Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

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 <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

2 1

Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 22 Sep '11

22 Sep '11

On Tue, Sep 20, 2011 at 15:00, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > what other information would you like? Can you remind me: are you running > on a cluster? Does this happen if you run on your local workstation? Do you > have limits on # of open files? Yes, I am running on a cluster with Gentoo (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) I runs without problems on the same data on a MAC The limits in the cluster are: ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 155648 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 155648 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited Still haven't resolved the problem. I was wondering, is there some way of forcing mri_ca_register to finish fast (to make error tracing easier)? I have tried using -tol [some large numer], but still it takes many hours before reaching the part where talairach.m3z is written (the part that fails). Best, Lauge

1 0

manual editting problem
by Jing Ming 21 Sep '11

21 Sep '11

Hi Bruce and Sita: Thanks for your relay. And Here are the images. Jing From: Jing Ming [mj_coming(a)hotmail.com] Sent: Thursday, September 15, 2011 7:31 PM To: Vy Dinh Subject: FW: [Freesurfer] manual editting problem > CC: mj_coming(a)hotmail.com; jennifer_g_goldman(a)rush.edu; vydinh(a)rush.edu; freesurfer(a)nmr.mgh.harvard.edu > From: fischl(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] manual editting problem > Date: Thu, 15 Sep 2011 20:07:41 -0400 > To: sita(a)nmr.mgh.harvard.edu > > Can you send an image? > > > > On Sep 15, 2011, at 6:38 PM, Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> wrote: > > > > > How does the wm.mgz look. Correcting the white surface will correct the > > pial surface as well. > > > > Sita. > > > > > > On Thu, 15 Sep 2011, Jing Ming wrote: > > > >> > >> Hi Surfers: > >> We have been coming > >> across several gray matter regions that are not included within the pial > >> surface (red line) when it should be (e.g., very anterior parts of the > >> temporal lobe). From my understanding of similar posts on the forum, it > >> seems that there isn't a way to add this region to the pial surface so > >> that the missing brain matter is included. We have tried using the clone > >> tool to fill in this region, as per the tutorial and have experimented > >> with this tool using the tutorial data. I followed the steps in the > >> tutorial but could not observe any changes when the middle button was > >> selected. Does anyone have any ideas on how to troubleshoot this > >> issue? Can someone please explain to me why this is not possible? Also > >> how does Freesurfer determine what regions to include within the pial > >> surface? If there is a way that has been developed recently, please > >> enlighten me. > >> > >> -Jing > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > 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 . 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. >

5 8

Re: [Freesurfer] please help, unsupported slice timing
by Greg Burgess 21 Sep '11

21 Sep '11

We've had a similar issue when using MRIconvert (mcverter) to convert dicom to nifti. Our anatomical images have this slice timing pattern 5, which isn't part of the Nifti standard. Also, mcverter outputs a blank sform matrix, which causes other problems. The easiest fix is to run the following magic: fslmaths /PATH/TO/IMAGE.nii /PATH/TO/IMAGE.nii A potentially better long-term fix is to switch dicom to nifti converters. We've been having success with dcm2nii, which is part of mricron. Good luck, --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

1 0

freesurfer problem?
by Nick Dery 21 Sep '11

21 Sep '11

Hi, I just downloaded the new version of freesurfer (5.1.0) with the hopes of completing hippocampal subfield segmentation. After running my data through the appropriate streams and trying to visualize it, ie: deryn(130)freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt I get the following feedback: freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory Any help would be appreciated. Thanks, Nick

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