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T1 and brainmask wonky: Pieces of putamen missing
by diana hobbs 20 Nov '17

20 Nov '17

Hello FreeSurfer Developers, I am running Recon1 to check/edit the Talairach and Brainmask. The process exits without error; however, I'm finding issues when I open T1.mgz and brainmask.mgz in freeview. Chunks of putamen seem to be boxed out as white matter, but this is not evident in the other files (orig.mgz or nu.mgz). Please see the attached images. The following is the code I am using: #007 recon-all -autorecon1 -subjid TEST007 -i [T1 file] -T2 [T2 file]; - freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - Linux MSI 4.4.0-43-Microsoft #1-Microsoft Wed Dec 31 14:42:53 PST 2014 x86_64 x86_64 x86_64 GNU/Linux - Recon-all.log; see attached. I haven't come across this error in my searches, but I may be using the wrong key terms. Would anyone be able to point me in the right direction or trouble-shoot fixing this? Thank you for your time, Diana <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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% overlap of multiple labels
by Yagmur Ozdemir 19 20 Nov '17

20 Nov '17

Hello Freesurfer experts, I am using the mris_compute_parc_overlap command to compute the % overlap of two labels of the same region. Is there a way to do this for multiple labels? Best Idil

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recon-all on previously segmented volumes
by Mcnorgan, Christopher 20 Nov '17

20 Nov '17

Hi, I’m having some issues generating surfaces for an individual and was hoping that a combination of tools might help. In this particular individual, the skull stripping went fine, but a fairly large proportion of the anterior temporal cortex (primarily inferior) volume is excluded from the data. My hunch is that it has to do with the fairly low contrast present in the images. Nonetheless, I had also worked on the data in SPM which did a fine job segmenting the wm/gm/other voxels when I inspect them as overlays in a program like MRICron. I tried an experiment wherein I used the SPM segmented volumes to create a composite brainmask.mgz where the wm voxels were set to exactly 110, the gm voxels were set to a somewhat lower value (I used element-wise multiplication, so the voxels vary in value, but were around 70-100) and all other voxels were set to 1. The resulting volume looks like a meticulously cleaned brain mask. Unfortunately, recon-all -autorecon-pial didn’t work any better afterwards. So that experiment was a dud. Assuming I can manipulate/combine the images in any manner, is there a way to take advantage of the segmented volumes that I was able to obtain from SPM? If I am going to be processing the data in SPM anyways, it would seem that having this information would make the process of tessellating the white and grey matter surfaces trivial. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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[Talairach failed when striping skull]
by Yi Li 20 Nov '17

20 Nov '17

Hi FS expert, When I run recon-all -autorecon1 -subjid <subjid>, the Talaitach transform failed. Please see the attached log file. Is there a way to correct the error? Thanks! Best Regards, Yi -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, November 13, 2017 5:48 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [strip skull for unregistered images] Hi Yi yes, brainmask.mgz is the skull stripped image. And no, n3 is pretty gentle so I would think letting our normal intensity normalization run would be fine (and better than not doing it) cheers Bruce On Mon, 13 Nov 2017, Yi Li wrote: > Hi Bruce, > > Thanks for the help! Is the skull-stripped image in Brainmask.mgz? > > Another question: since my raw image has gone through B1 correction > and > N3 normalization, will you suggest I omit the nu and normalize step in > -autorecon1? > > Best Regards, > Yi > > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Monday, November 13, 2017 10:50 AM > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [strip skull for unregistered images] > > Hi Yi > > autorecon1 should do the skull stripping, so there is no need for the > separate mri_mask call. The threshold of '5' is so to preserve edits > in which voxels are turned 'off' (they are set to 1 I believe, but we > reserve > 2-4 as additional 'off' values). > > The masking will not transform the voxel coordinates of the image > > cheers > Bruce > > > On Mon, 13 Nov 2017, Yi Li wrote: > >> >> Dear FS experts, >> >> >> >> I would like to strip skulls from unregistered images which have gone >> through GradWarp, B1-correction, N3 normalization and phantom-based scaling. >> I run the following two commands in freeSurfer: >> >> recon-all -autorecon1 -subjid <subjid> >> >> mri_mask -T 5 T1.mgz brainmask.mgz T1.final.mgz >> >> >> >> My questions are >> >> 1) Currently I use 5 as threshold (-T 5). Is there a guidance >> for the setting of this parameter? >> >> 2) In the output file T1.final.mgz, is the skull-stripped image >> represented in ijk space (image index space) or in XYZ space (via >> transformation matrix)? >> >> 3) If the skull-stripped image is represented in XYZ space, how >> do I get it in ijk space? >> >> >> >> Thanks in advance for the help! >> >> >> >> Best Regards, >> >> Yi Li (PhD) >> >> Senior Computational Scientist >> >> Computational Sciences >> >> The Jackson Laboratory >> >> Farmington, CT 06032 >> >> Tel: 860-837-2156 >> >> >> >> --- >> >> The information in this email, including attachments, may be >> confidential and is intended solely for the addressee(s). If you >> believe you received this email by mistake, please notify the sender >> by return email as soon as possible. >> > --- > > The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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XL Defect Detected
by Arsenije Subotic 20 Nov '17

20 Nov '17

Dear Freesurfer experts, I was processing one of my subjects, but ran into a problem as a XL Defect was detected. The following output was seen (attached screenshot). From examining all of my volumes it seems that they are tilted a bit, but I'm not sure if that is the reason. Thank you for your help. Best, Arsenije

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Re: [Freesurfer] TRACULA
by Yendiki, Anastasia 19 Nov '17

19 Nov '17

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eTIV as a covariate
by 郑凤莲 18 Nov '17

18 Nov '17

Hi Professor, I ran three steps of "recon-all" and get the cortical thickness, surfarea, GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use SPSS software for statistics， should I use eTIV as a covariate for everyone? Thank you very much. Sincerely, Zheng

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(无主题)
by 郑凤莲 18 Nov '17

18 Nov '17

Hi Professor, I ran three steps of "recon-all" and get the cortical thickness, surfarea, GrayVol in lh.aparc.stats and subcotical volume in aseg.stats. If I want to use SPSS software for statistics.

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hippocampus subfields
by 郑凤莲 18 Nov '17

18 Nov '17

Hi professor, I am using Freesurfer for DTI data. When I run 'mri_segstats', I got the result that there was anobvious difference in left hippocampus, but no difference in right hippocampus. Then, I run segmentation of hippocampus subfields.The result showed there is no difference in total left or right hippocampus, and only in two right hippocampus subfields has significant difference. Why is there inconsistent result in two means? Thank you very much. Sincerely, Zheng

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Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
by Manoj Kumar 18 Nov '17

18 Nov '17

Hello Dear Sir/Madam, Please provide your expert suggestions to resolve the above-mentioned error. Thank you very much, Best regards Manoj On Sat, Nov 18, 2017 at 11:05 AM, Manoj Kumar <vermanojk(a)gmail.com> wrote: > Hello Dear Sir/Madam, > > I am fairly new to the freesurfer and am getting an error "ERROR: > mpr2mni305 failed, see transforms/talairach_avi.log" > > When I run the "recon-all -all -subjid Anj commond. > > I looked for this error message on https://mail.nmr.mgh. > harvard.edu/pipermail//freesurfer/2014-August/039761.html > But could not resolve this issue by myself. > I am here also attaching the complete error log and recon-all-error file > for your find attention. > > Please kindly provide your expert suggestions to resolve this issue. > Please let me know if you need any additional information for further > diagnosis of the error. > > Thank you very much for all your help and support. > > Best > >

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