Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30133 discussions

mris_apply_reg
by Matthew Defenderfer 13 Dec '16

13 Dec '16

Hi All, I am trying to mirror labels across hemispheres and found various threads using mris_apply_reg. Unfortunately the version of that command I have does not recognize labels and all of the links in the mailing list seem to be broken. Would it be possible to get a link to the updated command? Thank you. -Matthew Defenderfer

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(no subject)
by Abigail Noyce 13 Dec '16

13 Dec '16

Hi Doug et al, I would like to get a different cluster summary stat out of mri_glmfit-sim. Rather than size, I'd like to use the "sum of t-scores" (after Maris & Oostenwald 2007, for example). That is, set a cluster inclusion threshold, and then for each cluster of adjacent vertices that clear the threshold, sum their t-scores. For the permutation significance testing, then, the largest such clusterwise sum would be the statistic used to generate the null distribution... I'm happy to write my own scripts, but can't figure out where to try to pull this number out. Thanks! Abby Noyce

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Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume
by Dowling, Kevin Francis 13 Dec '16

13 Dec '16

Hi Doug, Thank you for your note and my apologies for a delayed response. To create the sig.mgh file we used a volume specific mri_glmfit analysis, omitting the --surf flag and using our volume specific input (ces.nii.gz in SIRP_LoadRegression_Stable5.3_012616_sm5_mni305). I don't know if this information is helpful but when we've run a nearly identical analysis using almost all of the same participants and a different blood folate marker (serum folate) the volumes came out completely fine. I've tried de-meaning the RBC folate values and re-running the mri_glmfit, but the odd activation persists. This is our mri_glmfit command: mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/ces.nii.gz --fsgd /cluster/roffman/users/fsgd/GDD/137_GDD_Cond2vFix_Covary_RBC_Folate_linear_KDcorrect.fsgd --C /cluster/roffman/users/fsgd/TwoGroups1CovariateRegressOut1Covariate_KD --glmdir /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/GDD_Adults/137_GDD_RBC_Folate_Cond2vfix_KD/SIRP_LoadRegression_Stable5.3_012616_sm5_mni305/Cond2vFix/2vFix_ClassUsed_Covary_RBCFOLATE_Nuis_Age_Gender --fwhm 6 --no-prune Thank you very much, I am most appreciative of your help! Kind regards, Kevin Kevin F. Dowling Clinical Research Coordinator Brain Genomics Laboratory Division of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA, 02129 (p) 617.643.2479

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Freesurfer longitudinal analysis accuracy
by Gabor Perlaki 13 Dec '16

13 Dec '16

Dear all, We've run longitudinal Freesurfer on 30 healthy subjects. We have two subgroups (n=15) and we found a significant longitudinal change in the left and right cerebellar cortex in one of our subgroups. However, this change is very small: mean=0.67% range: -1.61-2.3% for the right cerebellar cortex; mean=0.86% range: -1.64-3.7% for the left cerebellar cortex. Although statistics indicate significant cerebellar cortex increase, we are sceptical that Freesurfer's accuracy allows reliable detection of such small differences. Is there any article on how accurate the longitudinal Freesurfer for cerebellum segmentation or any suggestion on how to decide whether our results are reliable? Best, Gabor

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MS Lesions effects on cortical thickness in FS 6.0
by Ismail Koubiyr 12 Dec '16

12 Dec '16

Dear Freesurfer experts, We are facing a problem in our study and would need your advice on it. We want to get an accurate measurement for the cortical thickness from our MS patients data. For that we are using 3D T1 and FLAIR (recon-all will be used with the FLAIR option so that we can a more accurate pial surface). However, we were wondering if running recon-all on the raw data would lead to some errors specially because of the juxtacortical lesions or not. Or, is it better to first apply a lesion filling using our lesion mask ? I should specify that we will use the longitudinal pipeline if it is of any use. Thank you all. Ismail PhD candidate Neurocentre Magendie, INSERM Bordeaux, France

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white matter segmentation incorrect after intensity change
by Rizvi, Batool 12 Dec '16

12 Dec '16

Hi FreeSurfer experts, After running -autorecon2 and -autorecon3, we're seeing issues for some of the subjects, which now start showing changes in intensity/brightness in some voxels, and this increased intensity is now missed by the white matter and grey matter segmentation, and is labeled as non-brain matter. Attached is an example of a subject's brain that was segmented incorrectly, which we think is due to the intensity around that frontal region. We hadn't added control points in that region, so we are unsure what the cause of the intensity change is. In our first pass before running -autorecon2 -autorecon3, we did not notice this error or the intensity values to be so bright for that region. Thanks for your help! BR

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longHippoSubfields
by Christian Krog Tamnes 12 Dec '16

12 Dec '16

Dear Juan and FreeSurfer team, We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can't seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build? Best regards, Christian

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Postdoctoral Fellowship in Memory
by Aneesha Nilakantan 11 Dec '16

11 Dec '16

*Full-Time Postdoctoral Fellowship in Memory * *Laboratory for Human Neuroscience Northwestern University* *Feinberg School of Medicine * http://www.lhn.northwestern.edu/Postdocsearch2017.pdf One full-time postdoctoral fellowship is available in The Laboratory for Human Neuroscience at the Northwestern University Feinberg School of Medicine, directed by Dr. Joel Voss (www.lhn.northwestern.edu) The research focus for this position is the effects of transcranial magnetic stimulation (TMS) on cortical networks of the human hippocampus and their contributions to learning and memory. The successful candidate would work with a large, longitudinal fMRI dataset collected from individuals participating in multi-week TMS experiments, including both young and elderly adults (supported by NIH grants R01MH106512, R01MH111790, and R01AG049002). The successful candidate would also be encouraged to develop an independent research focus, and would be provided with access to laboratory resources including equipment for TMS, high-density EEG, and eye-movement tracking studies of memory, a research registry of individuals with circumscribed neurological injuries, and excellent fMRI scanning facilities (www.cti.northwestern.edu) The Northwestern University Feinberg School of Medicine is a large academic medical center in the heart of downtown Chicago. It is home to a vibrant neuroscience community, structured around a multi-departmental neuroscience program (www.nuin.northwestern.edu) Position requires a Ph.D. or M.D./Ph.D. in a neuroscience-related field, broadly specified. We are seeking candidates with strong computational abilities, substantial experience in fMRI or EEG data analysis, and excellent written and verbal communication abilities. To apply, please send a cover letter, C.V. (or NIH-style biographical sketch), and the names of at least three individuals who could provide references if required. Contact name: Jonathan O’Neil Contact email: lhn(a)northwestern.edu

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Free surfer mri_convert and subjdir problems
by anand iyer 10 Dec '16

10 Dec '16

I wonder if anybody could help please? 1. I have converted DICOM to NIFTI and then when I try to apply mri_convert command to change it to .mgz; i cant locate the converted file! 2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient. 3. Thus i cannot apply the command recon-all. Is there any easy way to get the DICOM to load on to freesurfer without all this hassle? I am grateful for your help. Anand

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Freesurfer on Centos 7?
by Caspar M. Schwiedrzik 09 Dec '16

09 Dec '16

Hi! I was wondering whether there is an update from the 2014 thread on Freesurfer's compatibility with Centos 7? The old thread is here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html I have also come across this website mentioning some changes in the installation related to Perl and MNI tools: http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7 Any insights would be appreciated. Thanks, Caspar

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