Freesurfer June 2011

freesurfer@nmr.mgh.harvard.edu

118 participants
168 discussions

Regarding Installation
by Antonella Kis 20 Jun '11

20 Jun '11

Can you please let me know how I can install on top of an old version the new version FreeSurfer v.5.1.0? Thank you. Antonella -- ------------------------------ Dr.Antonella Kis, PhD Sessional Lecturer Life Sciences, Physics Department University of Toronto at Scarborough Clinical Research Project Coordinator The Hospital for Sick Children (SickKids) Diagnostic Imaging Department Neurosciences and Mental Health

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qdec roi analysis
by fabrizio piras 20 Jun '11

20 Jun '11

Dear all, I run a controls vs patients thickness analysis using qdec and got several results. Now, it is not entirely clear to me how to refine my surface-based analysis (still using qdec) into a ROI, the middle orbitofrontal region. Cheers, Fabrizio --------------------------- Fabrizio Piras Ph.D. --------------------------- Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213 Il giorno 18/giu/11, alle ore 18:00, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Automated QC of Freesurfer Images (West, John D.) > 2. [Fwd: Welcome to the "Freesurfer" mailing list (Digest mode)] > (Antonella Kis) > 3. Re: Automated QC of Freesurfer Images (Louis Nicholas Vinke) > 4. Re: Automated QC of Freesurfer Images (Douglas N Greve) > 5. Two timepoints - same subject, correlation matrix (Sudhin A. > Shah) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Jun 2011 20:11:55 +0000 > From: "West, John D." <jdwest(a)iupui.edu> > Subject: [Freesurfer] Automated QC of Freesurfer Images > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <793D43FE7976404CB5E172709AB1F4080DE8E659(a)IU-MSSG-MBX102.ads.iu.edu> > Content-Type: text/plain; charset="us-ascii" > > Hello. > > We are in the process of trying to develop a QC pipeline for our > Freesurfer processed images. I was wondering if anyone has > developed any type of automated QC they would be willing to share > with us or have any suggestions on how to proceed. > > Any help would be most appreciated. > > Thanks. > -John West > Systems Admin/Imaging Analyst > IU Center for Neuroimaging >

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Freesurfer New version Installation
by Antonella Kis 20 Jun '11

20 Jun '11

Good afternoon, It is for the first time I am using FreeSurfer and I used only a little the old version V.5.0. For this version my environment variable was FREESURFER_HOME. If I am still having my old version V. 5.0 and also I downloawded the new realeased version how I can install my new version, in other words how I can run it? Do I need to installed in fact or just to download this? I am not sure what executable to run for the instalation of the new version. I will be very grateful if you can give me more detailed directions about this. Also to set my new environment I have only to repalce the old environment (FREESURFER_HOME) while I am coding with the $FREESURFER_HOME/FreeSurferEnv.csh for example when I am gone run the recall-all? Thank you very much for your help. Best regards, Antonella

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Re: [Freesurfer] error while loading shared libraries:libtiff.so.3
by Daniel Ferreira Padilla 20 Jun '11

20 Jun '11

Dear all, I'm using Ubuntu 10.10 and have the same problem only when working with 4.5 version (I also use 5.1 version without any problem). I have followed previous suggestions making a symbolic link named libtiff.so.3, but it gives me back the message "denied permission". Also tried to install it with "sudo aptitude install ia32-libs" but it did not recognize "aptitude" command. So I tried with "sudo apt-get install ia32-libs" instead and it was ok, but I am still having the same problem. So, what could I do? Can I download libtiff.so.3 from somewhere? How can I avoid that "denied permission"? Thank you very much for your help. Daniel Ferreira #-------------------------------------------- #@# Cortical ribbon mask Sat Jun 18 17:57:36 WEST 2011 /home/neuroimagen/DANI/subjects/uu0148_36_1/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance uu0148_36_1 mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux neuroimagen 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 18 17:57:36 WEST 2011

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Access to download
by Gavin Cooper 20 Jun '11

20 Jun '11

I am having issue accessing the latest version of freesurfer for download (5.1.0) and was wondering if anyone else is having the same trouble. Chrome message: The web page at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux… might be temporarily down or it may have moved permanently to a new web address. Similar messages in Firefox, wget also not working. When FTP'ing to to pub directory no further folders/files are shown. Also tried the mirror link - but no luck there either. Thanks you in advance for any help. Cheers Gavin Gavin Cooper System Administrator/Programmer Schizophrenia Research Institute Mobile Number - 0403 337875 University Phone - 02 4921 5927 Gavin.Cooper(a)newcastle.edu.au Mailing Address: Gavin Cooper School of Psychology University of Newcastle Callaghan NSW 2308

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New version Installation
by Antonella Kis 19 Jun '11

