Re: [Freesurfer] Qdec - ROI - different thickness results
Thank you very much for the idea Nick, this explained everything. In qdec red means XY we didn't notice the thickness data on that plot at first :( Have a wonderful week ! Sincerely, Alex. --- En date de : Dim 27.2.11, Nick Schmansky ni...@nmr.mgh.harvard.edu a écrit : De: Nick Schmansky ni...@nmr.mgh.harvard.edu Objet: Re: [Freesurfer] Qdec - ROI - different thickness results À: Alex Hanganu hanganu.alexan...@yahoo.de Cc: FS Mailing List Freesurfer@nmr.mgh.harvard.edu Date: Dimanche 27 février 2011, 0h28 the easiest way to determine X from Y and blue from red (ie, which group is getting thicker or thinner) is to Ctrl-right click on a vertex within the region of interest on the cortex result display. a plot will appear showing the raw thickness values for your groups, and which-is-which should obvious. n. On Fri, 2011-02-25 at 15:33 +, Alex Hanganu wrote: Dear Freesurfer Experts, In qdec for question: Does the average thickness differ between X and Y we received blue colored regions, meaning that thickness for group Y is lower then X ? We created ROIs for each region, and extracted cortical thickness for each ROI for each subject using mris_anatomical_stats. in results: for each ROI, mean cortical thickness of Y group are higher then X. is it a mistake, or the question was misunderstood ? Sincerely, Alex. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Postdoctoral Fellowship in multimodal developmental neuroimaging
Applications are invited for an 18 month postdoctoral fellowship in the human multimodal neuroimaging project Linking the major system markers for typical and atypical brain development: a multimodal imaging and spectroscopy study (http://www.zihp.uzh.ch/1610.php#45) funded by the Zürich Institute of Human Physiology. This study will investigate the major physiological markers of brain development, using a combination of multimodal brain imaging (e.g., simultaneous EEG-fMRI, see Lüchinger et al., 2011, NeuroImage, in press) and MR-spectroscopy methods (i.e., GABA, see O'Gorman et al., 2011, J. of Mag. Reson. Img., in press). The initial phase of the study will establish baseline neurotransmitter levels, cerebral blood flow (e.g., perfusion MRI) and EEG frequency and power at rest in children, adolescents, and adults. Examining the interactions between these markers and the changes they demonstrate with age and hormone levels will allow to better understanding the global and regional processes underlying brain maturation. In addition, we will investigate changes in these physiological markers with (a) memory tasks (see Michels et al., 2010, PLoS ONE) and (b) attention deficit hyperactivity disorder (ADHD, see Doehnert et al., Biol Psychiatry, 2010). The starting date of the position is May 2011. Our department is equipped with 64-channel fMRI-compatible EEG equipment and a 3 Tesla GE scanner, which is mainly dedicated for research questions. The successful applicant will have a PhD research background in Cognitive Neuroscience, Neurophysiology, Psychology, Neuropsychology, or related fields. Fluency in English and the ability to work within a multidisciplinary team are essential. Applicants must be experienced at conducting fMRI and/or EEG studies -demonstrated by at least 2 first author publications in international peer-reviewed journals- and be familiar with analysis software such as SPM/Matlab, BrainVoyager and/or FSL. Experience with stimulus presentation software (such as Presentation), UNIX, and programming languages a plus. Salaries are in accordance with the Swiss National Research Foundation. APPLICATION INSTRUCTIONS: To apply, please send a curriculum vitae, a personal statement describing research interests, 3 letters of recommendations, and up to 3 article reprints/preprints (max. 2 MB!!!) to: Dr Lars Michels lars.mich...@kispi.uzh.ch MR-Zentrum University Children's Hospital Steinwiesstrasse 75 Zürich 8032 Switzerland Reviews of applications will begin on the 1st of March and will continue until the position is filled. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] residuals exactly zero
Hi, We have experimented a little with different ways of computing the p-values in a GLM analysis based on FreeSurfer data. The way the Matlab reference implementation (fast_fratio.m) handles a situtation where the residuals are exactly zero, seems to be to set those vertices to F = 0 and p = 1. Is this correctly understood? Is this also the case in the underlying C-code? Thank you! LMR -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] residuals exactly zero
