Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Optseq2 - Repeating Stimuli and Contrasting the Repetitions
by Ruthie Shaffer 10 Nov '16

10 Nov '16

Hi all, I’m posting to ask for advice on setting up certain parameters in optseq2: Specifically, in optseq2, how can one set up parameters to best optimize a task where there are say 20 items presented 3 times, where the relevant contrasts are between the first, second, and third presentations of the same items? Meaning the second presentation must come sometime after the first and the third presentation must come sometime after the second? Thank you so much for any help on this! Best wishes, Ruth

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aparcstats2table
by Martin Juneja 10 Nov '16

10 Nov '16

Hi everyone, I am trying to use following command to save stats from a set of subjects in a table format: aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt But after I run this, I get following error: Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 353, in <module> subj_listoftuples = assemble_inputs(options) File "/usr/local/freesurfer/bin/aparcstats2table", line 228, in assemble_inputs fsid=row['fsid'].strip() KeyError: 'fsid' My qdec.dat file looks like below: fsid HC003_1 HC004_1 HC006_1 HC015_1 This command works fine if I use subject IDs individually here e.g. aparcstats2table --subjects HC_Example HC003_1 HC004_1 HC006_1 HC015_1 --hemi lh --meas thickness -t zzz.txt Another question I have here is: How can I average these thickness stats and display it on standard fsaverage? Any help would be really appreciated.

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mri_average vs mri_concat
by Trisanna Sprung-Much 10 Nov '16

10 Nov '16

Hi Doug I spoke with you at the Freesurfer tutorial last week about using mri_average to average my sulcal labels and get a probability map on fsaverage. You had suggested using "mri_concat" instead, which is a newer command. So, I performed the following command: *mri_concat all files --o output.mgz --mean --keep-datatype* I had to put --keep-datatype or else it tried to create an annot file. This worked just fine. My question then is concerning *the min and max values *when this average is overlayed in Freeview. See the snapshot attached. The values seem to be based on 256 instead of percentage and this is what happens when I used "mri_average" without specifying the "-p". Is there a way to illustrate the values in percentage in a similar way with mri_concat? Many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Vertex-labeling
by Foteini Protopapa 10 Nov '16

10 Nov '16

Dear FS experts, I have a volume with specific clusters and I project it to a surface using mri_vol2surf. How can I determine the edges of my clusters now? By getting the surface I get a vector, but I don't know the "labels" of this vector. To which point (in mm) each value corresponds? Thanks in advance, Foteini.

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License on fsaverage datasets
by Marmaduke Woodman 10 Nov '16

10 Nov '16

hi As part of developing some tools [1] partly on the FreeSurfer ecosystem, we'd like to use the fsaverage5 dataset as a test data. In our workflow that would mean committing those files to our Git repo, pushing to GitHub, testing on Travis CI etc which makes them public in our repo. We have, however, no intention of otherwise redistributing the data. If we place the FreeSurfer license file next to the fsaverage5 folder in our repo, is this OK? or would you have a strong preference against this? Thanks, Marmaduke [1] The project in question is here https://github.com/ins-amu/bnm-recon-tools though not well developed at its current stage.

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FreeSurfer Dev Releases
by Elia S. 10 Nov '16

10 Nov '16

Dear FreeSurfer Developers, We have been trying out, for the past few months, the freesurfer dev releases, and in particular this one: freesurfer-X86_64-unknown-linux-gnu-dev5-20150924 My question is, does the above version classify as a nightly version of FreeSurfer 5, or as an early beta of the 6? Or......do the dev versions fall in some kind of grey area that are neither 5 or 6? Thank you in advance, Elia.

