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30132 discussions

Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 03 Oct '13

03 Oct '13

Hi, Thanks Marcos for your reply. My problem is that asegstats2table does not output values for eTIV. I do not manage to figure out why. But maybe your script could work. Anyone knows what is the corresponding FieldName Index for eTIV?? I checked a aseg.stats file and did not find it. Thanks a lot Dani Message: 7 Date: Wed, 02 Oct 2013 10:32:51 -0300 From: Marcos Martins da Silva <marcosm(a)hucff.ufrj.br> Subject: Re: [Freesurfer] missing eTIV in asegstats2table To: Daniel Ferreira <danifer(a)ull.es> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1380720771.1845.9.camel@alien> Content-Type: text/plain; charset="utf-8" You can use in a loop with your subjects. It extracts the fields I want and some others including the etiv to a table named AsegVol. You may change the number of the fields to get what you need. The code I am sending you addresses hippocampus, putamen and caudate (both sides). ________________________________________________________________________ for i in $(ls -d suj*) do asegstats2table --segno 11 12 17 50 51 53 -s $i --tablefile AsegVol done ________________________________________________________________________ Notice that suj is the prefix of all my subjects in freesurfer/subjects folder I hope it helps you. Em Qua, 2013-10-02

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Hippocampal subfield segmentation paused
by Irene Lee 03 Oct '13

03 Oct '13

Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas. Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the command recon-all -s my subject -all -hippo-subfields It was running well, however, it halted/paused after it displayed the following information:"final transformation (x=..,yr=..,zr=..) and a 4x4 matrix". For a week it is not going anywhere and not producing any output. The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer. Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!! -Irene

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Re: [Freesurfer] Effects of age on different parameters (thickness, lGI...)
by Daniel Klein 03 Oct '13

03 Oct '13

Hi Doug, I´m a bit unsure about polynomial fitting with qdec. So I want to demonstrate linear, quadratic and cubic effects of age on lGI. You wrote: If you need to test all 3, then you'll have to use mri_glmfit with and FSGD file. I want to be sure if it is correct to demonstrate: 1. age linear effects: age linear (for example 12 Years) as continous (covariate)? 2. age quadratic effects: age square (144 Years) as continous (covariate) and age linear (12 Years) as nuisance variable? 3. age cubic effects: age cubic (1728 Years) as continous (covariate) and age linear (12 years) as nuisance variable? Is it neccesary to include age square (144 years) in the model to show only the cubic effects? And if it is neccesary do I need mri_glmfit with a FSGD file or can I add age square (144 Years) as a seocond nuisance variable in qdec? Best wishes and thanks a lot Daniel

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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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