Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

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

2 2

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

2 5

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

2 4

Freesurfer software in stroke study
by Frank Robert 09 Dec '16

09 Dec '16

Dear Freesurfer experts I am curious whether Freesurfer segmentation tool is good at segment and quantify the stroke lesion size in T2 FLAIR image, GRE images, DWI images and Perfusion (DSC/ASL) images? If have a good tool, is there instructions how to use it? Many thanks Best Regards Frank Yu

1 0

poor segmentation and skull-strip = due to talairach?
by Rizvi, Batool 09 Dec '16

09 Dec '16

Hi FreeSurfer team, We have a couple of subjects that have really poor segmentation and skull-strip as well, that seem beyond fixing with just control points or WM edits. I'm wondering if this occurred because of earlier in the stream, there was a bad talairach transform? I went back to see the talairach, and it also looked irreparable. So this time, I tried using the other method of producing a talairach transform (mritotal), but this only made it much worse than before. How can I regenerate the talairach so that it will at least cleanly fit the lines of at least the target volume? Thanks very much! Batool

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Infant brain atlas
by Axelson, Eric D 09 Dec '16

09 Dec '16

Does the infant brain atlas mentioned in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ exist yet or will it be included in version 6? Thanks Eric Axelson Research Specialist Department of Psychiatry University of Iowa eric-axelson(a)uiowa.edu<mailto:eric-axelson@uiowa.edu> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Freesurfer December 2016