Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

Difference in GMV generated from qdec and mris_anatomical_stats
by Anupa AV 03 Oct '13

03 Oct '13

Dear FS experts, I was trying to find the gray matter volume of superior temporal gyrus (STG) for schizophrenia patients using freesurfer. I ran recon-all and generated the rh/lh.aparc.volume.stats using qdec. >From that, I got the volume for left hand lh_superiortemporal_volume,=11893. Out of curiosity, I separately found the STG volume for this patient alone using the follo. steps. 1. Saved the label lh.STG using tksurfer -annot aparc SZ01 lh pial 2. Then generated the volume using mris_anatomical_stats. 3. I found the value to be 16268. I'm wondering why there is so much changes in the generation of GM volumes. Can anyone please help me with my query?

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Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST OCTOBER 3rd, 2013)
by MCLAREN, Donald 02 Oct '13

02 Oct '13

Dear Colleagues, The Neurobureau is excited to announce a stipend program for Brainhack 2013. The stipend program was created following a generous grant from Siemens Healthcare to assist young investigators in attending Brainhack 2013. Without their support, the stipend program would not exist. The stipend program will provide at least 6 stipends for partial or full registration fees [if 24 attendees apply, you have a 25% chance of getting a stipend]. The exact breakdown of stipends provided will depend on the number of applicants and the cost of attending the conference for those applicants. The application for stipend requires: (1) A poster abstract (2) A 1-2 page Brainhack project proposal (pdf format) (3) NIH Biosketch/CV (pdf format) The Brainhack 2013 Organizing Committee will decide which applications will receive stipends based on their abstract and proposed brainhack projects. The deadline to apply for one of the stipends is 11:59PM EST on THURSDAY OCTOBER 3rd. All decisions will be made by October 6th and must be accepted within 24 hours of being awarded. Registration and payment will be completed by the organizing committee. Please mail the above application materials to mclaren.donald(a)gmail.com to apply. Good luck. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Visualize cortical projections of fiber pathways using FreeSurfer
by Longchuan Li 02 Oct '13

02 Oct '13

Hi, FreeSurfer experts I have a question regarding visualizing the cortical projections of a fiber bundle using FreeSurfer based on the data from a group of subjects. Since I am interested in seeing both the cortical projections on the surface and the trajectory of the fiber bundle derived from the group, I would like to have them in the same space. I wonder wether fsaverage surface template and mni305.cor.mgz have such a spatial correspondence. What I am planning to do: To show the cortical projections of the fiber pathways: (1) derive the fiber pathways using FSL (2) map the transformations between each subject's T1w image to mni305 (or any templates in FS that have spatial correspondence with fsaverage surface template) using non-linear methods, such as fnirt. (3) transform the fiber pathway from each subject's space to the mni305 space using the transformations derived earlier. (4) sample the projections to the surface using "mri_vol2surf" In this way, I will also have the volume average of the fiber pathways to show the trajectories of the fiber pathway. Do these steps sound ok? Is there any better way to do what I want to achieve here? Many thanks in advance! Longchuan

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Why don't no-mask flag work?
by SHAHIN NASR 02 Oct '13

02 Oct '13

Hi, I want to test activity outside the brain (around eyes/retina) but when I use "-no-mask" flag in my mkanalysis-sess (to be able to see activity outside brain) as below: mkanalysis-sess -analysis RetinaPrj_nomask -fwhm 2 -paradigm Conds.par -mni305 1 -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 3 -refeventdur 14 -force -runlistfile RunList -per-run -fsd bold -no-mask I get this error: outanadir = /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/RetinaPrj_nomask Error using MRIread (line 76) ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Retina_Prj/Sbj_53/abir/bold/008/masks/.mni305.1mm (MRIread) Error in fast_selxavg3 (line 146) runmask = MRIread(flac.maskfspec); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Note: ** I have already used -nomask and -no-subcort-mask in the preproc-sess *** If I remove this flag, everything looks fine except for the fact that all activity outside brain is masked! -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Error when running mris_anatomical_stats on a label
by Tara Ann Miskovich 02 Oct '13

02 Oct '13

Hello Freesurfer experts, I am having difficulty when trying to extract LGI values from a specific label I made. mris_anatomical seems to work when I run it with an annotation, so I am not sure why I am having this error. mris_anatomical_stats -l sub200/label/lh.precuneus.label -t sub200/surf/lh.pial_lgi -f sub200/stats/lh.precuneus_lgi.stats sub200 lh This is the output: limiting computations to label sub200/label/lh.trait_precuneus.label. using thickness file sub200/surf/lh.pial_lgi. reading volume /media/LGI/LGI/sub200/mri/wm.mgz... reading input surface /media/LGI/LGI/sub200/surf/lh.white... reading input pial surface /media/LGI/LGI/sub200/surf/lh.pial... reading input white surface /media/LGI/LGI/sub200/surf/lh.white... Segmentation fault (core dumped) Thank you for the help! Tara

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Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 02 Oct '13

02 Oct '13

Dear Douglas, Thanks for your quick answer. Yes, all my subjects have the measure " EstimatedTotalIntraCranialVol" in their "aseg.stats" file. The problem is that when I run "asegstats2table", this variable is not exported to the created text file. I wonder if there is some way to extract eTIV for all my subjects at the same time. I manage to do it with "mri_segstats", but what I get is individual values for all my subjects in the terminal, so it is quite boring to pass all the values to a table. Thanks a lot, Dani Message: 1 Date: Tue, 01 Oct 2013 11:58:57 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <524AF141.3060100(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed It should still be there. I changed the name to EstimatedTotalIntraCranialVol, eg the line now looks like # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1509814.835086, mm^3 On 10/01/2013 10:50 AM, Daniel Ferreira wrote: Hi, I just run my first asegstats2table in version 5.3 of FS. Is not eTIV included in the generated file anymore? I know that I can get eTIV with mri_segstats --subject subjid --etiv-only but, is it any way to get the values for all my subjects in a text file as asegstas2table does? Thanks a lot Dani _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 116, Issue 7

