Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30060 discussions

Re: [Freesurfer] Desikan-Killiany stats in FreeSurfer 6.0
by MIKHAEL Shadia 06 Jan '18

06 Jan '18

Dear Bruce, Thank you for your detailed reply at https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-January/055392.… . Just to be sure, could I please double check that I'm looking at the correct stats file for several parameters? All relate to cortical parcels derived using the DK protocol in FreeSurfer 6.0. 1. grey matter volume, or volume of just the grey matter (GM) layer: GrayVol from ?h.aparc.pial.stats ? ..although GrayVol values are identical in both ?h.aparc.pial.stats and ?h.aparc.stats 2. surface area of the GM-WM (grey matter/white matter) boundary: SurfArea from ?h.aparc.stats ? 3. mean grey matter thickness: ThickAvg from either of the 2 files Many thanks once again. Kind regards, Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 05 January 2018 15:36 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: Desikan-Killiany stats in FreeSurfer 6.0 Dear all, I'm wondering whether you could please clarify the differences between the ?h.aparc.pial.stats and ?h.aparc.stats files which are generated by the recon-all command in version 6.0. When comparing the content of the 2, some values are the same, while others (e.g., surface area) are different. I am seeking the stats for the Desikan-Killiany-based parcels which were previously summarized in ?h.aparc.stats in FreeSurfer 5.1. Thank you in advance. Kind regards, Shadia

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Re: [Freesurfer] FreeSurfer recon-all issue
by MIKHAEL Shadia 06 Jan '18

06 Jan '18

Dear Antonin, Thank you for your reply and clarification at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055331.… . I was changing the recon-all file in the subject folder rather than the one in the freesurfer/bin folder. The command recon-all now runs to completion following your recommendations (replacing ln with cp, and making a local copy of fsaverage in the subject folder). Many thanks once again! Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 31 December 2017 11:18 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: RE: FreeSurfer recon-all issue Dear Antonin, Thank you for your suggestions at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055319.… . I've tried both, but the process still fails at the same point. It appears that I now am left with a recon-all log file (attached) that is double in length (run 1 ending at line 4187, and run 2 ending at 8276), both of which have started from step 1, rather than run 2 resuming from where we last stopped. Should I be adding certain flags for recon-all to resume rather than start from the beginning? The way I did it was the same as before, but without the -I flag in the second run, as suggested by the recon-all prompt. Thanks again. Shadia -----Original Message----- From: MIKHAEL Shadia Sent: 28 December 2017 10:12 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: FreeSurfer recon-all issue Hello all, I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects: ..... mris_curvature -w lh.white.preaparc total integrated curvature = 6.657*4pi (83.654) --> -6 handles ICI = 129.9, FI = 1309.2, variation=20703.115 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: creating symbolic link `lh.white.H': Operation not supported Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/04047… , but I still get a message saying operation not supported ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H But again it says operation not supported. Recon-all log: attached Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Any advice? Thank you Shadia

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Demeaning Flag and DODS vs DOSS
by Hossein Rejali 05 Jan '18

05 Jan '18

Hello Freesurfer experts, I am doing a whole brain analysis using mri_glmfit to determine if there is a significant difference between two groups (controls-con VS Schizophrenic -Scz). I have set up the following fsgd file: [cid:8afe40fb-8a2d-433e-9a97-5ddebc7bde68] What I am wondering is if I should have a demeaning flag, there was not much documentation as to when or when not to do this but I was hoping I can get an answer here. Also below is the contrast vector that I am using: [cid:10993abb-2888-45d8-94ca-78110f8b2697] A follow-up question would be whether to use DODS or DOSS I am still confused which model to use? The independent variable is Myelin. Kind Regards, Hossein Rejali

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Postdoc position at the Center for Healthy Minds
by Audrey Jacobsen 05 Jan '18

05 Jan '18

The Center for Healthy Minds, at the University of Wisconsin-Madison, is looking for a postdoctoral fellow in affective, cognitive and aging neuroscience! The Center for Healthy Minds (CHM) was founded and is led by neuroscientist Richard J. Davidson. CHM's mission is to cultivate well-being and relieve suffering through a scientific understanding of the mind. CHM is a leader in rigorous, interdisciplinary basic and translational research aimed at understanding the mind and how to nurture well-being in ourselves and others. CHM communicates these findings to the world, inspires scientists to conduct further research, and influences a shift in culture to embrace well-being. The successful candidate will play a key role analyzing both extant and new neuroimaging data in relation to sociodemographic, behavioral, cognitive, and biomarker data from the Midlife in the US (MIDUS; http://midus.wisc.edu/) national longitudinal study. MIDUS is a collaborative, multi-site, national longitudinal study of health and well-being that has been following participants since 1995. The collective aim is to investigate the role of behavioral, psychological, and social factors in accounting for age-related variations in health and well-being in a national sample of Americans. Over 900 publications have been published using MIDUS data as of 2017. In addition to studying age-related variations in brain structure and function, the primary goal of the MIDUS Neuroscience Project is to identify how individual differences in the neural bases of different emotional response styles contribute to health and well-being vs. vulnerability to stress and disease throughout the lifespan. To learn more, please click here<https://drive.google.com/file/d/0B7nmWpuZRcWcakdXMUw5Vi13R00/view>. If you are interested in the position, send a cover letter and CV to Mike Kelly, at mkelly1(a)wisc.edu<mailto:mkelly1@wisc.edu>. Sincerely, Audrey Jacobsen Center for Healthy Minds University of Wisconsin-Madison

