Re: [Freesurfer] Cortical thickness values more than 5 mm
sure, you need to rerun mris_thickness with -max where N is the threshold you want to use (making it big enough and nothing will get thresholded) On Fri, 5 Apr 2019, Gonzalo Rojas Costa wrote: External Email - Use Caution Hi: How can I get cortical thickness surface image with values more than 5 mm? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Post-doctoral Position in Network Neuroscience at the University of Michigan
External Email - Use Caution Post-doctoral Position in Network Neuroscience at the University of Michigan A post-doctoral position is available in network neuroscience at the University of Michigan working with Chandra Sripada in Psychiatry, Liza Levina in Statistics, and Scott Peltier in Biomedical Engineering. The successful candidate will work on funded research projects that: 1) develop new methods for quantifying individual differences and longitudinal change in brain networks (functional and structural imaging modalities); 2) implement these methods in large datasets covering childhood (ABCD) and late adulthood (UKBiobank), with a focus on characterizing changes in neurocognition (executive functions, attention, learning and memory). Required Qualifications: a PhD in cognitive or computational neuroscience coupled with very strong quantitative skills; or a PhD in statistics, biostatistics, computer science, biomedical engineering, or another methodological discipline coupled with ability to work with brain and behavioral data. A strong background in the analysis and interpretation of neuroimaging data is a plus. Strong programming skills are a must; Matlab, R, and/or Python preferred. This is a 2-year position that has a possibility of being extended to a third. Start date is flexible, but September 2019 is preferred. If you are interested in this position, please send a CV and research statement to Chandra Sripada (srip...@umich.edu). -- Mike Angstadt Research Area Specialist Lead / PANLab Lab Manager Department of Psychiatry / University of Michigan (734) 936-8229 ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] aparc colours
External Email - Use Caution I was using the RGB values listed here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT as a lookup table for values in annotations. However, I find the left and right temporal lobes have different values. On the table they are dark grey [70 70 70] and in the aparc.annot they are purple [70 20 170]? What is the reason for this? The purple looks nicer Also, corpuscallosum is listed in the annotation aparc.annot but is not present in the vertices so I guess it does not matter. Thanks for your help Simon Mr P Simon Jones Research Associate University of Cambridge Department of Clinical Neurosciences Herchel Smith Building Forvie Site Robinson Way Cambridge Biomedical Campus Cambridge CB2 0SZ United Kingdom https://ftd.neurology.cam.ac.uk/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness values more than 5 mm
External Email - Use Caution Hi: How can I get cortical thickness surface image with values more than 5 mm? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Postdoc or Research Associate/Scientist at Northwestern in Chicago
External Email - Use Caution *Apologies for cross-posting* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease Imaging Core is seeking a research associate or postdoctoral fellow. Prior experience with Alzheimer's disease is *not a requirement*. The primary responsibility of this position is to develop and automate the preprocessing and analysis of large-scale neuroimaging datasets involving PET and MR imaging. This will involve implementing state of the art methodologies, including signal processing and statistical learning, on a high performance computing cluster. The individual may participate in publications and presentations resulting from the work. This individual will work with Emily Rogalski (Imaging Core Leader) and her collaborators Todd Parrish (director of the Center for Translation Imaging) and Lei Wang (director of the Applied Computational Anatomy Lab) at Northwestern University’s Feinberg School of Medicine. The Mesulam Center is located on the downtown campus, nestled between the Magnificent Mile and the city's beautiful lakefront. Successful candidates will have a Ph.D. or M.S. in computer science/engineering, biomedical engineering, neuroscience, or a related field. A successful applicant will be proficient in programming (Python or related language); be familiar with scientific-computing such as NumPy, SciPy, and Pandas and neuroimaging libraries such as FreeSurfer, FSL, AFNI, SPM; have the ability to work effectively in a multidisciplinary collaborative environment. Experience with a single imaging modality (sMRI, DTI, rsfMRI and/or PET) is required with a particular emphasis on multimodal approaches. Interested applicants should send a CV and cover letter stating experience and interests, two or three peer-reviewed publications, and at least two letters of recommendation to a...@northwestern.edu. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness values in the insula...
probably easiest to use matlab. see FREESURFER_HOME/matlab/read_annotation.m, which has an example On 4/5/2019 11:29 AM, Gonzalo Rojas Costa wrote: > External Email - Use Caution > > Hi: > >How can I get the different values of cortical thickness in the > insula? Not the mean and SD... > > >Sincerely > > > Gonzalo Rojas Costa > > ___ > 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
[Freesurfer] cortical thickness values in the insula...
External Email - Use Caution Hi: How can I get the different values of cortical thickness in the insula? Not the mean and SD... Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ERROR: Talairach failed!
