Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

Extend pial surface
by Noah Markowitz 31 Oct '16

31 Oct '16

Hi all, I’m trying to extend the pial surface to include missing GM. Part of the problem is that the wm.mgz seems to include the WM, but does not extend the border of the pial surface. I’ve attached links to pictures of the one of the scans. Any help would be greatly appreciated. Noah Without wm.mgz overlay: http://www.mediafire.com/view/9wsenfq2wdrtvcq/no_mwmask.png <http://www.mediafire.com/view/9wsenfq2wdrtvcq/no_mwmask.png> With mg.mgz overlay: http://www.mediafire.com/view/akdtms78iad5usu/with_wmmask.png <http://www.mediafire.com/view/akdtms78iad5usu/with_wmmask.png>

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[Question for recommended MRI protocols]
by 김정식 31 Oct '16

31 Oct '16

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Pial Problem #2
by Noah Markowitz 31 Oct '16

31 Oct '16

Hi, I just sent a question a few minutes ago but forgot to include an important bit in it. Some pial I’m trying to include doesn’t have WM to add that will push the pial surface back. I attached a link to an example. This happens in the parietal lobe, temporal pole, as well as frontal pole. Any suggestions? Noah http://www.mediafire.com/file/it2ukdeg15pphyk/missing_GM2.png <http://www.mediafire.com/file/it2ukdeg15pphyk/missing_GM2.png> http://www.mediafire.com/view/8x3avz4l9lxpoeg/missing_GM1.png

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Error long_mris_slopes
by tom parker 29 Oct '16

29 Oct '16

Dear FreeSurfers, I've been trying to run a longitudinal cortical thickness analysis in FreeSurfer but unfortunately, so far, it has not worked. After preprocessing the data following the instructions from the tutorial, I tried running: *long_mris_slopes --qdec /Volumes/WD/Long/qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Volumes/WD/Long/* And the following error came out: *Parsing the qdec table: /Volumes/WD/Long/qdec/long.qdec.table.datERROR: qdec table /Volumes/WD/Long/qdec/long.qdec.table.dat not found or empty?* The path is correct and there are no empty lines in the file. When I ran: *mris_preproc --debug --qdec-long qdec/long.qdec.table.dat* This comes out: *set echo = 1 ;set debug = 1 ;set debug = 1breakswbreakswendendwhile ( $#argv != 0 )while ( 2 != 0 )set flag = $argv[1] ; shift ;set flag = --qdec-longshiftswitch ( $flag )switch ( --qdec-long )if ( $#argv == 0 ) goto arg1err ;if ( 1 == 0 ) goto arg1errset fsgdf = $argv[1] ; shift ;set fsgdf = qdec/long.qdec.table.datshiftif ( ! -e $fsgdf ) thenif ( ! -e qdec/long.qdec.table.dat ) thenecho "ERROR: cannot find $fsgdf" ;echo ERROR: cannot find qdec/long.qdec.table.datERROR: cannot find qdec/long.qdec.table.datexit 1 ;exit 1* Do you have any idea why this is happening? Thank you so much!

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Questions about outputs in Longitudinal Stream
by Tamara Tavares 29 Oct '16

29 Oct '16

Hello, I am interested in looking at ventricular changes over time and thus, have ran the longitudinal stream on my participants scans. As suggested online, I am checking the ventricular segmentation in the longitudinal outputs and am planning on making any edits to the longitudinal stream if the segmentation of the ventricles are incorrect. I have a few questions related to this: 1) To check the segmentations, should I overlay the aseg.mgz with the brainmask.mgz or the brainmask_SubjID-Temp.mgz? 2) If I find that the segmentation of the ventricle is incorrect, should I make edits to the aseg output in the longitudinal outputs? What command line would I use to re-do the longitudinal stream with the corrected segmentation? 3) After looking to see whether there are errors in the longitudinal recon-all script output, are there any other things I should check to ensure that the base and longitudinal stream ran correctly? Thank you in advance for your help! Tamara

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Question regarding Checking Longitudinal Runs: Repost
by Tamara Tavares 29 Oct '16

29 Oct '16

Hello, I have a question regarding the outputs to the longitudinal processing stream. I ran my two participant's scans through the Cross, then created a Base and two longitudinal runs. I am primarily interested in looking at ventricular change over time. Other than the aseg output overlaid on the brainmask for each longitudinal time point, should I look at any other outputs to ensure the longitudinal process ran correctly? For example, should I inspect the templates to make sure they are not blurry? Should I also overlay the two longitudinal runs to inspect potential alignment problems? Thank you in advance for your help, Tamara

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Two Stage Longitudinal Model
by Timothy Hendrickson 29 Oct '16

29 Oct '16

FreeSurfer Experts, Hello I am attempting to perform a two stage longitudinal analysis. My entire data set has two time points for each participant. I understand that the subject order in the FSGD file should correspond with the QDEC file run through long_mris_slopes. In my case the FSGD file has half as many inputs as the QDEC file. My question is would I take the covariates from TP1 and TP2 and take the average to input into the FSGD file? If that is the case is there anything wrong with performing the long_qdec_table --qdec "qdec.table.dat --cross --out "cross.qdec.table.dat" command and using that co-variate data to input into the FSGD file? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Re: [Freesurfer] T2pial and [LONG]
by Antonin Skoch 29 Oct '16

29 Oct '16

Dear experts, I am potentially also interested in correct using of -T2pial feature with longitudinal stream. The first (standard cross-sectional) and third step (-long ) was already elaborated here, but I am, however, not sure how to process by T2pial in the second step ( -base), which creates the unbiased template and process it by (almost) standard cross-sectional stream. I did not find creation of unbiased template of T2 in the recon-all code. Therefore, in order to use -T2pial on -base run, I would probably need to create my T2 template by calling mri_robust_template on my T2's first, and then pass the created T2 template as input to recon-all -base run, like: recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all -T2pial -T2 path_to_T2_template I am correct? Regards, Antonin

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Question about mri_glmfit-sim
by neuroimage analyst 29 Oct '16

29 Oct '16

Hi FreeSurfer experts, I am currently performing some cortical thickness comparisons in my group of subjects and using mri_glmfit-sim --glmdir my_dir --cache 2.3010 --cwpalthresh 0.05 --2spaces found some clusters that have significantly different cortical thickness values, Given Eklund et al PNAS paper, do you suggest I should rather use mri_glmfit-sim --glmdir my_dir --sim perm 5000 1.3 perm.pos.13 --sim-sign pos in order to convince that the results are not due to false positive? Thanks Regards

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clinical pysch programs?
by Bruce Fischl 29 Oct '16

29 Oct '16

Hi All, just a note to say that if there are any faculty in clinical psychology programs looking for a grad student for next September, you would be extremely fortunate to convince our stellar RA, Allison Moreau, to come work for you. She has done outstanding research with us for a number of years, and is applying to graduate programs for the Fall. She knows how to analyze data, run a scanner, do histology, pack samples, keep track of expderiments, manage her time independently, problem solve on her own, research and implement solutions to difficult problems and is a lovely person to boot. I strongly advise recruiting her! thanks Bruce

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Freesurfer October 2016