Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

qdec problem
by Hannah 08 Feb '10

08 Feb '10

Hi, I have a problem using qdec, which I don't know how to solve- I get the following error message: Error in Analyze: command failed: mri_glmfit --y /Users/Hannah/ Borderline/subjects/qdec/Untitled/y.mgh --fsgd /Users/Hannah/ Borderline/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /Users/ Hannah/Borderline/subjects/qdec/Untitled --surf fsaverage lh --C / Users/Hannah/Borderline/subjects/qdec/Untitled/contrasts/lh-Avg- Intercept-thickness.mat --C /Users/Hannah/Borderline/subjects/qdec/ Untitled/contrasts/lh-Avg-thickness-alter-Cor.mat --C /Users/Hannah/ Borderline/subjects/qdec/Untitled/contrasts/lh-Diff-BPD-KG-Intercept- thickness.mat --C /Users/Hannah/Borderline/subjects/qdec/Untitled/ contrasts/lh-Diff-BPD-KG-Cor-thickness-alter.mat --C /Users/Hannah/ Borderline/subjects/qdec/Untitled/contrasts/lh-Diff-NonPTSD-PTSD- Intercept-thickness.mat --C /Users/Hannah/Borderline/subjects/qdec/ Untitled/contrasts/lh-Diff-NonPTSD-PTSD-Cor-thickness-alter.mat --C / Users/Hannah/Borderline/subjects/qdec/Untitled/contrasts/lh-X- diagnostik-PTSD-Intercept-thickness.mat --C /Users/Hannah/Borderline/ subjects/qdec/Untitled/contrasts/lh-X-diagnostik-PTSD-Cor-thickness- alter.mat Do you have any suggestions? Thanks a lot! hannah ----------------------------------------------------------------------------------------------- Dr. Hannah Bruehl Freie Universität Berlin Emotionspsychologie und affektive Neurowissenschaft Habelschwerdter Allee 45 - Raum JK 25/222h 14195 Berlin +49 30 838 564 72 -----------------------------------------------------------------------------------------------

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Error mris_thickness_diff
by Jürgen Hänggi 08 Feb '10

08 Feb '10

Dear FS experts when running mris_thickness_diff the following error occurred: mris_thickness_diff \ ? -src_type curv \ ? -out amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness_diff.mgh \ ? -register \ ? -abs -S amblyo_pat01_tp3.long.amblyo_pat01_base1_3 \ ? -L amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh_thickness_diff.log \ ? amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.white \ ? amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.thickness \ ? amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.white \ ? amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness Output differences to file amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness_diff.mgh Do a rigid alignment of two surfaces before mapping to each other logging results to amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh_thickness_diff.log Reading first surface file amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.white Surface1 has 137991 vertices Reading in first data file amblyo_pat01_tp3.long.amblyo_pat01_base1_3/surf/lh.thickness Reading second surface file amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.white Surface2 has 137991 vertices Reading in second data file amblyo_pat01_tp1.long.amblyo_pat01_base1_3/surf/lh.thickness Register surface 2 to surface 1 (rigid mapping using ICP) ERROR: FindClosest: MHTfindClosestVertexNo returned annIndex=-1, which is invalid! What does it mean? 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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Segmentation fault?
by Raghav Puranmalka 08 Feb '10

08 Feb '10

Hi all, I am running recon-all as follows: recon-all -subjid subj1 -all and (after about 4 hours of running,) get this error: 0516: dt=0.000000, rms=0.507 (0.000%), neg=0, invalid=766 Segmentation fault ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Sat Feb 6 02:56:03 EST 2010 /usr/local/freesurfer/subjects/be496/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 It seems that perhaps this is because it cannot find "transforms/talairach.m3z" - indeed, this file doesn't exist. But should this be something generated by recon-all? Should I be running recon-all differently? Thanks for your help, Raghav

2 1

longitudinal design
by Casper van Oers 07 Feb '10

07 Feb '10

Hi, I am trying to specify a longitudinal design in an fsgd file. there is 2 groups and each subject has 3 timepoints. can I use a similar approach as paired-diff in the tutorial, but now using 3 timepoints like this: GroupDescriptorFile 1 Title ALL_subjects Class Stroke Class Control Input subject1 Control Input subject1_time2 Control Input subject1_time3 Control Input subject2 Stroke Input subject2_time2 Stroke Input subject2_time3 Stroke ... as I fear the approach above will not work, is there another way? thanks, casper -- Casper A.M.M. van Oers, MD Department of Neurology, C03.236 University Medical Centre PO Box 85500 3508 GA Utrecht the Netherlands T: +31 30 2503184 F: +31 30 2542100 (Dept. of neurology)