Hi Abby if you upload an image that fails we will take a look. If I had to guess, I would say it is because you have so much non-brain tissue (neck and even shoulders). YOu could try cropping your rawavg.mgz with the freeview tools->crop tool to elimate stuff below brainstem and see if that helps cheers Bruce On Fri, 5 Apr 2019, Abby tang wrote: External Email - Use Caution I load my original nifti through freeview and they are right directions display. I attached two picture which are different subjects with letter. one of them,called correct,processed as normal. Another is the subject with problem as mentioned. I hope you can give me some other advises.Thank you so much. Bruce Fischl 于2019年4月4日周四 下午9:42写道： Hi Abby if you load your original nifti do the directions display properly? That is, are right/anterior/superior as shown by freeview in the correct directions anatomically? cheers Bruce On Thu, 4 Apr 2019, Abby tang wrote: > > External Email - Use Caution > > Hello FreeSurfer Developers, > > I'm attempting to recon_all my subjects which is .nii file. But I usually meet this error. > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0 > 000 < threshold=0.0050) > Command exited with non-zero status 1 > @#@FSTIME 2019:04:04:10:30:25 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 50% M 6252 F 7 R 243 W 0 c 1 > w 8 I 1384 O 0 L 1.11 0.48 0.21 > @#@FSLOADPOST 2019:04:04:10:30:25 talairach_afd N 4 1.11 0.48 0.21 > Manual Talairach alignment may be necessary, or > include the -notal-check flag to skip this test, > making sure the -notal-check flag follows -all > or -autorecon1 in the command string. > See: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > ERROR: Talairach failed! > Linux abby-virtual-machine 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_6 > 4 x86_64 GNU/Linux > recon-all -s 0306A_T1_w4 exited with ERRORS at Thu Apr 4 10:30:25 CST 2019 > For more details, see the log file /home/abby/freesurfer_data/M_W4_T1_NONfreesurfer/W4_1/0306A_T1_w4 > /scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > I've searched the list and they advised to check with this website https://surfer.nmr.mgh.harvard.ed > u/fswiki/FsTutorial/Talairach_freeview. however,my subject's recon_all folder doesn't have T1.mgz a > nd brainmask.mgz. it just has mri_nu_correct.mni.log orig orig_nu.mgz transforms mri_n > u_correct.mni.log.bak orig.mgz rawavg.mgz > > I run ten files, and almost all of them go wrong, which is very strange.I need your help. please giv > e some advises with program statements in detail. > > I really appreciate your help > > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz > 2) Platform: ubuntu 18 > 3) recon-all.log:see attached > >___ 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
[Freesurfer] FSFAST group analysis problem: dimension mismatch between y and X
External Email - Use Caution Hi Freesurfer experts I'm having a problem running an FSFAST group analysis. When I try to run the second level GLM, I get the following error: keri@buddha:~/audio_108_no_stc_tau1,5$ mri_glmfit --y ~/audio/all/audio.lh/tones/ces.nii.gz --wls ~/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls --nii.gz gdfRead(): reading 2groups.fsgd INFO: gd2mtx_method is dods Reading source surface /home/keri/recon_all/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.984375 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /home/keri/audio_108_no_stc_tau1,5 cmdline mri_glmfit.bin --y /home/keri/audio/all/audio.lh/tones/ces.nii.gz --wls /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz --fsgd 2groups.fsgd --C groupdiff.mtx --surface fsaverage lh --glmdir all_tones_left_glm.wls --nii.gz sysname Linux hostname buddha machine x86_64 user keri FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/home/keri/audio/all/audio.lh/tones/ces.nii.gz logyflag 0 usedti 0 FSGD 2groups.fsgd labelmask /home/keri/recon_all/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir all_tones_left_glm.wls IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /home/keri/audio/all/audio.lh/tones/cesvar.nii.gz weightinv 1 weightsqrt 1 Creating output directory all_tones_left_glm.wls Loading y from /home/keri/audio/all/audio.lh/tones/ces.nii.gz ... done reading. INFO: gd2mtx_method is dods Saving design matrix to all_tones_left_glm.wls/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1.34783 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 66097 voxels in mask Saving mask to all_tones_left_glm.wls/mask.nii.gz Reshaping mriglm->mask... search space = 31233.070725 ERROR: dimension mismatch between y and X. y has 116 inputs, X has 108 rows. 108 is the number of subjects that I have. I can see that the y file with 116 inputs is /home/keri/audio/all/audio.lh/tones/ces.nii.gz , and checking the dimension of it, it confirms that it is a 4D matrix with the 4th dimension of 116. It seems as if this file is created during isxoconcat-sess, and I have checked and the session ID file being used here has only 108 entries. It appears that 108 subjects are being used in this step, as part of the output is: ninputs = 108 Checking inputs nframestot = 108 Allocing output Done allocing nframes = 108 I think that a source of the error could be the fact that at one time I did have 116 subjects. I've created a new folder, copying in the unpacked files for each subject, and repeating from the preprocessing step, but this doesn't make any difference. Is there are chance that there's a file outside the functional directory that has stored this 116? Any help is greatly appreciated. Best wishes, Keri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
