -invert-and-save transforms/talairach.m3z GCAMread: encountered error executing: 'zcat transforms/talairach.m3z' Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux imageserver1 2.6.20-gentoo-r8 #2 SMP Fri May 25 10:23:59 CEST 2007 x86_64 Intel(R) Xeon(R) CPU X5355 @ 2.66GHz GenuineIntel GNU/Linux Best, Lauge

3 2

distortion metric question
by Ritobrato Datta 22 Sep '11

22 Sep '11

Hi All, Is there a way to examine the distortion metric of the freesurfer surface normalization ? Please let me know. Thanks Ri

2 1

time course within ROI
by YUMI MAEDA 22 Sep '11

22 Sep '11

HI, I am trying to get timecourse from each subject within a ROI with GUI as follows, in tksurfer GUI, Tools > timecourse > Write summary of marked vetices/label, I would like to do it command line, would you tell me what line I can use? I tried to use mri_segstats --i ./filtered_func_data.nii --subject subj1 --sum ./test_summary --avgwf test_output --annot subj1 aparc lh --seg ./testaseg-in-func.img the output has 7 columns and does not seems to be timecourse and also it is different from the one that I get when I use GUI as I described above. thank you very much. YUMI

3 10

thickness-age correlation
by Antonella Kis 22 Sep '11

22 Sep '11

Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age 2)what is the best iteration number for the simulation? Should be 5000 or 1000 or greater? 3)why when I run the simulation for 5 iterations I've got zero clusters? 4)can I derive the thickness from the significant clusters of glm analysis? Do I need to run QDEC after GLM? Thanks for any enlightenment. Antonella

2 18

Fwd: FW: flipped orientation in tksurfer and tkmedit
by Ilana Hairston 22 Sep '11

22 Sep '11

from my research assistant - On XXX the coordinates on the right side of the screen in tkmedit always start with a negative number. So that part is correct. Our problem is that the brain is not flipped - if freesurfer displays radiological and SPM8zero displays neurological, then when you compare the 2 side by side, the brains should be mirror images. Ours are not, they are the same. Make sense? On Tue, Sep 20, 2011 at 2:26 PM, Ilana Hairston <hairstonster(a)gmail.com>wrote: > could you check this? > this a followup on my original email after looking at 110???yl with Barbara > and Steve. > thanks > i. > > On Tue, Sep 20, 2011 at 2:23 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> What are the talairach coords for the left hemi? The first coordinate (x) >> should always be negative. >> doug >> >> Ilana Hairston wrote: >> >>> Hi Doug, >>> No, we had the lh loaded in tksurfer, and when saving a point it showed >>> up on the _left_ in tkmedit (i.e., the right side). >>> thanks >>> ilana >>> >>> >>> On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara < >>> bweiland(a)med.umich.edu <mailto:bweiland@med.umich.edu**>> wrote: >>> >>> >>> -----Original Message----- >>> From: freesurfer-bounces(a)nmr.mgh.**harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer-bounces@**nmr.mgh.harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu> >>> > >>> [mailto:freesurfer-bounces@**nmr.mgh.harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu> >>> <mailto:freesurfer-bounces@**nmr.mgh.harvard.edu<freesurfer-bounces(a)nmr.mgh.harvard.edu>>] >>> On Behalf Of >>> Douglas N Greve >>> Sent: Wednesday, September 14, 2011 6:10 PM >>> To: Ilana Hairston >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.**harvard.edu<freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> >>> Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit >>> >>> When you say on the "right hemi in tkmedit" do you mean on the >>> right side of the image (which is the left side of the brain)? >>> doug >>> >>> Ilana Hairston wrote: >>> > Hi there, >>> > We recently had a problem that tksurfer and tkmedit were flipped >>> > relative to each other. Basically, when saving a point in the left >>> > hemisphere in tksurfer it it loaded in the right hemisphere in >>> tkmedit. >>> > Any ideas how this could have happened? >>> > Thanks >>> > 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 <tel:734-232-0232>; Mobile: 650-906-8449 >>> <tel:650-906-8449> >>> >>> >> >>> >> ******************** >>> >> Reminder: Women do 66% of the work worldwide, earn 10% of the >>> income, >>> >> and own 1% of the world's property >>> > >>> > >>> > >>> > >>> ------------------------------**------------------------------** >>> ---------- >>> > -- >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> Fax: 617-726-7422 <tel:617-726-7422> >>> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> >>> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> 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<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. >>> >>> >>> >>> >>> -- >>> >>>> ****************************** >>>> 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 >>>> >>>> ******************** >>>> Reminder: Women do 66% of the work worldwide, earn 10% of the income, >>>> and own 1% of the world's property >>>> >>> >>> >>> ------------------------------**------------------------------** >>> ------------ >>> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> > > > -- > > ****************************** > 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 > > ******************** > Reminder: Women do 66% of the work worldwide, earn 10% of the income, and > own 1% of the world's property > > > -- ****************************** 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 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

2 3

Manual editing after recon-all
by Sindhuja Tirumalai Govindarajan 22 Sep '11

22 Sep '11

Hi all, I ran into an issue similar to the manual editing problem discussed yesterday and earlier today. The pial surface seems to cut into the gray matter regions. However, there seems to be no wm problem in the neighborhood. Are there any tools to fix this? I have attached snapshots for your reference. Any advice on how to include the gray matter would be helpful! Thanks, Sindhuja

3 8

Stupid FsFastTutorialV5.1/TutorialData question
by Carl Anderson 22 Sep '11

22 Sep '11

Dear Free Surfer, At the bottom of http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/TutorialData it is stated: "You will also need to link the FreeSurfer<http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> anatomical subjeccts (data in fsfast-tutorial.subjects) into your $SUBJECTS_DIR" My stupid question: Could this be accomplished by creating subdirectories or links in $SUBJECTS_DIR? Thanks, -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Freesurfer September 2011