Freesurfer March 2013

freesurfer@nmr.mgh.harvard.edu

155 participants
331 discussions

FDR questions
by Yang, Daniel 06 Mar '13

06 Mar '13

Dear Freesurfer experts, I am interested in a specific brain region that is based on the 2009 atlas. I used Qdec to 'Generate Stats Data Tables' to get the cortical thickness info for this region and saved them in a file. Then I used SPSS and did an ANOVA test. The ANOVA test reveals that the patient group (versus the neurotypical group) has significantly cortical thinning in this region (p < .05). I am also able to see this significant effect in this region using 'Display' in Qdec. However, once I hit 'FDR' button (q = .05), the minimum t-value associated with significant data increased from around 2 to more than 4. And the significant effect in this region does not survive FDR, as seen in the Display. My questions: 1. Is what I did the usual procedure to do FDR correction? How do I see the significance value of this region under FDR (q=.05)? 2. Is the normal that the minimum t-value increased so much when doing FDR? 3. Do I have to do FDR since I'm only interested in a very specific region? Thank you! Daniel

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recon_all exited with errors
by Sinead Kelly 06 Mar '13

06 Mar '13

Dear members, I am currently conducting cortical thickness analysis and I have ran the recon_all step. The appropriate files have been created including aseg.mgz, brainmask.mgz, aseg.stats etc. and therefore volumes and cortical thickness measures have been calculated, however, when I look at the output of my script it states that the job has exited with errors (see below) mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 001 mris_volmask.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Linux tcin-n05.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 1 20:00:42 GMT 2013 I'm not too sure what the error is or how to fix it. However, as the relevant files have been created, should I be too concerned about this? Also, I should mention that I am running my scripts on a high performance computing cluster and not locally on my linux. Thank you for your help! Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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entorhinal thickness
by stdp82＠virgilio.it 06 Mar '13

06 Mar '13

Hi Bruce and other users, I have read the article on EC that you have suggested. But, I do not understand how I should obtain the EC thickness outcomes /statistical maps from my analysis. I have some question, please. I have already performed recon-all and cortical thickness analysis. For entorhinal cortex thickness analysis, should I run again mris_prep, surf2surf and glmfit for EC files only? If yes, which are the files that should I use? Which are their names and where these files are locate? An additional question on other matter, please. If I'd like perfomed a ROI based cortical thickness (for example on occipital lobe), can I use a mask that is builded by recon-all? How can I extract it for example from aseg (do you advise it)?About the occipital lobe, I do not understand from tutorial if already exist a particular modality to calculate the cortical thickness specifically in that region. Thank you very much for your patience and kindness, Stefano Hi Stefano look on the wiki and search for entorhinal. In particular, this paper:http://surfer.nmr.mgh.harvard.edu/pub/articles/YNIMG6159.pdf describes how we estimate the location of EC in vivo cheers Bruce On Fri, 1 Mar 2013, std...(a)virgilio.it wrote: > Hi list,Where Can I find basic information about entorhinal cortex > analysis?Thank you very much.Stefano > _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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tkmedit segmentation color offset
by Natalie Han 05 Mar '13

05 Mar '13

Hi, all, I have a tkmedit display issue when I try to add transformation to the main volume, but the segmentation volume won't conform to Talairach domain accordingly. Here is the commandline tkmedit subject norm.mgz -main-transform talairach.xfm -seg aseg.mgz really appreciate any feedback on how to add transformation on this segmentation results. Thanks. Natalie

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Post-doctoral research fellow position in neuroimage analysis at MGH/Harvard Medical School
by Mert Rory Sabuncu 05 Mar '13

05 Mar '13

A post-doctoral research fellow position is available in the Laboratory for Computational Neuroimaging (with PI's Bruce Fischl and Mert Sabuncu) at the Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging and the Department of Radiology at Harvard Medical School. Responsibilities: The position will involve developing novel computational image processing and statistical analysis tools for longitudinal neuroimaging studies. A minimum commitment of two years is required. Salary will be competitive and commensurate with experience. Requirements: The candidate should have: • A PhD in computer science, electrical engineering, statistics or a related field • Research experience in image processing and/or computational image analysis, preferably in biomedical applications • Excellent oral and written communication skills using the English language. • Strong organizational skills • The ability to work independently within the research lab on assigned projects as well as the ability to work well with others on a research team • Strong coding skills (e.g. in Matlab, Python, C/C++, Unix scripting) There is no formal application deadline and candidates are encouraged to apply as soon as possible. The search will continue until position is filled. The start date can be as soon as possible (latest Fall 2013, but preferably sooner). Please email Mert Sabuncu (msabuncu(a)nmr.mgh.harvard.edu with subject line "Longitudinal Post-doc application" ) with questions and/or applications. To apply please send a cover letter, CV and the names/contact information of 3 people who could provide letters of reference. --- Mert Rory Sabuncu Assistant Professor of Radiology A.A. Martinos Center for Biomedical Imaging MGH/Harvard Medical School Research Affiliate Computer Science and Artificial Intelligence Lab, MIT http://people.csail.mit.edu/msabuncu Google Scholar Page

