Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Matlabpool has been removed
by Kasper Jessen 23 Mar '16

23 Mar '16

Dear FreeSurfer experts, Thanks again for a great FreeSurfer forum. I have been trying to run the linear mixed effects model on a longitudinal dataset. However, i get the an error in matlab: "matlabpool has been removed. Use PARPOOL instead". I can see in the forum that others have experienced the same. Unfortunately i cannot find the answer, which fixes the problem. As far as i understand, it may be because i am using a new version of Matlab. However, is there a way to fix the problem? Best regards, Kasper Jessen MD, PhD student

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mris_anatomical_stats on more than one subject at a time?
by Elissa Ash 22 Mar '16

22 Mar '16

Dear experts, Is there any way to run the mris_anatomical_stats command on more than one subject at a time? Thanks, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

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mris_flatten error
by Ji Won Bang 22 Mar '16

22 Mar '16

Dear. Freesurfer experts. Hi. How are you? I'm trying to flatten the visual cortex using the command mris_flatten (freesurfer version 5.3.0). The command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat The error I get is: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with 27964 vertices (19.0% of total) MRISreadPatch: bad vertex # (147220) found in patch file No such file or directory Previously, Bruce advised me to recut it, so I deleted the lh.oc.patch.3d and recut it. However, freesurfer gives me the same error message... Could you please help me fix it? Thank you so much. Best, Ji Won

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PET voxelwise
by Elijah Mak 22 Mar '16

22 Mar '16

Hi Freesurfer Community, I am trying to run a vertex-wise analyses of PET data. I have already performed bbregister. Next, I did mri_vol2surf for each subject, left and right hemispheres. for i in `cat subjects`; do mri_vol2surf --src FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out FS6_${i}_MPRAGE_Neuro.nii/surf/lh.PETSurface.mgh --hemi lh --regheader FS6_${i}_MPRAGE_Neuro.nii --projfrac 0.5 --interp nearest; done Is this command correct? Visual inspection on freeview looks OK. How may I derive the group average from these individual surfaces and perform the mri_glmfit? Any help will be greatly appreciated. Best Wishes, Eli

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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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Freesurfer March 2016