Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mri_glmfit-sim ( cluster wise analysis)
by Alshikho, Mohamad J. 22 Mar '16

22 Mar '16

Dear FS experts, I ran cortical thickness analysis as previously explained in Wiki : Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis My data is previously cached so I ran the command : mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh GLM analysis: mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir Correction for multiple comparison mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces In order to do cluster-wise correction for multiple comparisons, I ran the command "mri_glmfit-sim" (step3). This command is calling, internally, the command "mri_surfcluster" as follow: mdline mri_surfcluster --in lh//2G0C/sig.mgh --csd /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd --mask lh//mask.mgh --cwsig lh//2G0C/cache.th13.pos.sig.cluster.mgh --vwsig lh//2G0C/cache.th13.pos.sig.voxel.mgh --sum lh//2G0C/cache.th13.pos.sig.cluster.summary --ocn lh//2G0C/cache.th13.pos.sig.ocn.mgh --oannot lh//2G0C/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf lh//2G0C/cache.th13.pos.pdf.dat --cwpvalthresh 0.05 --o lh//2G0C/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Kindly, I have the following questions: 1. How the command mri_surfcluster choose the fwhm=?? for the flag "csd" . In the previous command it shows fwhm=15. Is this depends on how much I am smoothing in the previous steps? 2. What is purpose of using the flag Bonferroni in the previous command 3. If we are doing cluster wise correction, what is theexact usage of the flag "--vwsig" ? Thanks for your patience ! Looking forward to learn from you Mohamad

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Using digital tablet pen
by Mahmoud 22 Mar '16

22 Mar '16

Dear Experts, I was wondering if someone could share with me and others the experience using digital tablet pen and those sort of things instead of mouse to edit and touch the images especially the masks. I appreciate your help. Thank you! Mahmoud

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Asegstats2table: insula and Substantia nigra volumes are not reported
by Morten Sejer Hansen 22 Mar '16

22 Mar '16

Dear Experts, I am interested in retrieving the volume of the insula and substantia nigra from T1W structural scans converted to nii.gz files. All scans have undergone the recon-all process without error. I have seen volume estimations of Insula and substantia nigra performed in several studies, but I can't seem to figure out how I retrieve these volumes. I ran the command: asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to Subcortical.txt following this I get at fine output with several volume estimation of subcortical structures, but without the Insula (left and right), and without the substantia nigra (left and right). I tried to run the same command on "Bert", and ended up with the same result (with the insula and substania nigra still missing). I also tried to add the --all-segs But without any change in the output. On the FreeSurferColorLUT (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurf…) I can see that the structures I am interested in have the following numbers: 19, 27, 55 and 59. Could you provide me answers on how to extract the volumes of the insula and substantia nigra? Thanks a lot! Kind regards Morten Sejer Hansen Morten Sejer Hansen MD Direct: + 45 26373611 Mail: morten.sejer.hansen(a)regionh.dk / morten.sejer.hansen(a)dadlnet.dk<mailto:morten.sejer.hansen@regionh.dk%20/%20morten.sejer.hansen@dadlnet.dk> Department of anaesthesiology 4231 Centre of head and orthopaedics Copenhagen University Hospital, Rigshospitalet Blegdamsvej 9 2100 Copenhagen Tel: +45 35 45 35 45 Web: www.regionh.dk<http://www.regionh.dk/> This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message. ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

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Troubleshooting for error - neither NIfTI-1 qform or sform are valid
by Reema Jayakar 22 Mar '16

22 Mar '16

Hello FS list subscribers, Is there a way to manually feed FS with NIfTI-1 qform or sform information? Or correctly add this information to the original .nii files? My sense of the problem is that there is a problem with the header information in my .nii files and FS cannot tell what is anterior, posterior, left, right. That said, I am very new to FS and my interpretation of the error could be wrong. So I am laying out the details below (recon-all.log is also attached to this email): - When I try to run recon-all there are no output images/files generated and the message I get is that the Talairach transform failed - When I try to run autorecon1 an autorecon2 with the "-notal check" flag, FS does not give me any error message and proceeds with generating output. However, I can visually see (via brainmask.mgz) that oreintations are messed up (e.g., tried to register coronal orientation on top of sagittal orientation) - This problem only occurs with .nii files from a particular study that came out of a specific scanner. All my other data are running through FS smoothly, which is why I think there is some problem with the .nii files - Also, when I view my raw .nii images in FSL view none of the usual orientation markers are visible to me, which again suggest that they may be missing? - Unfortunately, I do not currently have the original .dcm files available as this is a multi-site archival study Any help you can provide to resolve this issue would be really appreciated! Thank you, Reema -- *Reema Jayakar, M.A.* Doctoral Candidate - Clinical Neuropsychology Health Resources and Services Administration (HRSA) Fellow Department of Psychology Georgia State University Email: rjayakar1(a)student.gsu.edu

