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30089 discussions

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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Ask for unsubscribe from the mailinglist
by Ying Wang 21 Feb '18

21 Feb '18

Hi, Can I unsubscribe from the FreeSurfer mailing list? My email address is: neuying(a)gmail.com Thanks! Ying

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How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST
by Axelson, Eric D 21 Feb '18

21 Feb '18

We are using N4 to correct some large inhomogeneities in some samples and wanted to insert these images into the v6.0 pipeline and bypass the N3 bias correction done within. What would be the correct sequence of freesurfer commands to achieve this? Thanks Eric ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Freeview mac OSX firewall setting
by Seung-Goo KIM 20 Feb '18

20 Feb '18

Dear all, Has anyone using mac OSX experienced constant popping-up of a window asking firewall setting every time when you open FreeView although you have already set it? It's not critical but kind of annoying... so hope you one of you already solved it. Best, -- Seung-Goo ("SG") KIM, Ph.D. Research associate Department of Psychiatry, University of Cambridge. Postal: Box 189, Level E4, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom. Phone: +44 (0) 1223 761 360 https://sites.google.com/view/sgkim/ <https://sites.google.com/view/sgkim/>

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Re: [Freesurfer] Freesurfer Recon all {Disarmed}
by Shim Hee Youn 20 Feb '18

20 Feb '18

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