Freesurfer April 2016

freesurfer@nmr.mgh.harvard.edu

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Extract random effects for correlation
by Lim Kai Wei, Joseph 13 Apr '16

13 Apr '16

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mri_surfcluster issues
by Antonin Skoch 12 Apr '16

12 Apr '16

Dear FreeSurfer experts, I am using mri_surfcluster to compare results from PALM and FreeSurfer cluster extent inference. I came across several issues in mri_surfcluster I cannot cope with. 1. I observed that --mask option in mri_surfcluster does not prevent cluster to growing outside the mask. When I run mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum summary.txt --subject fsaverage --surf white --hemi lh --thmin 0 --ocn cluster_summary.mgz --mask ./mask.mgh the cluster is growing outside mask and covers all surface including non-cortical (masked) regions. Is this intended behavior? This behavior (allowing clusters leak outside mask) seems strange to me since it could possibly influence results of cluster-extent inference in case of mask-constrained analysis. 2. How behaves mri_glmfit-sim in permutation-based building cluster-extent null distribution with mask? Is in this case also allowed to clusters to leak outside mask? 3. Another issue is concerning reported cluster area. I tested mri_surfcluster on data where overlay values (lh.thickness.fsaverage.mgh) were set to 0 outside cortex mask (they were non-zero also in some portion of non-cortical vertices). When I set thmin to non-zero value in mri_surfcluster mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum summary.txt --subject fsaverage --surf white --hemi lh --thmin 0.00001 --ocn cluster_summary.mgz --mask ./mask.mgh I get cluster comprising (almost) all cortex, not leaking to non-cortical areas. But what is strange, the reported cluster size is far larger than area of the whole cortical surface. number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 5 at vertex 817 overall min = 0 at vertex 8 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=0.000100 (0.000100), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 2 clusters Max cluster size 76431.562500 Saving cluster numbers to pok.mgz Here is output of mri_surfcluster: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs 1 5.000 817 76431.56 -25.8 4.6 -37.5 149874 2 2.670 144205 0.53 -15.8 -40.4 -3.8 1 How it is possible? 4. Does the fsaverage/surf/lh.area correspond to area of particular vertices on fsaverage/surf/lh.white? I expect yes. 5. How it is possible to calculate area of specified vertex of surface? I tried to do that by creating .label file with particular vertex number and running mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum summary.txt --subject fsaverage --surf white --hemi lh --thmin 0.00001 --clabel myVertex.label I indeed got report of 1 cluster with 1 vertex, with VtxMax value identical to vertex index in myVertex.label but the area value in summary.txt is different that value in fsaverage/surf/lh.area. Thank you very much in advance for clarification, Antonin Skoch

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FSFAST with reoriented reconstruction
by Julio Alberto González Torre 12 Apr '16

12 Apr '16

Hi Freesurfer users. I performed the recomended reconstruction of 82 subjects with Freesurfer. The images used for this reconstruction were previously reoriented to AC-PC position, because they were previously used for SPM purposes. Now I'm trying to perform the FSFAST workflow, and I had to unpack the original functional DICOMs for each subject. Those images are not reoriented because they were not used until now. The question is: The functional images should be previously reoriented to the same position as the anatomical used in Freesurfer? Should I perform the recomended reconstruction again with the original DICOMS? Or it doesn't matter the reorientation of the functional/anatomical images and Freesurfer would perform correctly the FSFAST? (I hope so, so I could skip the reconstruction, which involves many hours of processing) Thanks.

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Group level analysis: Specifying contrasts
by Afzal, Afsana 12 Apr '16

12 Apr '16

Hi, I want to perform a linear regression for a task with 3 different risk conditions (low, medium, high) with the following linear trend: low = 1, medium = 2, high = 3. Right now I'm specifying the above weighted under each risk condition in my contrast matrix. Is this the correct approach? I want to make sure I am calculating a regression and not a weighted average. Thank you for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Bad Segmentation in Left Thalamus
by Grant O'Brien 12 Apr '16

