Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

smoothing data
by Tamara Tavares 12 Jul '17

12 Jul '17

Hi All, I was hoping someone can help me with two naive questions I have: I have read on the Freesufer wiki that you should smooth surface data before analyzing. Should I smooth the data only after I have ran recon-all and have made edits? Also, should volumetric data be smoothed or is this limited to surface data? Thank you in advance for your help. Best, Tamara

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Simple math with freesurfer surfaces
by Van Der Deijl, Rosanne 12 Jul '17

12 Jul '17

Dear Freesurfer team, Is it possible to add/subtract/compute the average of freesurfer surface .mgh files? And how would I do this? Thank you in advance. Kind regards, Rose

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Re: [Freesurfer] GLM question
by Yann Ying Chye 12 Jul '17

12 Jul '17

Thanks for your reply, I have a follow up on my first question - if however I was not looking for a main effect of gender, but for the main effect of something else (e.g. diagnosis), will it then be ok to include the unbalanced group (i.e. A-male), to control for gender? Thanks! Regards Yann On 7 July 2017 at 18:34, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > > > On 7/7/17 1:58 PM, Yann Ying Chye wrote: > > Dear FreeSurfer mailing list, > > > > I've got two questions regarding the freesurfer GLM analysis. > > > > 1. I am trying to run mri_glmfit on the cortical thickness of a > > dataset that has a few interacting factors of unequal levels. > > For example, my dataset may have groups A, B, C, and D. Within the > > groups, subjects are further divided by gender - male and female. > > However, group A only has males, such that the classes in my FSGD file > > = A-male, B-male, B-female, C-male, C-female, D-male, and D-female. > > Will this design be a problem? Will it be statistically sound? > > Additionally if I was looking for an effect of gender, how would I > > weigh my contrast? I was thinking 0.25 0.25 -0.33 0.25 -0.33 0.25 > > -0.33. Would that be valid? > I think I would lean against including A-male. Otherwise, what is the > null hypothesis? Without A-male, it would be that males and females > differ when regeressing out the effect of group, but you can't say that > if you include A-male. Eg, if there were no difference between A-male > and A-female but A tended to be larger than the other groups, then > including A-male and not A-female would create a confound making males > look bigger than females. > > 2. Does mri_glmfit have a limit to the number of subjects it can run > > with? If I have say upwards of a few thousand subjects, will this be > > possible to run/how long would that take? > I don't think it has a limit. > > > > Thanks for your help! > > > > Regards > > Yann > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 161, Issue 17 > ******************************************* >

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Subject with missing fMRI data
by Sadie Marvel 12 Jul '17

12 Jul '17

Hi List, I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of filling the missing data. Alternatively, is there a way to only use the portions of the brain that have data when doing mri_glmfit? Does freesurfer do this automatically? Thanks.

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mkbrainmask-sess: couldn't find register.dof6.lta
by Li Guo 12 Jul '17

12 Jul '17

Dear freesurfer developers, I’d like to ask about an error I encountered in Freesurfer v6.0 with mkbrainmask-sess. I am using macOS Sierra. Here is the error: error:"ERROR: cannot find /Users/lguo15/Documents/MATLAB/fMRI_P3/Fisch_P3_01/bold/register.dof6.lta, you might need to run register-sess” The error goes away if I run register-sess before mkbrainmask-sess. However, my lab mates use v5.3 and ran the exact same preprocess pipeline without this error. The order for them is mkbrainmask-sess first and register-sess later. I’d like to ask whether it is true that maybe in v6.0 mkbrainmask-sess now depends on register-sess to generate the register.dof6.lta file? Or how should I interpret this? Does running registration and masks have some fixed order at all or it doesn’t matter? Best, Li

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petsurfer stats for multiple segmentations
by Lu Zhao 12 Jul '17

12 Jul '17

Dear freesurfer support, I am using the PetSurfer to process our PET data. But by default, it would only generate stats for the segmentation with the aparc atlas. However, I want to obtain the stats for different freesurfer atlases, like in the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, ?h.aparc.DKTatlas.stats, etc.) How should I set the ‘gtmseg' to make it produce segmentations for the GTM with different freesurfer atlases? I checked the help doc of gtmseg. The annotation to use for GM/WM segmentation can be set using --ctx-annot --wm-annot. However, I still don’t know how exactly these should be set. I will be very grateful if you could give me some suggestions and detailed guidance to help me obtain the PetSurfer stats for different freesurfer segmentations. Best regards, Lu

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Pial surface editing
by Michelle VanTieghem 12 Jul '17

12 Jul '17

Hello, We have assessed freesurfer output for 160+ brains, and about 50% have poor segmentation of pial matter that includes too much skull. Manual edits and re-running does work to improve the problem, but is very time/labor intensive for so many scans. I saw on the freesurfer wiki that you can include T2 or Flair images to improve the segmentation for this problem. However, we do not have these extra scans. What do you recommend to do otherwise? Thank you! -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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Re: [Freesurfer] dmri_pathstats error
by Yuwen Hung 12 Jul '17

12 Jul '17

Dear DTI experts: I am wondering if anyone knows a solution to this tracula script error: dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.200000 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Your help would be greatly appreciated, Yuwen

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Re: [Freesurfer] dmri_pathstats error
by Yuwen Hung 12 Jul '17

12 Jul '17

Dear DTI experts: I am wondering if anyone could help find the solution for this tracula script error: RuntimeError: Command: dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Below I pasted the last bits of the log including the error messages. Your help is being greatly appreciated. Yuwen ---- 170712-12:28:30,168 interface INFO: stdout 2017-07-12T12:28:30.165030:Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... 170712-12:28:30,168 interface INFO: stdout 2017-07-12T12:28:30.165030:ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Traceback (most recent call last): File "/home/yuwenh/script/dti_2017pipeline_YHMK.py", line 292, in <module> make_tables(args.subject) File "/home/yuwenh/script/dti_2017pipeline_YHMK.py", line 262, in make_tables cmd.run() File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1085, in run runtime = self._run_wrapper(runtime) File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1728, in _run_wrapper runtime = self._run_interface(runtime) File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1762, in _run_interface self.raise_exception(runtime) File "/om/user/yuwenh/envs/CEMO_env/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1686, in raise_exception **runtime.dictcopy())) RuntimeError: Command: dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Standard output: cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.200000 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Standard error:

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Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0
by Torben Lund 12 Jul '17

12 Jul '17

Hello FreeSurfer Developers I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the Freeview program. For version 1.0 superimposing a gifti surface on top of a nifti volume works beautifully, but with the new version 2.0 the orientation is messed up, for the exact same files (see screenshots in attached jpeg’s). Has anybody else experienced this problem, and could it potentially be caused by recent changes in the minc tools which nifti converter I know have been changed between the two Freeview versions, or are they not used in Freeview. Best Torben Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Building 10G, 5th floor, room 31 Noerrebrogade 44 8000 Aarhus C Denmark Phone: +45 7846 4380 Fax: +45 7846 4400 http://www.cfin.au.dk <http://www.cfin.au.dk/> torbenelund(a)cfin.au.dk <mailto:torbenelund@cfin.au.dk> (for official stuff) torbenelund(a)me.com <mailto:torbenelund@me.com> (for faster response)

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Freesurfer July 2017