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30060 discussions

regional gray matter volumes and corticl thicknesses analysis in children
by Liu Y 15 Jan '18

15 Jan '18

Dear Experts, Is there an acurate way to anayze the longitudianl changes in regional gray matter volumes and corticl thicknesses in children (several months to 8 years). How accurate are freesurfer of fsl-FIRST? Best regards, Yawu

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White/pial surface failure
by Trevor K Day 12 Jan '18

12 Jan '18

Hello, We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our subjects. Two images from recon_checker are attached. I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there no obvious indication of any error. I’m not sure what to search because I don’t have an error message. Recon-all.log is attached. The brainmask is fine. Not perfect, but certainly not poor enough to cause this. The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in the frontal lobe, but nothing that freesurfer hasn’t handled before. Others have suggested that this seems to extreme to fix with control points, are the other approaches to take? The command used was: /usr/local/freesurfer/stable6_0/bin/recon-all \ -all -s 170661.s1 -hires -cw256 -qcache \ -i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \ -expert /mnt/panuc/udallp2/lib/expert.opts (Again, T1_256.nii.gz looks totally fine.) The contents of expert.opts are mris_inflate -n 30 * Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 * Platform: Debian GNU/Linux 8.9 (jessie) * Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64 GNU/Linux Where can I start to debug and fix this? Thanks, Trevor Day

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no skullstrip
by Dijkshoorn, A.B.C. (Aicha) 12 Jan '18

12 Jan '18

Dear free surfer developers, Because I work with neonatal scans the skullstrip phase cannot be applied correctly (it removes too much skull). To avoid this problem I added the -noskullstrip option. However, I do still need the brain mask output of this phase. How can I work around this? Kind regards, Aicha

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Re: [Freesurfer] making masks with subfields etc
by Iglesias Gonzalez, Eugenio 12 Jan '18

12 Jan '18

Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon(a)rcsi.ie> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 12 January 2018 at 13:07 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] making masks with subfields etc Hi FS experts, I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography. 1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to? 2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps? 3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths <input imgae> -thr LUT number of the subcorical structure -uthr lut number again <output filename> first and then regsiter them to the rawavg.mzg? Thanks for any guidance which is always greatly appreciated. Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D38BB0.B4949E20] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.ie<http://www.rcsi.ie/> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE

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Dear freesurfer users
by 주요한 12 Jan '18

12 Jan '18

Dear all, I’m a beginner in FreeSurfer. Actually I tried to get an information for cerebellum volume. Thus I installed the FreeSurfer and typed recon-all ~ ... After the processing, I got an information from aseg.stats in the stats folder. The information is here. # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 8186 8459.1 Left-Lateral-Ventricle 39.5864 11.4363 22.0000 93.0000 71.0000 2 5 141 190.2 Left-Inf-Lat-Vent 56.3475 10.4033 34.0000 78.0000 44.0000 3 7 12336 13138.8 Left-Cerebellum-White-Matter 87.7091 6.0827 35.0000 103.0000 68.0000 4 8 55173 55127.2 Left-Cerebellum-Cortex 66.0291 11.1028 8.0000 95.0000 87.0000 (I guess the information is..) The volume of Left cerebellum-white-matter : 13138.8 mm3 The volume of left cerebellum-cortex : 55127.2 mm3 However, as you know I’m only a beginner. Thus I guess the information is as that, but I cannot sure. Would you let me know - is this correct information or not? If it is not, please let me know how to get the information for cerebellum volume. Thank you. Best Regards John.

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making masks with subfields etc
by Erik O'Hanlon 12 Jan '18

12 Jan '18

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why freesurfer is not able to segment frontal cortex
by Vidhu Agrawal 12 Jan '18

12 Jan '18

Respected Sir Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_middle.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_operacula.nii --match 1106 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_orbital.nii --match 1107 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_triangula.nii --match 1108 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_middle.nii --match 1109 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_superior.nii --match 1110 but it is not segmenting any region Looking forward for your reply. Thanking you With regards vidhu agarwal

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Recon-all Hires Segmentation Failure
by Giovana dos Santos Cover 12 Jan '18

12 Jan '18

Dear Freesurfer Developers, I am trying to segment the grey matter and pial surface using the FreeSurfer command recon-all with the hires flag. But even though there is no error while executing my code, when I analyze the output surfaces, the segmentation is missing some areas in the brain (I attached an image to show these brain regions). My command is: recon-all -all -s $SUBJ -hires -i $IMAGE -expert $EXPERT_FILE My expert file contains: mri_em_register -p .5 mris_fix_topology -s 50 mris_inflate -n 100 Does anyone have any thoughts on how to troubleshoot my problem? Thanks in advance, Gio. 1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. u-name -a: Linux ubuntu 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux [cid:b5b990e1-aacc-4a2f-a73e-0d92496f8736]

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Amygdala segmentation runtime error
by Emily K Clarke 11 Jan '18

11 Jan '18

Hi Freesurfer developers, I’m attempting to run the new amygdala segmentation command (segmentHA_T1.sh) using the developer version of Freesurfer 6.0. However, when I run my script I receive the following error — error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory I checked with our cluster administrator, and we do have the Matlab R2012 runtime installed. Does anyone have any insight into what could be causing this error? I’ve attached my full output as well as my script in case that’s any help! Thanks, Emily K. Clarke Duke University

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Description of a few files generated by
by Aaron Tanenbaum 11 Jan '18

11 Jan '18

I would like to get a clarification on what some the the files generated by FreeSurfer recon-all based on the URL https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles The web pages says the nu.mgz "This is a intensity normalized volume generated after correcting for non-uniformity in the orig.mgz". I just need a clarification the intensity normalized is just a global scaling and the correction for non-uniformity is the bias field correction. I was wondering if the orig.mgz is bias field corrected to generate the orig_nu.mgz and the intensity normalized to generate the nu.mgz. Finally what is the norm.mgz image. I cannot final details on how it is created.

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