When the residual variance is exactly 0, this is what the matlab code. In the C implementation, if (glm-rvar FLT_MIN) glm-rvar = FLT_MIN; which will have similar results. doug Lars M. Rimol wrote: Hi, We have experimented a little with different ways of computing the p-values in a GLM analysis based on FreeSurfer data. The way the Matlab reference implementation (fast_fratio.m) handles a situtation where the residuals are exactly zero, seems to be to set those vertices to F = 0 and p = 1. Is this correctly understood? Is this also the case in the underlying C-code? Thank you! LMR -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Baseline Offset in Stable 5 funcroi
Hi Freesurfers, When conducting ROI analyses in Stable 5, is there a way to generate a mean functional baseline offset value within the ROI which can be used to help calculate percent signal change? This would correspond to the value from row 4 in the output file generated by roisummary-sess in Stable 4. Thanks, Adam PS: Here are examples of the commands I've used in Stable 5 to generate ROI Data: funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs -thresh 1.3 funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH funcroi-table-sess -roi MTH_7vFix_DLPFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH -c Cond7vFix -o /cluster/roffman/users/Stable5_PerRun/DLPFC_ROI_7vFix_MTH Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] thickness analyse
wang, i think having the imported roi thickness data in your qdec.table.dat file is confusing you. you should just delete that data from your qdec.table.dat, keeping just 'fsid' and 'addiction' columns. from looking at your analysis (which appears you have done everything right), it is not used anyway, as it appears just the discrete factor 'addiction' was selected in your analysis, which is the right thing to do for a straightforward two-group analysis. Your display image doesnt show insula, so i cant say whether the effect would survive multiple corrections (there is an option to run this in qdec), but your highlighted vertex has a log-p of -3.7, which is a p of 0.002 for that vertex. The roi data that you imported is the average thickness value for that roi for that subject prior to any kind of statistical analysis (freesurfer recon-all automatically creates rois in the cortical parcellation stage). generally you would use those outside of freesurfer in another analysis package. you can import them into qdec and select them in an analysis if you wanted to conduct some rather unusual analyses, like asking does the thickness of the roi 'entorhinal' affect overall cortical thickness? (which can be a good question for aging research, but in general is kind of unusual). n. On Mon, 2011-02-28 at 17:19 +0800, 汪贵宏 wrote: Dear all, I try to analysis the thickness difference between the patient vs. control for several days, but I fail to explain the results.Although I had read the wiki on the website,it not works for me. Here,I list the procedures which I took for my study,I really hope somebody can help me. My research is to analysis the thickness difference between the control vs.patient which are addicted on the internet. Firstly,as the papers says,FREESURFER divided each cortex hemisphere into 33 areas,but why did there has only one thickness value per area?there is the thickness information for all of controls and patients in the first file which I add in the appendix. Secondly,why did the thicknesses are not in the same value for the same area between the qdec.table.dat (in the first appendix)and which in the first picture in the appendix below? Thirdly,the detail steps I took in the qdec are also list in the appendix pictures,is it right? Thanks a lot. Sincerely, wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] win xp shared drives
Hi, I have recently installed freesurfer 5.0.0 on top of a Xubuntu Linux distribution on an virtualBox/WIN XP computer. I can run freesurfer without a problem. My problem is with accessing Host drives from linux system. How am I going to get the image data to my linux virtual system if I cannot access host USB drives from my guest linux system? I looked on your archives and found nothing on shared drives. Your help is appreciated. Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] win xp shared drives
saad, i dont have the information directly on-hand, but in your virtual box configuration (independent of freesurfer) there should be an option to map a USB drive into the linux virtual machine. others have done this successfully. you'd have to google the help docs for your virtual box to learn about this (or maybe someone on this list will respond). n. On Mon, 2011-02-28 at 12:01 -0500, Saad Ramadan wrote: Hi, I have recently installed freesurfer 5.0.0 on top of a Xubuntu Linux distribution on an virtualBox/WIN XP computer. I can run freesurfer without a problem. My problem is with accessing Host drives from linux system. How am I going to get the image data to my linux virtual system if I cannot access host USB drives from my guest linux system? I looked on your archives and found nothing on shared drives. Your help is appreciated. Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] NIFTI-2 public announcement
