Freesurfer

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30065 discussions

mri_robust_template output data size
by Chang, Yulin 20 Feb '18

20 Feb '18

Hello, Synopsis I have 5 longitudinally acquired high-res volumes at 0.8 mm isotropic resolution. The matrix size is 320x320x240 (240 is long left-right), covering an FOV of 256x256x192 mm3. I've used mri_robust_template to create a template out of these 5 volumes, preferably at the same matrix size and FOV. However, sometimes the matrix size of the created template is 321x321x321, resulting in the FOV of 256.8x256.8x192.8 mm3. This non-standard FOV would lead to error in the subsequent FreeSurfer segmentation analysis. Details The command I used was: $ mri_robust_template \ -- mov sub1_rep01.nii sub1_rep02.nii sub1_rep03.nii sub1_rep04.nii sub1_rep05.nii \ -- template sub1.nii \ -- lta sub1_rep01.lta sub1_rep02.lta sub1_rep03.lta sub1_rep04.lta sub1_rep05.lta \ -- mapmov rep01_to_mean.nii rep02_to_mean.nii rep03_to_mean.nii rep04_to_mean.nii rep05_to_mean.nii \ -- average 0 \ -- iscale \ -- satit The size of the output is NOT consistent: Sometimes the matrix becomes 320x320x320 (with the left-right FOV extended), but at other times it becomes 321x321x321. In the latter case, the FreeSurfer recon with -hires flag $ recon-all -i sub1.nii -subject recon_sub1 -all -hires -expert hires.expert-options would fail with the error message (from recon-all.log) ************************************** ERROR! FOV =256.799 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. ****************************************** (I am reluctant to explore the flag -cw256 for workflow reasons.) So why the output of mri_robust_template not consistent? Is there anything intrinsic in the data that would affect the output data size? 1) FreeSurfer version: freesurfer-Linux-centos_x86_64-stable-pub-v6.0.0-2bed96c 2) Platform: CentOS Linux release 7.4.1708 (Core) 3) uname -a: Linux host 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

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Goodness of fit
by Sarah Cole 20 Feb '18

20 Feb '18

Hi Doug, I have used spmhrf 0 in my FS-FAST analysis. I was wondering if there is any way to check the variance explained and fits on the model? Thank you, -S

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Error in running make_average_subject
by M Janani 20 Feb '18

20 Feb '18

Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt relabeling unlikely voxels interior to white matter surface: norm: mri/norm.mgz XFORM: mri/transforms/talairach.m3z GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /home/lakshman/freesurfer/subjects subject avgsubject1 outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white Reading lh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial Loading lh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Reading rh white surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white Reading rh pial surface /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial Loading rh annotations from /home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from Could you please help us in resolving the issue. Have also attached the recon-all log for reference. Thanks & Regards, Janani ::DISCLAIMER:: -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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Segmenting the Corpus Callosum
by Benjamin Yeske 20 Feb '18

20 Feb '18

Hello Freesurfer Experts, I was looking through your website to see if I could find any info/papers that explained what landmarks you use for segmenting the corpus callosum, but I couldn't find anything on the topic. Could you please point me to a paper or resource that explains how freesurfer captures the corpus callosum and what landmarks it use to segment it out? We'd like to be able to hand check this region for accuracy in our TBI patients brain scans. Thank you, Ben

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Requesting to unsubscription
by neha hooda 20 Feb '18

20 Feb '18

Dear Admin , Can you please remove me from the mailing list of freesurfer. With warm regards Neha

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mris_flatten error: bad vertex
by Ji Won Bang 20 Feb '18

20 Feb '18

Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d So I think I made the patch correctly. ! weird thing that I suspect is that when I click save patch as, the default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf Could you please help me? Thanks a lot! Best, Ji Won

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V6.1
by Eduard Vilaplana Martinez 20 Feb '18

20 Feb '18

Dear freesurfer experts, Some days ago I unexpectedly found a thread (about including the flair in the pipeline) in which you mentioned the v6.1. In my lab we are thinking about doing the major 5.1 to 6.0 upgrade, but given that we have a huge database of subjects N~2000) we are wondering about the status of the 6.1 version. Is there any estimation about the v6.1 release? And based on that, would you wait for the v6.1? Thanks in advance, Best,, Eduard. Memory Unit, Neurology Dept. Hospital de la Santa Creu i Sant Pau, Sant Antoni Maria Claret 167 Barcelona, Spain

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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 20 Feb '18

20 Feb '18

Dear Iglesias, We set up our our hippocampal subfield T2 protocol based on the ADNI protocol (with some minor differences). However, we see an artefact similar to the image found in ADNI2 training manual (page 28): http://adni.loni.usc.edu/wp-content/uploads/2012/10/ADNI2MRITrainingManual_… Please see the hyperintense artefact in the anterior part of the sagittal and axial images. Do you also see this artefact in your images? Do you have any idea about the cause of the artefact or do you have any suggestion on how to get rid of it? Thanks, Gabor <petzinger.gabor(a)gmail.com>

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Re: [Freesurfer] Question regarding exporting subcortical segmentation to
by Simon, Joe 20 Feb '18

20 Feb '18

Hi Bruce Thanks, mri_binarize works great! Best, Joe ---------------------------------------------------------------- Dr. Dipl.-Psych. Joe Simon Universitätsklinikum Heidelberg Klinik für Allgemeine Innere Medizin und Psychosomatik Im Neuenheimer Feld 410 69120 Tel.: ++49(0)6221-56-38667 joe.simon(a)med.uni-heidelberg.de ---------------------------------------------------------------- Date: Thu, 15 Feb 2018 12:08:12 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question regarding exporting subcortical segmentation to .nii ROIs for further analysis in SPM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1802151207140.11691(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Joe you can use mri_convert to convert the .mgz volume to nifti if that is what you want: mri_convert aseg.mgz aseg.nii.gz should do the trick. Not sure if that counts as an ROI for SPM. If you want separate volumes for each structure I think you can use mri_binarize with the --match flag cheers Bruce

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Re: [Freesurfer] Read 13, expected 64, could not read .nii.gz as type 24
by Ben Smith 19 Feb '18

19 Feb '18

Thanks for your help on this! It was a corruption problem, just as you said- didn't seem to be a disk space problem, but I deleted the file, re-ran, and things went fine. Cheers Ben _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz On Mon, Feb 19, 2018 at 9:11 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Ben > > we find the CC as the region where there is the largest left/right WM > connection. We then orient it to be vertical and find principle directions, > and divvy it up into however many segments you want (I think the default is > 5 but this can be changed). We then grow it out laterally as far as your > specify > > cheers > Bruce > > > On Mon, 19 Feb > 2018, Benjamin Yeske wrote: > > > Hello Freesurfer Experts, > > I was looking through your website to see if I could find any > info/papers that explained what > > landmarks you use for segmenting the corpus callosum, but I couldn't > find anything on the topic. > > Could you please point me to a paper or resource that explains how > freesurfer captures the corpus > > callosum and what landmarks it use to segment it out? We'd like to be > able to hand check this region > > for accuracy in our TBI patients brain scans. > > > > Thank you, > > Ben > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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