Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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

2 1

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

2 1

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

2 1

tmp directory not created
by Sneha Pandya 28 Oct '16

28 Oct '16

Hi all, I am running recon-all stream for ~200 subjects and after successful run of them I observed that for some of the patients recon-all ran successfully without error but it did not create "tmp" sub-folder. Can anyone please advice when recon-all stream does not create "tmp" folder and do I need to run these subjects again even after its successful completion? Thanks, Sneha

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How to get numerical r values from analysis
by Marissa Pifer 28 Oct '16

28 Oct '16

Hi freesurfer experts, I've run into a problem of not being able to generate the numerical results of the analysis I've run through qdec.After I ran the analysis in qdec I opened the overlay in tksurfer, applied a label, and found a significant negative correlation between cortical thickness and one of our variables. I cannot figure out how to get the numerical r value of this correlation. How can I get this value? Thanks in advance Marissa

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