Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

iSurf Brainview now ported to Mac
by Pedro Paulo de Magalhães Oliveira Junior 03 Jan '12

03 Jan '12

Today Apple released in the Mac Store, for free, the version of iSurf BrainView for Mac. It's yet not as complete as the iPad and iPhone version but it has some nice features to help you or your students to learn neuroanatomy using FreeSurfer automated parcellation and subcortical segmentation. You can download it at: http://itunes.apple.com/us/app/isurf-brainview-desktop/id491367143?ls=1&mt=… As usual, suggestions are welcome. Happy 2012 for everyone. PPJ --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

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Re: [Freesurfer] get_4dfp_dimoe problem
by Bruce Fischl 03 Jan '12

03 Jan '12

Hi Avi just running recon-all I think. Is there an env variable you use to specify a tmp dir or something? thanks Bruce On Tue, 3 Jan 2012, Snyder, Avi wrote: > It looks like both the command (imgreg_4dfp) and argument > (.../711-2B_as_mni_average_305_mask.4dfp.img) fields are garbled. > Evidently, operating system paths have not been correctly set. > The 4dfp suite of tools is available and probably could be installed but > I'm not sure that is what is wanted. > I don't understand what LAOUCHEDI MAKHLOUF is trying to do. > > > AZS > ----------------------------------------------------- > On 1/3/12 10:40 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> this is actually not part of FreeSurfer proper, but rather something that >> Avi Synder (ccd) was kind enough to contribute. Avi: can you comment? >> >> thanks >> Bruce >> On >> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote: >> >>> hi everyone >>> we run recon-all on a cloud and we obtained this error: >>> >>> mpr2mni305 failed, see transforms/talairach_avi.log >>> >>> The log says the file name is too long perhaps because of the tmp dir >>> file >>> names: >>> >>> >>> get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/htt >>> ps_3a_2f_2fwms01. >>> >>> ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e >>> 5- >>> >>> ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/71 >>> 1- >>> 2B_as_mni_average_305_mask.4dfp.img filename too long >>> ERROR: >>> 'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/https_ >>> 3a_2f_2fwms01. >>> >>> ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-47e >>> 5- >>> >>> ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/71 >>> 1- >>> 2C_as_mni_average_305 >>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i >>> >>> e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/ >>> .t >>> >>> mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask8201883777111446775 >>> /f >>> reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none >>> talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 >>> >>> >>> knowing that it is difficult for us to do things differently (to change >>> the >>> path); is it possible to do something in freesurfer to work with thesse >>> filenames ? >>> >>> thanks for your help > > > >

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Transformation Matrix from 3D Space to Flattened Surface
by warre295＠umn.edu 03 Jan '12

03 Jan '12

Hello gurus, Thank you in advance for any assistance. I have seen questions similar to this in the archives, but I believe this is a distinct problem. I apologize if this has been addressed previously. I am trying to obtain a retinotopic map, but for reasons of compatibility and future analysis I would like to keep as much of the work in MATLAB as is possible. To date, I have used FreeSurfer to generate a flattened cortical surface with great success. I would like to at this point exit the FreeSurfer world and perform the remaining analysis in MATLAB. What would be most ideal is if I could obtain a matrix which I can import into MATLAB and calculate a statistic for a point on the *flattened* cortical surface as a function of that statistic calculated for each voxel. This includes the phase information for a retinotopic map, but really I am looking for a solution to a more general problem. In other words, I need the matrix T in the equation... T*[Statistic from each voxel] = [Statistic for each point of Flattened Surface] where T describes how each point on the surface is derived from some set of voxels. I imagine this is an incredibly naive question, and that this would require a fair amount of work involving multiple transformations if it is even possible at all. I appreciate any and all advice. Best wishes, Scott Warren Graduate Student, Department of Neuroscience University of Minnesota

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Destrieux atlas 2002
by Klein, Holger 03 Jan '12

03 Jan '12

Dear freesurfers, dear Mr. Destrieux, I have a question concerning the destrieux atlas 2002: I need a distinct label "G_temp_sup-G_temp_transv_and_interm_S" , which is only available in this atlas version. I tried using "?.atlas2002_simple.gcs", but this atlas does not output the requested label - but the labels of the default ?.aparc.annot. How can I get the mentioned label (with the original boundaries of this region). Would be glad about any help, THX Holger

