Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Lesion Volume Analysis
by Ledesma, Jason 08 Jan '18

08 Jan '18

Hi, I am aware that the recon-all command ultimately calculates statistics on a given MRI sequence, including what is referred to as "aseg.stats". "Aseg.stats" includes the "WM-hypointensities" calculation, which I was told would be an equivalent to white matter lesion volume. Is there a way to calculate the WM-hypointensity volume without doing the complete "recon-all" analysis to reduce processing time for this particular aspect of study? Thank you. Sincerely, Jason Ledesma Staff Research Associate Phone: 1(424)571-7755 E-mail: jason.ledesma(a)labiomed.org<mailto:jason.ledesma@labiomed.org> ________________________________ LA BioMed Warning: This email (and any attachments) is intended for the use of the person to which it is addressed. It may contain information that is privileged and confidential. As the recipient, you are obligated to maintain it in a safe, secure and confidential manner. Unauthorized disclosure or failure to maintain confidentiality may subject you to governmental penalties. Should you not be the intended recipient, please notify us by return email, and delete this message from your computer at once. ________________________________

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make_average_subject for skull-stripped data
by Duran, Tugce 08 Jan '18

08 Jan '18

Hi FS Experts, I want to make sure that the make_average_subject on my pre skull-stripped data is accurate. I check the avgsubj volume and surfaces using the following command: tkmedit avgsubject orig.mgz lh.white and as a result, I get the attached. Though the shape looks elongated in other analyses. Any thoughts? Thanks! Tugce Duran, B.S. Research Technologist II [cid:image001.png@01D38882.8FF43A70]<https://medicine.iu.edu/departments/neurology/research/> Indiana Alzheimer Disease Center (iADC) Office: 317-278-7015 durant(a)iupui.edu<mailto:durant@iupui.edu>

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asegstats2table error message
by Hugh Pemberton 08 Jan '18

08 Jan '18

Hi, I'm getting the following error when trying to use the asegstats2table command, I can't see anything similar from previous emails, any ideas what the issue is? Thanks v much in advance. asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile aseg_stats.txt File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' SyntaxError: invalid syntax

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viewing the flatten sheet
by N Saf 08 Jan '18

08 Jan '18

Dear experts, I cut the inflated surface in tksurfer and obtain the flatten sheet by mris_flatten but I can not load the $h.flaten.patch.3d not in freeview nor in tksurfer it somehow collapse! my laptop is RAM:6G , core i5 , would you please help me how can I see the 2D flatten sheet ?? many thanks to any help you can provide me. BRG, Nazanin

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Re: [Freesurfer] Freeview
by Samir Rekic 07 Jan '18

07 Jan '18

Hi Ruopeng, I have the libpng16.so.16 installed on my system And tried to install the libpng12.so.0 but the apt-get install order nor Synaptics could not find anything Rekic

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Re: [Freesurfer] Desikan-Killiany stats in FreeSurfer 6.0
by MIKHAEL Shadia 07 Jan '18

07 Jan '18

Perfect. Many thanks once again. Best wishes, Shadia -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----Original Message----- From: MIKHAEL Shadia Sent: 07 January 2018 00:41 To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: RE: Desikan-Killiany stats in FreeSurfer 6.0 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 -----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] 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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Freesurfer January 2018