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Variations in results in different versions of QDEC
by Vikas Bandalli 05 Jan '18

05 Jan '18

Dear Freesurfer Team, I was previously using qdec v1.4 for my analysis and I had compiled the results,However,I could not publish my results at that time due to various reasons. Now,I decided to re-run the analysis from the scratch before sending for publication to cross-checl for any errors . I am currently using qdec v1.5 I noticed that there is variations (slight) in the CWP values of the significant clusters.However,there is no change in the regions of significance and the new values almost correspond to the older results tha I had obtained (for example if 'A' cluster's CWP was 0.0007 now it is 0.0008) I wanted to make sure if the newer results are due to version change or if I am probably going wrong somewhere. Thank you, Regards, Vikas Bandalli Raju -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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Desikan-Killiany stats in FreeSurfer 6.0
by MIKHAEL Shadia 05 Jan '18

05 Jan '18

Dear all, I'm wondering whether you could please clarify the differences between the ?h.aparc.pial.stats and ?h.aparc.stats files which are generated by the recon-all command in version 6.0. When comparing the content of the 2, some values are the same, while others (e.g., surface area) are different. I am seeking the stats for the Desikan-Killiany-based parcels which were previously summarized in ?h.aparc.stats in FreeSurfer 5.1. Thank you in advance. Kind regards, Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Freeview
by Samir Rekic 05 Jan '18

05 Jan '18

Dear FreeSurfer Team, I just wanted to ask you a quick question about installing Freeview on a Ubuntu 17.04, 32-Bit Computer. I couldn’t find an appropriate answer in you archives so I decided to write you. I could not find an 32 bit Version of Freeview in your archiv of previous releases so I installed the latest version. Everytime I try to run it there is an Error appearing that says ‚cannot open shared object file libpng12.so.0‘. Wanted to ask if you know if this Problem has already been solved by another Freeview user. Or is there a 32 bit Version that I missed? Thank you in advance Kindest regards Rekic Samir – Carinthian University of Applied Sciences, Austria

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Correcting for dura/pia mater
by Leavitt, Mackenzie 04 Jan '18

04 Jan '18

Hello Freesurfer Developers, I am brand new to Freesurfer, so I'm just getting acquainted with how to use the program. Our clinic is attempting to run quality control on our imaging data for the last five years. One issue that I've noticed many times in our sample is that the Freesurfer program includes portions of the dura and pia mater in the brain mask volume after running reconstruction. On particularly bad images, it looks like a small part of the skull is included too. I've browsed through the tutorial datasets on Freesurfer, but it seems like there isn't an obvious way to make edits to images to correct for this. Please let me know what edits I should make if I want to correct for this. In addition, let me know if there is a way to correct for this error that can be quickly applied to a large number of subjects at once. There are at least 150 brains that have this issue, so it would be helpful if there was a way to correct this error quickly. Best, Mackenzie =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Change the location of SUBJECTS_DIR
by zuxfoucault Wong 04 Jan '18

04 Jan '18

Dear list, If I changed the location of subjects_dir (via `export SUBJECTS_DIRS=/new_location/) after `source $FREESURFER_HOME/FreeSurferEnv.sh`, could I still completely run the `recon-all -all`? I mean some folders in the default location of subjects_dir, such as fsaverage, would not be included in the new subjects_dir. Would this cause trouble to the subsequent freesurfer routine? Thanks for your time! Best, Foucault

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Postdoctoral position available in the Poldrack Lab
by Chris Gorgolewski 04 Jan '18

04 Jan '18

Apologies for cross-posting. The Poldracklab at Stanford is looking to hire a postdoc with expertise in fMRI data analysis, starting as soon as possible. Our lab is a dynamic and collaborative group that includes basic cognitive neuroscience researchers focused on the study of decision making and executive function alongside methodological researchers focused on reproducible data analysis and data sharing. Stanford University is located in sunny northern California, deep in the heart of Silicon Valley and a short train ride to San Francisco. The postdoc will be able to contribute to a number of ongoing research projects in our lab and collaborating labs by analyzing fMRI data from those studies. In addition, the postdoc will have the opportunity to develop their own research program with the domain of scientific or methodological problems currently being investigated within the lab ( https://poldracklab.stanford.edu/projects) The successful candidate should: - Have a PhD in a relevant field of study and demonstrated experience with the processing and statistical analysis of fMRI data. - Have strong and demonstrated computer programming skills, including Python. Experience with Nipype is strongly preferred. Candidates will be asked to submit a link to their open source code repository for review. - Have strong skills in statistics and machine learning. - Have solid experience with computational data analysis, including strong UNIX/Linux skills and experience using high performance computing clusters. Experience with cloud computing platforms is also preferred. - Be dedicated to open source software development and data sharing. The Poldracklab is strongly committed to diversity in science, and we particularly welcome applications from members of traditionally underrepresented groups. Eligible candidates will be asked to complete a data analysis problem using a specified dataset and present a report of their results as well as sharing their analysis code, in order to demonstrate their expertise with data analysis. Interested candidates should email the following to russpold(a)stanford.edu: - A cover letter describing your background and research interests - CV (including a link to code repository, e.g. Github, Bitbucket) - Names and email addresses of two references

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