Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

Update: asymmetric parcellation error
by Dijkshoorn, A.B.C. (Aicha) 22 Feb '18

22 Feb '18

Dear Freesurfer developers, When I was troubleshooting my data I came across an odd parcellation error that I can not place. When looking at the reconstructed surface parcellation (freeview -f {$subject}/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ --viewport 3d) I noticed that in a large proportion of my subjects the parcellated errors are not placed correctly. Moreover, the error mostly seems to apply to the right cortex and not the left. I adjusted foto's for visual information. I already checked the brain mask.mgz file and the rh.white and rh.pial surfaces I cannot find any segmentation errors either. Do you have any idea what could have gone wrong and how I can correct for this? Kind regards, Aicha

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asymmetric parcellation error
by Dijkshoorn, A.B.C. (Aicha) 22 Feb '18

22 Feb '18

Dear Freesurfer developers, When I was troubleshooting my data I came across an odd parcellation error that I can not place. When looking at the reconstructed surface parcellation (freeview -f {$subject}/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ --viewport 3d) I noticed that in a large proportion of my subjects the parcellated errors are not placed correctly. Moreover, the error mostly seems to apply to the right cortex and not the left. I adjusted foto's for visual information. Do you have any idea what could have gone wrong and how I can correct for this? Kind regards, Aicha

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Freesurfer equivalent to fslmaths?
by Zimmerman, Jared 22 Feb '18

22 Feb '18

Hi all, Is there an equivalent of fslmaths in Freesurfer? I would like to add two scalar value images (.mgh files) that are registered to the fsaverage6 surface but I’m not seeing an obvious way to do it. Right now I’m reading the images into Matlab to add them, but this is a bit inconvenient because what I would like to do is smooth an image by a small amount, add the original image back to it, then smooth again marginally and iterate until I get to a target fwhm. Since I can’t smooth inside Matlab this necessitates writing out a temp image for each smoothing step then reading it back into Matlab for the adding. Obviously this is a solvable problem, but as someone only marginally proficient in Matlab it’s something I’d like to avoid, plus it seems like a lot of I/O for this task. A little more detail on my data and what I’m trying to do: The scalar images I’m working with are network confidence maps, basically like the spatial maps from an ICA dual-regression. I want to combine the confidence maps together into a hard partition and write it to an annot file, but I want to smooth them first. I’m concerned, however, that smoothing is going to bias the parcellation against small network parcels and in favor of large network parcels because in each confidence map the small parcels will be surrounded by lots of zeros (does this make sense?). To correct for this, my idea was to iteratively smooth by small amounts and to add the original confidence values (or some fraction of them) back to the smoothed map after each iteration so that regions of high confidence with a small/narrow spatial spread do not become diluted by the smoothing and don’t get taken over by larger high confidence regions in nearby networks. One final question would be how to smooth on a surface without resampling. Right now I’m using mri_surf2surf and smoothing when I resample to the native mesh, but if I take the above approach I would not want to resample at each smoothing step. Could I just use mri_surf2surf with –srcsubject and –trgsubject pointing to the same subject? Thanks, Jared ____________________________ Jared P. Zimmerman jaredz(a)pennmedicine.upenn.edu Neuroscience Graduate Student Oathes Lab University of Pennsylvania

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Longitudinal analysis using SLURM {Disarmed}
by Backhausen, Lea 22 Feb '18

22 Feb '18

Dear FS experts, I am trying to do a longitudinal analysis of around 250 adolescents with up to 4 data points each. Given the complexity I would like to use the long_submit_jobs script which is described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts Unfourtunately it does only run on launchpad and I would do the analyses with SLURM using bash system. Has anybody adopted the script so i will run with SLURM or does anybody know where I should look to get information on this? I have little scripting experience so any help would be greatly appreciated! Best, Lea Backhausen, B.Sc. Research assistant Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Tel. +49 (0)351 458-7166 Fax +49 (0)351 458-5754 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de<https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=htt…> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Problem with cortical parcellation of rh but not lh
by Amal Achaibou 22 Feb '18

