Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

mri_cvs_register failure from missing shared lib
by Michael Waskom 25 Apr '17

25 Apr '17

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: -------------------- FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 ---------------------- Any thoughts on how to proceed? Thanks! Michael

3 4

Help on "mris_anatomical_stats"
by Lim, Lena 06 Apr '17

06 Apr '17

Dear Experts, I ran a group analysis in Qdec for the left volume and found a region of significant group difference. I wanted to extract this ROI. I defined this label and used the "map label to subjects" option in Qdec and ran the following but encountered the following error. Please kindly help... [spjwker@nanlnx2 FSL]1% mris_anatomical_stats -l lh.HCA_vol.label \-b -f PAC07/stats/lh.HCA_vol.stats PAC07 lh limiting computations to label lh.HCA_vol.label. reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz... reading input surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... reading input pial surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial... reading input white surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... Segmentation fault Many thanks, Lena

2 1

ExploreDTI Workshop!
by Szabolcs David 02 Apr '17

02 Apr '17

Thrilled to announce that we are going to hold an ExploreDTI workshop in Utrecht (July 4-6)! More details can be found here: http://www.exploredti.com/workshop. We hope to see you there! Cheers, Szabolcs

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LME mass univariate model
by Bronwyn Overs 22 Mar '17

22 Mar '17

Dear mailing list, I am trying to run a LME model using the matlab tools, but I’m unsure how to specify the model we wish to run. We have a qdec file that contains the following columns: fsid, fsid-abse, years between scans, age at baseline, gender, group We want to specify a model where we can examine four interaction terms (years*age, years*group, age*group, years*age*group), as well as random effects for the intercept, years and age. My questions are: 1. How do we specify a model that will include the random effects we want? 2. How do we compare our full model (3 random effects) with a model excluding the random effect for age? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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TRACULA and priors problem
by Juergen Haenggi 16 Mar '17

16 Mar '17

Dear TRACULA experts I run TRACULA FS 6.0 on a Mac and get the following error: #@# Priors Fri Feb 24 17:11:18 CET 2017 /tmp/subj33.interpreter_control_01/.15208.txt: No such file or directory. In the FS archive I found the following email https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50778.html However, in my situation, the directories of the FS preprocessed subjects are in /Applications/freesurfer/subjects folder, and therefore to solution proposed in the email (make symbolic links) does not make sense for me. Is there another work around? Thanks in advance Regards Jürgen ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology 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(a)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. -----------------------------------------------------------------------------------------------------

2 1

Inflation of one hemi only
by Kang, XJ 10 Mar '17

10 Mar '17

Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang

3 6

Different segmentation atlas
by Julie Hall 08 Mar '17

08 Mar '17

Dear all, I would like to use the Gordon Parcellation as segmentation atlas for my subjects. I have warped this atlas into individual subject space. Then I wanted to use mris_sample_parc to apply this parcallation, but I have a few questions.. 1. Is this the right command to use? 2. When I use this command, I get the following error: could not open translation file /Applications/freesurfer/cma_parcellation_colors.txt I don’t have this color table, should I create one (and how?)? Thank you Julie

3 6

Strange wm error
by Melanie Ganz 07 Mar '17

07 Mar '17

Dear list, we are experiencing a strange wm surface error that we are not quite sure about how to fix. The errors is at a location where the wm.mgz look absolutely fine as well as the brainmask.mgz. Also the intensities in the norm.mgz look fine. Please find 6 pics showing the error highlighted by the cursor on the brainmask.mgz and the wm.mgz in all three views. Cheers, Mel -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

4 4

Question on saving interim files when generating an fsavearge
by West, John D. 07 Mar '17

07 Mar '17

Hello. We are looking to save the interim subject files generated when creating an fsaverage. These seem to be automatically deleted at the end of the process so we were wondering if there is a flag or script that would save these for us? Thanks for your help. John D. West, M.S. Principal Systems Analyst | Center for Neuroimaging Indiana University School of Medicine 355 West 16th Street | GH 4100 Indianapolis, IN 46202 317-963-7510 jdwest(a)iupui.edu<mailto:jdwest@iupui.edu>

3 5

mri_vol2surf
by Redwan Maatoug 06 Mar '17

06 Mar '17

Hi all ! I would like to convert my files : volumetrics nifti files to surfaces files. My volumetrics nifti files come from an Atlas and I would like to convert them to surfaces files (i need the surfaces files). Could you please tell me the process because I have tried many things like : mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out thepathwayIwantToputmySurfaceFileAfterConversion And it did not work. Thank you for your help, Redwan

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Freesurfer February 2017