19 Jun '11

Hello, I just started to use the FreeSurfer software and until now I used an old version V. 5.0.0. I wonder if to install the new version I have first to remove the old one or I can do just updates for the old version. If I downloaded the new version V.5.1.0 what will be the next step, how I can install the new version if I have the old version on the computer? Some help would be most appreciated. Thanks. Antonella ------------------------------ Dr.Antonella Kis, PhD Sessional Lecturer Life Sciences, Physics Department University of Toronto at Scarborough Clinical Research Project Coordinator The Hospital for Sick Children (SickKids) Diagnostic Imaging Department Neurosciences and Mental Health

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Resampling from MNI 152 to MNI 305 - Problem with orientation
by Balaji Goparaju 17 Jun '11

17 Jun '11

Hello Freesurfers, I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired using WFU_PickAtlas toolbox in SPM. These masks are .nii files, and have a RAS orientation. I am trying to resample these masks into the fsaverage MNI 305 space, specifically with the dimensions matching the "mni305.cor.subfov2.mgz" file found in the $FREESURFER_HOME/average file. This file is in the LIA orientation. However, the mni152.register.dat file seems to be transforming volumes from the MNI 305 space to the MNI 152 Space in LAS orientation (MNI152_T1_2mm.nii in FSL). Should I transform my Brodmann Area masks from the RAS orientation to a LAS orientation? If so, how can I achieve this? The RAS orientation is correct, so I know using mri_convert --out_dimension is out of the question. I have tried to use *mri_label2vol --seg {BA_mask} --temp {$FREESURFER_HOME/average/mni305.cor.subfov2.mgz} --o {output_file} --reg mni152.register.dat --invertmtx* Also, I have tried to use the inverted matrix from mni152.register.dat and use it with *mri_vol2vol -mov {BA_mask} --reg {inverted_mni152.register.dat} --o {output_file} --tal --talres 2* However, the output files had interchanged posterior (P) and anterior (A), and superior (S) and interior (I) orientations. What is the best way to achieve the resampling? Any guidance is really appreciated! Regards, Balaji Goparaju

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[Fwd: Welcome to the "Freesurfer" mailing list (Digest mode)]
by Antonella Kis 17 Jun '11

17 Jun '11

Hello, I just received my confirmation for posting on the mailing list. ---------------------------- Original Message ---------------------------- Subject: Welcome to the "Freesurfer" mailing list (Digest mode) From: freesurfer-request(a)nmr.mgh.harvard.edu Date: Fri, June 17, 2011 4:25 pm To: akis(a)utsc.utoronto.ca -------------------------------------------------------------------------- Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! To post to this list, send your email to: freesurfer(a)nmr.mgh.harvard.edu General information about the mailing list is at: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer/akis%40utsc.uto… You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: araukana Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you. 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. -- ------------------------------ Dr.Antonella Kis, PhD Sessional Lecturer Life Sciences, Physics Department University of Toronto at Scarborough Clinical Research Project Coordinator The Hospital for Sick Children (SickKids) Diagnostic Imaging Department Neurosciences and Mental Health

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dmri_train error
by Michielse Stijn (SP) 17 Jun '11

17 Jun '11

Hello FreeSurfer users, Currently I'm trying to analyze DWI data using the new TRACULA package. The packages looks promising and I managed to process a few tracts (the ILF and UNC) But now I would like to process more tracts at once. So I ran the trac-all subroutines to check every step. All goes well until the Pathway priors have to be generated. The subroutine is "trac-all -prior -c dmrirc" with all 18 tracts specified in the configuration file. My dataset contains 4 participants for the first run. The error occurs in "dmri_train" and says: dmri_train(75687) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort So there is something wrong in the dynamic memory allocation. The process takes up to 3GB of memory. The system contains: Memory: 16 GB 1066 MHz DDR3; Model Identifier: MacPro4,1; Processor Name: 2 x Quad-Core Intel Xeon; Processor Speed: 2 x 2.93 GHz System Version: Mac OS X 10.6.7 (10J869) Kernel Version: Darwin 10.7.0 Can someone help me out on this error? Kind regards, Stijn Michielse Maastricht University

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Unsupported slice timing problem
by Louie Perkins 17 Jun '11

17 Jun '11

We recently ran into an issue with Freesurfer's mri_convert tool where it gives an error of "unsupported slice timing pattern". We have some NIFTI MPRAGE files that have a "slice_code" with a value of NIFTI_SLICE_ALT_INC2 (=5). Issue arises in utils/mriio.c (line 9549 of rev:stable5), two slice_code possibilities are not included in the if-statement, NIFTI_SLICE_ALT_INC2 and NIFTI_SLICE_ALT_DEC2. These are defined in include/nifti1.h (comment says they were added in 2005), so I'm checking to see if there is a reason they are not allowed, or if this bit of code was just never updated to reflect the latest nifti1.h. Thanks for any help, -Louie Perkins

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Freesurfer June 2011