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Running mri_anatomical_stats on many subjects
by Klein, Holger 03 Jan '12

03 Jan '12

Dear Freesurfers, Is there a possibility to run mri_anatomical_stats on many subjects? Otherwise it would be quite time_consuming. Many thanks, Holger

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Linear Regression Analysis - Significant Slope?
by Adam Nitenson 03 Jan '12

03 Jan '12

Hi Doug et al, *I think this email got lost in the cracks before the holidays, so I am reposting* We have been working on a linear regression-type analysis (see attached analysis.info for analysis and slopepar for a sample paradigm file) that involves task-related activation in a working memory test. For each participant, there are four conditions: 1, 3, 5, and 7 items that need to be remembered. The question that we would like to ask is: for each voxel, does the slope of activation (i.e., the slope of the best-fit line as you move from 1 to 3 to 5 to 7 items, as calculated separately for each subject) differ from zero? The second-level analysis would determine if there is a significant difference in activation-related slope between groups. Based on previous discussion, the way we have been doing this is to modify the paradigm file to create the following contrast: Condition 2: activation during working memory, but weighted by condition so the 1 item condition is weighted as 1, the 3 item condition as 3, etc. Condition 0: fixation The contrast is Condition 2 minus Condition 0. However, this method of weighting does not appear to answer the question about slope, but rather focuses on a weighted average. Consider the following scenario, involving 5 subjects (A through E): The SLOPE column is calculated using the slope function of the spreadsheet (i.e., slope of best fit line, using values of 1...3...5...7 for the x-axis, and, say, for subject A, the values of 2...4...6...8 for the y-axis). The WEIGHTED column is calculated in the way that I think FS-FAST is doing it, which is as follows: ((1 * 1 item activ. value) + (3 * 3 item activ. value) + (5 * 5 item activ. value) + (7 * 7 item activ. value))/4 The SLOPE and WEIGHTED values (regardless of their different scale) are not really comparable. For example, for Subject A, the SLOPE value is 1 and the WEIGHTED value is 58, while for Subject E, the SLOPE value is 1.1 and the WEIGHTED value is 28. So when looking at the paradigm file, take the lines 76.57 2 3.4 5 213.42 2 2.29 7 Does this mean that the activation at the first timepoint is accounted for 5-fold and the second timepoint 7-fold? If this is the case then this analysis may not best represent what we are looking for. Is there a way to modify the paradigm file so that the analysis can focus on slope of the best fit line as opposed to the weighted average? Thanks, Josh Forwarded from: Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Join my network on LinkedIn
by Sinem Erdoğan via LinkedIn 03 Jan '12

03 Jan '12

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bbregister coordinates
by Gregory Kirk 02 Jan '12

02 Jan '12

Happy new year folks, i would like to get info on which axis the transformation info in the fregister_XXX.dat.param is w.r.t. comparing the log files with the values i think the first 3 are the translations and the next 3 the rotations. but i did not see w.r.t. which directions, i.e. LR,AP,IS for the 3 translations for the rotations w.r.t. which planes , i.e. 1st rotation LR&AP , 2nd etc. all w.r.t. conformed space, i.e. the directions w.r.t. brain.mgz did i miss a doc. that tells me this thanks Greg

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recon all problem
by LAOUCHEDI MAKHLOUF 02 Jan '12

02 Jan '12

hi everyone i run recon-all on 200 subjects on a cloud system and i had the following message : mpr2mni305 failed, see transforms/talairach_avi.log so i attached the corresponding log to this message. does anyone have an idea of the error thanks andhappy new year

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Fw : recon all problem
by LAOUCHEDI MAKHLOUF 02 Jan '12

02 Jan '12

--- En date de : Lun 2.1.12, LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> a écrit : De: LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> Objet: recon all problem À: freesurfer(a)nmr.mgh.harvard.edu Date: Lundi 2 janvier 2012, 11h15 hi everyone i run recon-all on 200 subjects on a cloud system and i had the following message : mpr2mni305 failed, see transforms/talairach_avi.log so i attached the corresponding log to this message. does anyone have an idea of the error thanks andhappy new year

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Freesurfer January 2012