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Re: [Freesurfer] Error running TRACULA
by Anastasia Yendiki 02 Oct '13

02 Oct '13

Hi Lucia - You are using an older version of tracula (from freesurfer 5.1 instead of 5.3). This version used to have memory issues in the mac build. There is an update of the 5.1 mac build that addresses the memory issue, but since you are just starting out, I *highly* recommend to use the 5.3 version. It has improved both speed and performance. All this info is here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates Also, please make sure to send these messages to the freesuerfer list and not just to me personally. This way the messages are archived, which reduces the replication of questions. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ Thanks! a.y On Wed, 2 Oct 2013, Lucia Billeci wrote: > I found this: > build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > Lucia > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > Dr. Lucia Billeci, PhD > Institute of Clinical Physiology (IFC) > National Research Council (CNR) > via Moruzzi 1, 56124, Pisa > ITALY > Tel: +39-0506213204 > e-mail: lucia.billeci(a)ifc.cnr.it > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > > > Il giorno 02/ott/2013, alle ore 16:38, Anastasia Yendiki ha scritto: > > build-stamp > > > >

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Re: [Freesurfer] Error running TRACULA
by Anastasia Yendiki 02 Oct '13

02 Oct '13

Thanks. And can you also check which freesurfer build you're using? Look for the line that says "build-stamp" towards the beginning of your trac-all.log file. On Wed, 2 Oct 2013, Lucia Billeci wrote: > Hi Anastasia > These are the information: > > Mac OS X 10.7.5 > Processor 3.4 Ghz Intel Core i7 > Memory 4 GB 1333 MHz DD3 > > > Lucia > > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > Dr. Lucia Billeci, PhD > Institute of Clinical Physiology (IFC) > National Research Council (CNR) > via Moruzzi 1, 56124, Pisa > ITALY > Tel: +39-0506213204 > e-mail: lucia.billeci(a)ifc.cnr.it > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > > > Il giorno 02/ott/2013, alle ore 16:21, Anastasia Yendiki ha scritto: > > > Hi Lucia - Glad to hear the bvecs problem got solved. > > About the memory problem: Can you please click on the apple on > the top left of your screen and go to "About This Mac" and give > me the info on the little window that pops up? > > Thanks, > a.y > > On Wed, 2 Oct 2013, Lucia Billeci wrote: > > Dear Anastasia, > > > using the command you told me I solved the problem > with the bvecs file, however I get this error > > > dmri_train(8994) malloc: *** mmap(size=159744) > failed (error code=12) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > MRIalloc(218, 182, 182): could not allocate 158704 > bytes for 14th slice > > > Cannot allocate memory > > Darwin dhcp-71-112.ifc.cnr.it 11.4.2 Darwin Kernel > Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; > root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 > > > trac-preproc exited with ERRORS at Wed Oct 2 > 10:04:53 CEST 2013 > > > Is it a memory problem? Do I need to change memory > allocation? > > > Thanks again. > > > Lucia > > > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > Dr. Lucia Billeci, PhD > > Institute of Clinical Physiology (IFC) > > National Research Council (CNR) > > via Moruzzi 1, 56124, Pisa > > ITALY > > Tel: +39-0506213204 > > e-mail: lucia.billeci(a)ifc.cnr.it > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > > > > Il giorno 27/set/2013, alle ore 18:08, Anastasia > Yendiki ha scritto: > > > > Hi Lucia - The bvecs file is full of > "0,0000000". I'm guessing the problem is > that your environment is set to use the > comma instead of the point as the > decimal separator. Can you try this and > then rerun? > > > setenv LANG en_US.UTF-8 > > > Hope this helps, > > a.y > > > On Fri, 27 Sep 2013, Lucia Billeci > wrote: > > > Hi Anastasia > > > here are the files > > > Thanks > > Lucia > > > > > > > > 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. > > > > > > > > >

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Re: [Freesurfer] Problems with LME-Setup
by Vivian R. Steiger 02 Oct '13

02 Oct '13

Hi Jorge Thank you for your answer our question about CM. I worked so far and the results are in line with glm_fit as you predicted. If we would like to compare the groups (4th column in our qdec.table, with (responder = 1), (non-responder = 2) coded) the CM.C would be [0 0 1 0] ? We have unbalanced group sizes here 14 responder vs. 9 non-responder. Thanks for your assistance Best, Vivian

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Error running TRACULA
by Lucia Billeci 02 Oct '13

02 Oct '13

Dear all, I am trying to apply TRACULA on my DATA (GE data) but when I run the following command: trac-all -prep -c /Users/Desktop/FreesurferData/SUBJECT1/dmrirc_subject1 after eddy current correction, I obtain this error: mv -f /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot xfmrot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.ecclog /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs.norot /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/bvecs printf: -.999993: expected numeric value printf: -.003594: expected numeric value printf: .000852: expected numeric value R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. fslroi /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/dwi.nii.gz /Users/luciabilleci/Desktop/FreesurferData/FRANCINI1/dmri/lowb.nii.gz 0 Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Darwin dhcp225.ifc.cnr.it 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Gio 26 Set 2013 10:12:38 CEST I attach my bvals and bvecs Could you help me? Thanks Lucia

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Freesurfer October 2013