22 Feb '18

Hello, I'm new to freesurfer and have been trying to use it for cortical parcellation of individual T1s running recon-all -s subID -i sunT1 -all command. I'm specifically interested in getting parahippocampal and perirhinal ROIs for each individual. It appears that the parcellation is correct for the left hemisphere but not for the right hemisphere... I found that there were also mislabeling for precentral and postcentral gyrus (as easy gyri to identify), and that regardless of if I looked at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme. Is there any reason why I have this systematic mistake? Attached is the example for one subject (others looked very similar). Thanks Amal ________________________________

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Unsubscribe Mailing List
by Duy Nguyen 22 Feb '18

22 Feb '18

Hi Freesurfer Team Please unsubscribe my email from the list Email: duynguyen.bme(a)gmail.com Thanks -- Sent from Iphone

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Extracting the centroids from Desikan-Killiany atlas
by zuxfoucault Wong 21 Feb '18

21 Feb '18

Dear Freesurfer experts, Based on this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03333… , I wrote a short script to extract the centroids from Desikan-Killiany atlas. ###### for hemi in lh rh; do mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels for label in ${labels}; do mri_surfcluster --in /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 --hemi ${hemi} --subject fsaverage tail -1 ./labels/sum.${label} | sed 's/ */ /g' | cut -d' ' -f6-8 >> ./labels/68parc.centroids.txt done done ####### However, 1) the value is not precise enough, it is only one digit after decimal point. And 2) I kept getting the same value for each hemisphere. Eg,. 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 29.8 -20.7 18.0 I would appreciate if you have any suggestions regarding extracting centroids and the aforementioned issues! Thank you for your time! Best, Foucault

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Search angle limitation in the flirt registration
by Yixin Ma 21 Feb '18

21 Feb '18

Hi freesurfer developers and users, I'm writing to ask about the search angle limitation (--searchrx, -- searchry and --searchrz) in the flirt function. I use the search angle option a lot for limited angle search, which usually generate a better registration result compared with the broad angle search. But I still don't quite understand how rx,ry and rz are defined and how negative and positive angles affect the result. Because sometimes I find the result after the angle limitation does not align well with my expectation of rotation angle. Thank you for your help, Yixin Ma Brain Image and Analysis Center Duke university

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Lookup Table
by Ledesma, Jason 21 Feb '18

21 Feb '18

Hi, When viewing MRI mgz images in Freeview, is it possible to only look at certain structures specified in the look up table? That is, to only view colorization of one structure to view it more concisely? Specifically, we want to look at wm-hypointensities to see lesion approximations. Thanks. 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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Fwd: Re: recon-all stage 3: mri_vol2surf cannot load label file lh.cortex.label
by Anna Chen 21 Feb '18

21 Feb '18

Hello FreeSurfer Developers, I'm attempting to run the Human Connectome Project's FreeSurferPipeline.sh script (https://github.com/Washington-University/Pipelines/blob/master/FreeSurfer/F…) on a test subject, but am encountering the following error during the "WM/GM Contrast lh" step, when pctsurfcon is called: mri_vol2surf --mov /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/surf/tmp.pctsurfcon.32625/lh.wm.mgh --regheader hcptest8_1mm --cortex No such file or directory mri_vol2surf: could not open label file /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/label/lh.cortex.label ... Loading label /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/label/lh.cortex.label Invalid argument mri_vol2surf: could not load label file /data/EDresearch/Temperament_fMRI/hcptest8_1mm/proc/T1w/hcptest8_1mm/label/lh.cortex.label Invalid argument I looked in the subject's /label/ folder, and only found one file: lh.aparc.annot; furthermore, no right hemisphere files have been created yet. I've searched the mail archives and no similar errors have been reported. I also tried to backtrack to find out which step of recon-all creates the lh.cortex.label file (is it step 11, "CA Label"?), but instead of finding the step that creates this file, I found commands that used it (i.e., mris_anatomical_stats). Please let me know if I'm approaching this incorrectly. I'm not sure how to proceed from here. I've attached the recon-all.log and recon-all-status.log in case they're of any use. 1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 2) Platform: CentOS 4 3) uname -a: Linux induction.sdsc.edu 2.6.18-419.el5 #1 SMP Fri Feb 24 22:47:42 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Many thanks, Anna

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Freesurfer February 2018