Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

postdoc ad
by Lilla Zollei 07 Aug '17

07 Aug '17

Please, see attached or below for details. Lilla >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Postdoctoral Research Fellow Position in Infant Brain MRI analysis at the A.A. Martinos Center, MGH and Harvard Medical School under Dr. Lilla Zöllei A postdoctoral fellow is recruited for an NIH funded project for developing Freesurfer-compatible brain image analysis tools for children. Code development will focus on pair- and group-wise registration tools, segmentation methods and surface-based image analysis algorithms. The successful applicant should have a doctoral degree in a field related to medical imaging (e.g., computer science, electrical engineering, biomedical engineering, applied mathematics, computational neuroscience). She/he is expected to have a strong research background in method development and brain image analysis and should be able to work independently. Strong programming skills (for example, C/C++, MATLAB, and/or Python) are a must and prior experience with brain image-analysis packages (such as SPM, FSL, FreeSurfer, AFNI) is desirable. In addition, the candidate must also possess excellent English verbal and written communication skills. This position will be jointly hosted by the Laboratory of Computational Neuroimaging, MGH and the Department of Psychology, Harvard University, thus the position offers great opportunities to collaborate with a large group of scientists from diverse research disciplines. Approximate start date is fall 2017. For consideration please send a statement of interest, a CV and a list of three potential references via email to Lilla Zöllei, PhD (lzollei(a)nmr.mgh.harvard.edu) The search will continue until the position is filled.

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mri_glmfit-sim output
by Van Der Deijl, Rosanne 07 Aug '17

07 Aug '17

Dear Freesurfer team, In the mri_glmfit-sim summary output file, I get a number of output variables, and I'm not sure what some of them are. Could you explain the ones in bold to me? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPH NVtxs WghtVtx Annot 1 2.015 134872 355.89 -36.3 -9.7 -1.4 0.96620 0.96390 0.96850 841 1298.68 insula 2 1.652 71259 154.25 -49.4 -52.7 39.2 1.00000 -0.00010 1.00000 363 526.18 supramarginal 3 -1.521 91550 39.92 -37.1 -26.5 -23.3 1.00000 -0.00010 1.00000 90 -125.33 fusiform 4 1.322 139141 0.76 -36.4 3.5 -10.7 1.00000 -0.00010 1.00000 2 2.62 insula 5 1.312 73658 0.47 -36.0 -4.4 9.6 1.00000 -0.00010 1.00000 1 1.31 insula 6 1.387 133422 0.44 -5.1 -17.2 51.7 1.00000 -0.00010 1.00000 1 1.39 paracentral I know CWP stands for Cluster-wise P-value. But what is the low and the high number, a confidence interval? And isn't it odd that my p-values are (almost) 1? Thank you in advance. Kind regards, Rose

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susceptibility-induced distortions
by John Anderson 07 Aug '17

07 Aug '17

Dear Freesurfer experts, I want to inquire if there are any tools or any methods to improve T1 images which has "susceptibility-induced distortions" - attached an example. I need to fix these distortions outside the brain. In the mouth area and I am wondering what is the best approach to deal with it and fix it. I highly appreciate any help John

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Sampling vertex-wise data across various distances from the core of a mask to a somewhere else on fsaverage
by Elijah Mak 07 Aug '17

07 Aug '17

Hi Doug and Freesurfer Experts, I am trying to see whether cortical thinning gets progressively less severe as we move further away from a seed/voxel (e.g. precuneus). Is it possible to perform correlations between the (a) distance between a given vertex to specific point on fsaverage, and the (b) measurement (i.e. thickness) of the vertex? Say I have a binary mask of the precuneus seed, as well as a second binary mask that surrounds it. How may I go about getting the thickness values at various distances, starting from the central core of the precuneus seed to the outer boundary of the second mask? I was thinking of something analogous to the proj-frac function in mri_vol2surf where we could sample PET/fMRI data at different values along the cortical ribbon. Apologies if that was rather confusing. If you like, I could make a drawing of what I am trying to do. Thanks for your time. Best Wishes, Elijah

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installtation error
by 水墨丹青 07 Aug '17

07 Aug '17

TO: freesurfer(a)nmr.mgh.harvard.edu FROM: fsuser(a)worlduniversity.edu SUBJECT: installation error error: there is no setupfreesurfer.sh file Hello FreeSurfer Developers, I'm attempting to install freesufer on my computer(linux ubuntu 14).But there is on setupfreesurfer.sh file.I can find a setupfreesurfer.csh file on installation directory.I think I should install it using bash rather than tcsh.Thank you every much! I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: CentOS release 6.7 (Final) 3) uname -a: Linux ubuntu 14.0.4 LTS 4) recon-all.log: see attached

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Need Urgent Help!! Regarding FreeSurfer Installation
by Tabassum, Ruchira 05 Aug '17

05 Aug '17

Hi, I need Freesurfer for my windows OS. Is there any windows version of FreeSurfer? Please let me know ASAP. Kind Regards Ruchira Tabassum

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Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation
by Matt Glasser 05 Aug '17

05 Aug '17

No. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Tabassum, Ruchira" <Ruchira_Tabassum(a)student.uml.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Saturday, August 5, 2017 at 12:22 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation Hi, I need Freesurfer for my windows OS. Is there any windows version of FreeSurfer? Please let me know ASAP. Kind Regards Ruchira Tabassum _______________________________________________ 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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Co-ordinate systems in FS
by Martin Juneja 04 Aug '17

04 Aug '17

Hi FreeSurfer experts, I am trying to correlate my behavioral data with whole brain cortical measures using cortical measures as IVs and behavioral data DV. Somehow the significant clusters I get from cortical thickness, area and volume are in MNI co-ordinates but significant clusters from local gyrification-behavioral data are in Talairach co-ordinates. I used identical procedures to preprocess my data but still I am getting my results in different co-ordinate systems (thickness, volume, area in MNI and gyrification in Tal). I would really appreciate any help. MJ

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label2annot issue
by Redwan Maatoug 04 Aug '17

04 Aug '17

Hi all, So my issue is the following : I have 112 mgh files. (They come from the Yeo 17 Network atlas (we split the atlas in smaller regions). I have extracted the coordinates with : mri_surfcluster (playing with the thmin option) mri_vol2label and then I have used mri_label2annot with my own color lookup table to combine the 112 files into 1 file. (I have played with --noverbose, --maxstatwinner) When I try to display, I have the feeling that there is some overlapping because what tksufer dispays, is not very relevant and it is spotty. I have attached some screenshots Thank you very much for your help, Redwan

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Optseq2 onset times
by Ruthie Shaffer 04 Aug '17

04 Aug '17

Hi, I’m using Optseq2 to generate stimulus / jitter schedules, and, depending on the TR used, in the output timing files I see several event onset times very close to the correct time, but slightly off (for example, something like 124.7999, instead of 124.8). I’ve used the following command to generate timing files: optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 --nkeep 6 --o CRtiming.2017 --nsearch 100000 --tnullmin 0 --tnullmax 6.4 Should I be concerned about optimal onset times that are slightly off from the actual possible onset times based on the TR, or is it correct to assume it should be 124.4, instead of 124.4001 or 125.8, instead of 125.7999, for example? Thank you in advance for any help on this! Best wishes, Ruth Shaffer

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Freesurfer August 2017