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question, how to copy the liscence.
by jijun wang 06 Feb '10

06 Feb '10

Dear expert, I can not find the file of ".license" in the Freesurfer folder when I finishing the installation. who could give me some hints? Thanks a lot. -- Best regards, Jijun Wang, MD & PhD Shanghai Mental Health Center 600 Wanping Road Shanghai 20030, China. E-mail: jijunwang27(a)gmail.com

2 1

user specified output orientation using mri_convert?
by Michael Harms 05 Feb '10

05 Feb '10

Hello Doug, Is it possible using mri_convert to just reorder the way in which the data is stored, without any resampling of the actual voxel values? i.e., I have Siemen's MPRAGE DICOMs, and if run mri_convert, I get a default "PIL" orientation. I would like to just reorder the way in which the data is stored, to get a "LAS" orientation instead. I tried using "--out_orientation LAS", but that does a resampling (interpolation) such that the resulting xform has strictly 0's on the off-diagonal. And reading the mri_convert help, it clearly states that the --out_orientation flag is to be used when the input orientation is WRONG, which is not the case here (since I presume that the input orientation is correctly read out of the DICOMs). I tried "--reorder 2 1 3", to see what effect that has on a file already in nii format, but I got the message: in nii format, but I got the message: reordering axes... MRIreorder: incorrect dst width error reordering axes I've checked the archives, and read through the mri_convert help, but just can't seem to figure out if reordering from one orientation to another (without resampling) is possible using mri_convert. thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Difference in sub-cortical volumes
by Walimuni, Indika S 05 Feb '10

05 Feb '10

Hi I noticed in my FreeSurfer runs, that there is a significant volume difference for sub-cortical structures obtained using the aseg.stat file and the mri_binaraize command. For example I got 14454mm3 for Thalamus-Proper (obtained by summing up the values for Left_Thalamus-Proper and Right-Thalamus-Proper) using aseg.stats file. For the same subject I got 15091mm3 using the command " mri_binarize --i aseg.mgz --match 10 --match 49 --o Thalamus-Proper_mask.nii.gz". Is this normal ? If so what is the most accurate method ? Thanks in advance, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX.

2 1

sliver problem remains after going through relevant wiki page
by dahlia＠nmr.mgh.harvard.edu 05 Feb '10

05 Feb '10

Hi, I have just installed freesurfer on a CentoOS5 virtual machine (VMware), where the host OS is Windows. I am experiencing the "sliver problem" - only a sliver of the brain is being rendered to view. I have gone through the steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems, as follows: 1. NVidia driver update: the virtual machine doesn't have a /usr/bin/nvidia-installer, but I updated the driver installed on the host machine. Is this good enough, or should I update it somewhere under the virtual machine too? 2. doublebufferflag - I tried setting it to 1, but that didn't help 3. VirtualGL - since I'm sitting directly at the virtual machine, I didn't install this. 4. Override native graphics libraries: tried it too (copied the relevant file from the Martinos Center and set the LD_LIBRARY_PATH to its directory), no change. 5. VirtualBox - I didn't install this since the virtualization tool I'm using is VMware Workstation, not VirtualBox. Is there a way to run the relevant freesurfer version on a VMware virtual machine? I have done enough installation work on this machine that the option of using VirtualBox instead is strongly unappealing. Can anyone instruct me how to resolve this issue? Thanks!! Dahlia.

2 3

2010 FSL & FreeSurfer course in Heidelberg, Germany
by Bruce Fischl 05 Feb '10

05 Feb '10

if you missed it the first time... > > We are pleased to announce the 2010 FSL & FreeSurfer course in > Heidelberg, Germany. It will run immediately before the Human Brain > Mapping conference, which will be in Barcelona - a 2-hour flight > from the Heidelberg area. The course is an official satellite > meeting of the HBM conference. > > The course lasts 5 days, from May 31 to June 4. > Numbers of attendees are strictly limited and are available on a > first-come-first-served basis. > > For full information and to register for the course, please go to: > > http://www.fmrib.ox.ac.uk/fslcourse/heidelberg2010.html > > Regards, course organisers. > > > > > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve(a)fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------

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use of Freesurfer in 2-4 year olds
by Naama Barnea-Goraly 05 Feb '10

05 Feb '10

Dear Freesurfer experts, We would like to use Freesurfer in a group of children 2-4 years of age. Is there a pediatric template in the works? How valid is it to use Freesurfer currently in this age group? Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you.

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