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Create a surface overlay with statistic results using AAL ROI
by carolina.mr 22 Mar '16

22 Mar '16

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Re: [Freesurfer] epidewarp.fsl for FSL 5.x
by Douglas Greve 22 Mar '16

22 Mar '16

It is there again. I don't know what the status if it is in terms of the version. Try it and let me know doug On 11/25/14 4:34 PM, Morgan Hough wrote: > Hi Doug, > > Could you put the epidewarp.fsl script back on your ftp site? I don’t > see it at the link in the archives: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl > > BTW, is the script updated in some way for 5.x or can I can the old > script just be changed to accept 5.x version numbers. > > Cheers, > > -Morgan

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extracting pial surface area numbers...
by Karl Liu 22 Mar '16

22 Mar '16

Dear FS team, My question is how I should extract the measure of pial surface area from a significant cluster after group-analysis. I performed statistical analysis in QDEC, choosing pial surface area as the measure. I found a significant cluster. Now I would to extract the surface area of this cluster from each subject, so that I can plot the group means. But the numbers I got from the "cache.th20.neg.y.ocn.dat" file are quite small (mean centered at ~1). I am wondering how I should get the correct numbers from each subject. thank you in advance Karl

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Regarding: Freesurfer 6.0 dev version
by Dr Sampada Sinha 22 Mar '16

22 Mar '16

Dear freesurfer experts, I am trying to do hippocampal subfields segmentation on Mac. I will greatly appreciate if freesurfer 6.0 version link is forwarded to me. With thanks and regards, Sampada Pre-doctoral student KGMU, Lucknow India

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"Bump" - Fwd: lGI value is aberrantly high and misalignment fix
by Marco Bucci 22 Mar '16

22 Mar '16

Dear all, I forward again my original post. I also attach the recon-all.log of one of the several faulty cases. I run freesurfer (freesurfer-Darwin-lion-stable-pub-v5.3.0) in Mac OS X 10.9.4 and -lgI option with Matlab_R2013a and I have fixed the SearchProjectionOnPial.m. I also had to fix line 51 of make_outer_surface.m "v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different orientation" with "v2=[vol.vox2ras1(1,4)-v(:,1) v(:,3)+vol.vox2ras1(2,4) vol.vox2ras1(3,4)-v(:,2)];" in order to use the image coordinate to fix surface orientation and alignment. If I would use the original line 51, the surface produced by recon -lgi results misaligned with the reference pial and image. My problems remains the aberrantly high lgI value in most of my subject images. Can you help me? Yours, Marco Bucci ---------- Forwarded message ---------- From: Marco Bucci <bucci.marco(a)gmail.com> Date: 2015-12-22 23:49 GMT+02:00 Subject: Re: [Freesurfer] lGI value is aberrantly high To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Dear all, I have a problem with the LGI module. At the step when the software computes the LGIs for the vertices, In one vertex the lGI results aberrantly high and the software exits with ERRORS. I tried the solution suggested by Marie Schaer to rereconstruct The images with "randomness" Recon-all -autorecon2-wm -randomness -autorecon3 I tried this fix on two of my subjects With errors. Not all subject resulted Errors in the computation of the gyrification. Can you help me? Marco Bucci Turku Pet Center Sent from my iPhone -- **************************************************** Marco Bucci, PhD in Clinical Physiology and Nuclear Medicine Turku PET Centre Turku University Central Hospital (TUCH) PL 52, Kiinanmyllynkatu 4-8, 20521 Turku, Finland tel. +358 2 3132798 fax. +358 2 2318191 mobile: +358 40 6873976 UTU e-mail: marbuc(a)utu.fi ****************************************************

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Postdoctoral Position in Infant Brain MRI Analysis
by gangli 21 Mar '16

21 Mar '16

Postdoctoral research associate positions are available at the Infant Brain Mapping Lab in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill. Our current focuses are to better understand the dynamic and critical early brain development in health and disease, via multimodal neuroimaging analysis. The successful candidate will support our efforts either in advancing neuroimaging analysis technologies or in neuroscience applications. We are seeking highly motivated individuals who have extensive research experience in neuroimaging analysis (e.g., structural, diffusion or functional MRI) and demonstrated academic excellence, including publications in first-class journals and conferences. The candidate for Postdoctoral Research Associate should have a Ph.D. (or equivalent) in Neuroscience, Computer Science, Applied Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or related fields. Good command of programming tools including Matlab, C/C++, Linux, and scripting are necessary to carry out the research work in this group. The successful candidate will be part of a diverse group including neuroscientists, radiologists, psychologists, physicists, biostatistician, and computer scientists, and will build upon the group's extensive foundation on neuroimaging analysis. If interested, please email resume to Dr. Gang Li (gang_li(a)med.unc.edu)

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