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mris_flatten_cuda
by James Gao 05 Mar '13

05 Mar '13

Hi, I'd like to use mris_flatten_cuda to accelerate the flattening process. However, it seems that the code doesn't handle ripped vertices correctly. mris_flatten by itself works correctly, but attempts to run mris_flatten_cuda results in thousands of "PANIC: RIPFLAG IS NOT SUPPORTED !" messages. The result is a completely folded surface. Peering through the code, it seems that the MRISremoveRipped command is being run (line 236 in mris_flatten.c), but somehow doesn't operate correctly. Is there any way to get the cuda version to run correctly, or is that not supported at this time? -James Gao -- University of California - Berkeley Vision Science Graduate Group

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FIR analysis, time window question
by Cesar E Echavarria 05 Mar '13

05 Mar '13

Hi Freesurfers, I did an FIR analysis to get the BOLD response over time, the following way mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR 1.000 -nconditions 8 -force -fsd bold -fir 4 14 I then generated the relevant contrasts, ran the funcroi-config command, and the func-roi-table-sess command to create 14 files for my ROI, each containing the signal value at 14 different time points. i.e. funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame0 -frame 0 funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame1 -frame 1 . . . funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct -o ROI/frame13 -frame 13 My question is this: To what time point (relative to stimulus onset) does the value in the frame0 file correspond? As I understand it, the first 4 frame values should correspond to activity pre-stimulus. However, this expectation is not corroborated by the timing and pattern of the BOLD response I am observing. I would appreciate any guidance on this issue. Thanks, Cesar Echavarria

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question stats
by j janssen 05 Mar '13

05 Mar '13

Hi Doug, using mri_glmfit with DODS and mri_glmfit-sim with a fsgd-file and contrast (attached) that looks like (2 discrete factors: 1 with 2 levels (diagnosis) and 1 with 4 levels (Site) and 1 continuous covariate (age)): GroupDescriptorFile 1 Title AGE-subj Class PatSite1 Class PatSite2 Class PatSite3 Class PatSite4 Class ConSite1 Class ConSite2 Class ConSite3 Class ConSite4 variables Age Input $FSGDID PatSite1 12.8 .. Input $FSGDID PatSite2 9.3 .. Input $FSGDID PatSite3 15.1 .. Input $FSGDID PatSite4 10 .. Input $FSGDID ConSite1 7.6 .. Input $FSGDID ConSite2 8.9 .. Input $FSGDID ConSite3 10.2 .. Input $FSGDID ConSite4 14 .. mri_glmfit --y lh.justmen.NOTmatched.CT.fwhm10.mgh --fsgd fsgd_justmen_NOTmatched_only_age.txt --C contrast_justmen_DODS_GxA.mtx --surf fsaverage lh --cortex --glmdir lh.justmen.NOTmatched.all.GRxAge.CT.fwhm10 for the contrast attached (which i thought is the interaction between diagnosis and age, independent of 'Site') i found 3 clusters using mri_glmfit-sim (attached). i saved these clusters as labels and transformed them to native space (cluster appeared in the correct location in native space): mri_label2label --srclabel cluster-001.label --srcsubject fsaverage --trgsubject $subject --trglabel $subject_cluster-001.label --regmethod surface --hemi lh and extracted mean CT from the cluster in native space: mris_anatomical_stats -l $subject_cluster-001.label -t lh.thickness -b -f $subject_cluster-001.stats $subject i plotted mean thickness for each cluster against age but did *not* see an interaction between groups. even though this is mean thickness for the cluster on non-smoothed native space thickness i would have expected to see some interaction but the slopes for both groups are almost parallel. any thoughts? i can provide more info if needed. -joost

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Some basic cortical thickness questions
by Rongxiang Tang 05 Mar '13

05 Mar '13

Dear All, I have some basic questions about groups analysis for cortical thickness, and I looked over the list and tutorial, but still have questions. I have two groups, experimental and control, and both were tested before and after training... I plan to use qdec to run the group analysis, and I finished the recon-all, and -qcache processing for each subject. My question is that: 1.Is it necessary to select a ROI prior to my cortical thickness analysis? 2.For the .dat text file, which stats (for cortical thickness) output should I use for the continuous factors such as left hemi thickness, right hemi thickness? Thanks, Catherine

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mprage resolution for surfaces/thicknes?
by Inati, Souheil (NIH/NIMH) [E] 05 Mar '13

05 Mar '13

A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in plane, 1.3mm thick. The SNR and CNR are pretty good. I figured I'd ping the list to see if anyone have any experience running scans with the slightly thickish voxels through the recon-all pipeline. Anything I ought to look out for in particular? Thanks, Souheil ---------------- Souheil Inati, PhD Staff Scientist, Functional MRI Facility NIMH/NIH/DHHS souheil.inati(a)nih.gov

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Freesurfer March 2013