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Manual pial and white matter corrections cause irregularities
by Cleo Vandervost 10 Nov '16

10 Nov '16

Hi Bruce, As you asked, I uploaded the recon-all log-file for that subject, edited and unedited. We're using version 5.3. How can you check for sure that the WM significantly gets >110? I also uploaded the pictures once again. Thanks, Cleo ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Verzonden: vrijdag 21 oktober 2016 02:14 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Manual pial and white matter corrections cause irregularities Hi Cleo can you upload a subject before and after editing so we can replicate what you are seeing? And what version of FreeSurfer are you using? Does the WM after editing get signifcantly >110? If so, you may have accidentally placed a control point in a gray matter voxel cheers Bruce On Thu, 20 Oct 2016, Cleo Vandervost wrote: > > Hello Freesurfer team, > > > For my thesis I'm researching the differences in grey and white matter and cortical thickness between > children with and without dyslexia. My supervisor advised me to manually edit the Freesurfer-generated > data. I've been editing my data as follows: > > - adding control points to (larger) WM-areas that FS did not include > > - manually editing (smaller) WM-areas through recon-editing > > - correcting the pial surface through recon-editing > > > After finishing and saving my edits I reran recon-all with this command: recon-all -autorecon2-cp > -autorecon -subjid (subject number). When I opened my data again in Freesurfer to check my edits, I saw > that there were two big problems: > > - 'distortions' in the pial surface > > - sometimes large areas of WM suddenly were excluded, even when I didn't make any edits in that area > > It makes the edited data look much worse than the original data, which is weird I suppose. > > > I've included some pictures so you can see what I mean. > > - Picture (a) is the original unedited version. > > - Picture (b) is the edited version: control points and WM edits. You can see that there's a large area > in the left hemisfere excluded from the original WM area > > - Picture (c) is the re-edited version of (b), control points added in that large area. This time it's > included but the pial surface shows a lot of irregularities. > > > Me and my supervisor tried a couple of times with other data, but we still had the same results. We also > tried by only adding control points and editing manually, without the pial-corrections. > > > Do you have any idea of what's going wrong in the editing proces? > > > Thank you very much, > > > Kind regards > > > Cleo Vandervost > > 1st master speech and language therapy > > Katholieke Universiteit Leuven > > > > >

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Extracting structural measures from trend-level PET clusters
by Elijah Mak 09 Nov '16

09 Nov '16

Hi Freesurfer Team, 1) We've found some subtle differences in tau accumulation between two groups. Unfortunately, it does not survive mri_glmfit-sim (voxel threshold 0.001, cwp < 0.05). Still, I would like to extract the structural measures from the uncorrected tau clusters (p<0.001). What is the most convenient approach for this? Could the following URL (http://www.mail-archive.com/f reesurfer(a)nmr.mgh.harvard.edu/msg16268.html ) be a solution? Can mri_label2label work for sig.mgh with multiple clusters? 2) A slightly unrelated question: how can I go about using this particular cluster as a seed for functional or tractography analysis in other softwares (i.e. FSL or MRTRIX) or even within Freesurfer if possible? Thanks again. Really appreciate your help! Best Wishes, Elijah

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Re: [Freesurfer] Assessing local correlations across 2 modalities
by Elijah Mak 09 Nov '16

09 Nov '16

Hello, Thanks Doug for your help on this previously. I am quite puzzled by the vertex-wise local correlations that I've found (i.e more tau thicker cortex)... and before I go down the rabbit hole of trying to dissect what could be happening, I'd like to check if one of the steps in my workflow has gone wrong? 1) My FSGD is a simple one group design with no other covariates. 2) mri_concat --f stacks_cth_rh15 --o concat_cth_rh15_.mgh **stack of thickness maps after qcache 3) C_pvr_cth.mtx = 0 1 4) mri_glmfit --y concat_tau_lh_sm8.mgh --pvr concat_cth_lh15.mgh --fsgd FSGD_tau dods --C C_pvr_cth.mtx --surf fsaverage lh --cortex --glmdir pvr_lh.glmdir Thanks a lot! :) Best Wishes, Elijah Writing results C_pvr_cth maxvox sig=4.6783 F=34.7936 at index 31050 0 0 seed=1479612145 mri_glmfit done Thanks a lot for your help. Best Wishes, Elijah

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mri_convert slope scale
by Rockers, Elijah D. 09 Nov '16

09 Nov '16

Hello, We have been using mri_convert to convert our dicoms into .nii niftis. There is an entry in the .nii header for the slope scale, but mri_convert appears to discard this value instead of copying it into the header (whereas mricron retains this value) We prefer to use mri_convert. Is there a way to have mri_convert carry this value over? Why is it being discarded? Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Freesurfer November 2016