12 Apr '16

Hello, I’m an undergraduate at Duke University working on a study of pediatric structural imaging. We’ve recently come across some segmentation issues with the left thalamus (and very rarely the right thalamus) on many of our scans. Although our study isn’t looking at the thalamus as a region of interest, we’re concerned that it could be indicative of more global segmentation issues. Freesurfer appears to be incorrectly labeling segments of the left thalamus as “left cerebral white matter." We initially thought that perhaps the errors were due to motion artifacts, but we have observed this phenomenon in some scans with striping and some scans without striping (as demonstrated in the two screenshots). My questions are: What could be the possible reasons for this incorrect segmentation? Would scans with this problem need to be excluded? What steps could we take to fix it? Why might it only be occurring in the left thalamus? Thanks so much for your help. Best, Grant O'Brien Duke University Class of 2017 704-467-5449 [cid:BCEC92F0-59BE-4FBC-8E1B-B4DA90099CFB@dhe.duke.edu][cid:5CA3D954-63A9-4C96-B716-817AFCCB25D0@dhe.duke.edu]

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TRACULA
by Jasmin Alves 12 Apr '16

12 Apr '16

Hello Freesurfer Team, I attended the conference last week in Boston and really enjoyed all I learned! But while trying to run through the Tracula tutorial with my own data, I am having an error with my configuration file: ERROR: must specify as many DWI dicoms as subjects. My files are in nifti format, could this possibly be the cause of this error? I have attached my configuration file for reference. FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 Thanks so much! Jasmin Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Re: [Freesurfer] mri_vol2surf misaligment
by Francesca Strappini 12 Apr '16

12 Apr '16

Hi, I used load_nii and save_nii to read and write out the volume. Thank you! Francesca 2016-04-11 14:33 GMT+02:00 Francesca Strappini <francescastrappini(a)gmail.com >: > Hi, I used load_nii and save_nii to read and write out the volume. > > Thank you! > Francesca > > 2016-04-08 18:31 GMT+02:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> can you show a pic? What were your matlab commands to read in and write >> out the volume? >> >> On 04/04/2016 07:36 AM, Francesca Strappini wrote: >> > Dear Freesurfers, >> > >> > I run the preprocessing step of some functional data with >> > preproc-sess, then the Fourier analysis with matlab. Now, I'm trying >> > to plot this data on the surface: >> > >> > mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh >> > --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz >> > >> > I used as registration matrix the one produced by the preprocessing >> > step but when I try to visualize the map on the surface it looks like >> > completely misaligned. >> > >> > Thank you >> > Best >> > Francesca >> > >> > >> > >> > -- >> > Francesca Strappini, Ph.D. >> > Neurobiology Department >> > Weizmann Institute of Science >> > 234 Herzl Street, Rehovot 7610001 Israel >> > Tel.: +972 58 444 2584 >> > E-mail: francesca.strappini(a)weizmann.ac.il >> > <mailto:francesca.strappini@weizmann.ac.il> >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> > > > -- > Francesca Strappini, Ph.D. > Neurobiology Department > Weizmann Institute of Science > 234 Herzl Street, Rehovot 7610001 Israel > Tel.: +972 58 444 2584 > E-mail: francesca.strappini(a)weizmann.ac.il > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Segmentation of supplemental motor area
by Morten Sejer Hansen 12 Apr '16

12 Apr '16

Dear Freesurfer experts, I need to extract the volume of the supplemental motor area (cortical structure) I have used the aparch.stats2table and applied the both the ?h.aparc.stats and the ?h.aparc.a2009s.annot.stats atlas; However, I am having trouble identifying the supplemental motor area. Do you know if it is possible to extract volumes of this area using Freesurfer? Thank you. 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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3T or nuintensitycor3t
by Kasper Jessen 12 Apr '16

12 Apr '16

Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag? Best regards, Kasper -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

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August FreeSurfer course in Copenhagen, Denmark
by Allison Stevens 11 Apr '16

11 Apr '16

There are still some spots available in the Copenhagen FreeSurfer Course which will be held from August 10th to 12th, 2016. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. The course will be a three-day course for beginners and experienced users of FreeSurfer and the lectures will be held by FreeSurfer developers from the Laboratory for Computational Neuroimaging. For further information and to register for this course, please visit: http://fscph2016.nru.dk/ Please feel free to contact my friends at NRU (cc'd) with any questions. Allison Stevens Lab Manager/Course Organizer Laboratory for Computational Neuroimaging FreeSurfer Development Team

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Freesurfer April 2016