FYI _* _* _* _* _*A 64-bit update to the NIfTI format*_ *_ *_ *_ *_ The NIfTI committee are proposing the creation of a NIfTI-2 format that is a very simple extension of the current NIfTI-1 format, but updated to allow 64-bit storage and addressing for large images and matrices. _ _ It is intended that this format: - will enable the storage of large images and matrices, with all dimensions being coded by 64-bit integers rather than the current limitation of 16-bit signed integers (which currently gives a restrictive 32767 size limit in each dimension) - will be very simple to implement and update software (a couple of hours coding or less generally) - contains the same information as a NIfTI-1 file (no new fields and all current fields still retained) - will support the existing file formats and naming: a .nii single-file, a .hdr/.img file-pair and their gzipped versions - has a very simple test (see below) to determine if the file is NIfTI-1 or NIfTI-2 - does not replace NIfTI-1 in the short term but is supported alongside it *_Comments_* This announcement is intended for public comment. Please post any comments on this NIfTI-2 proposal to the NITRC discussion list (www.nitrc.org/forum/forum.php?forum_id=1941 http://www.nitrc.org/forum/forum.php?forum_id=1941) We ask that comments relating to larger-scale changes and requests for other types of format change be posted instead to a separate NITRC discussion list for more advanced neuroimaging formats (www.nitrc.org/forum/forum.php?forum_id=1942 http://www.nitrc.org/forum/forum.php?forum_id=1942) _* *_ _*Supporting software*_ - AFNI, BrainVoyager, Caret, Fiswidgets, FreeSurfer, FSL, ITK, LONI-DIRAC, MRIcron, NiBabel and SPM have all agreed to support the NIfTI-2 version in their upcoming releases, but that NIfTI-1 will remain a default output, or a configurable default, in the short-term - the sourceforge supporting libraries in niftilib will be updated so that they seemlessly support both NIfTI-1 and NIfTI-2 - conversion utilities to and from NIfTI-1 will be made available via sourceforge as well as in some of the software packages mentioned above _*Changes to the header *_The changes to the NIfTI header structure are the following: - short dim[8] becomes int64_t dim[8] - float intent_p1 becomes double intent_p1 - float intent_p2 becomes double intent_p2 - float intent_p3 becomes double intent_p3 - float pixdim[8] becomes double pixdim[8] - float vox_offset becomes int64_t vox_offset - float scl_slope becomes double scl_slope - float scl_inter becomes double scl_inter - float cal_max becomes double cal_max - float cal_min becomes double cal_min - float slice_duration becomes double slice_duration - float toffset becomes double toffset - float quatern_b becomes double quatern_b and similarly for quatern_c, quatern_d, qoffset_x, qoffset_y, qoffset_z - float srow_x[4] becomes double srow_x[4] and similarly for srow_y[4], srow_z[4] - char magic[4] becomes char magic[8] - char unused_str[12] is added after char magic[8] The order, size and type of all other fields remains unchanged. The sizeof_hdr must store 556 for a NIfTI-2 file instead of 348 for NIfTI-1. Extension information is still held in the first 4 bytes after this header (bytes 557-560) in the same way as in NIfTI-1. Note that the total block size of 560 (header + 4 bytes) retains the 16-byte alignment in NIfTI-1 (348+4=352), as needed for convenient memory-mapping. The changes of float to double are generally made to allow for more accurate mapping of intensities or indices when dealing with very large arrays, and unused_str is added to ensure the 16-byte alignment holds. _*Compatibility*_ This format is not, and cannot be, bit-wise compatible with the previous NIfTI-1 (or ANALYZE) formats and so will not work with existing NIfTI-1 software directly. In the short term this can be solved via conversion utilities. A NIfTI-2 image will not be recognised as a valid NIfTI-1 image by existing software and so no incorrect processing or analyses should occur. In the longer term most code should be very easily converted to work with both NIfTI-2 and NIfTI-1 by using the updated sourceforge libraries or making equivalent changes internally. The change in format is intentionally very minimal and should be very easy to code. *_Determining the NIfTI version_* The following pseudo-code shows how a file can be tested to see: (a) if it is a NIfTI image file, (b) what version of NIfTI it is, and (c) whether byte-swapping is required. read in the first 4 bytes from the file let d = the content of these bytes, formatted as a 32-bit int if (d==348) then it is a NIfTI-1 file, no byte-swapping required else if (swap_4bytes(d)==348) then it is a NIfTI-1 file, but with byte-swapping required else if (d==556) then it is a NIfTI-2 file, no byte-swapping required else if (swap_4bytes(d)==556) then it is a
