Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Topological White Matter Correction
by Kiersten Snyder 02 Mar '16

02 Mar '16

Hello FreeSurfer Experts, What image processing technique is behind the Topological White Matter Correction to correct topological defects? Is it true that FreeSurfer take into account your edits as a "suggestion" and incorporates into some type of algorithm? I would like to have a more thorough understanding of the image processing that this function utilizes. Thanks for the help! Kiersten

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hippocampus subfields
by Kanel, Prabesh 02 Mar '16

02 Mar '16

Freesurfer List, I ran recon-all to segment hippocampus subfield using the development version of freesurfer.V6.Beta. To get the better segmentation, I have used both T1 and T2 images. But for some of the scans, the process stops at a point and doesn't seem to progress further. That happens in only a few cases and only when the data are run using the flag -hippocampal-subfields-T1T2. I have attached a log file of one of the case in this email. Another query that I have is to get T2 segmented subfields images (one with intensity values rather than labels). Is there an easier way to get T2 subfields segmented images using the segmentation volumes and T2.FSspace.mgz. Sorry, if this question seems too trivial. Regards, Prabesh

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Unknown option DKTatlas40
by marmaduke woodman 02 Mar '16

02 Mar '16

hi I'm using the dev version of FreeSurfer on 64-bit Fedora 23. Recon-all runs fine but at the end I see $ recon-all -s tvb -aparc2aseg ... mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40 ERROR: Option --DKTatlas40 unknown Running that command $ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos without the --DKTatlas40 appears to run correctly. Is this just an issue with the dev version or have I done something silly? thanks, Marmaduke ps bugr output FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229 RedHat release: Fedora release 23 (Twenty Three) Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64

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Re: [Freesurfer] running two versions of fs in the same
by Fengji Geng 01 Mar '16

01 Mar '16

Hi Bruce, The command that we ran is recon-all. Below is the error msg: mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = HMN122 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Invalid argument ERROR reading /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN122 exited with ERRORS at Tue Feb 23 16:40:01 EST 2016 ---------------------------------------------------------------------------------- Hi Fengji you need to give us more details about the problems before we can help you. What commands failed? What was the screen output? Note that there is still no such thing as FS 6.0. We are hoping to have it in the relatively near term, but it doesn't exist yet. cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: > Dear fs developers,? > > we are attempting to use the stable version of fs 5.1 for processing while > also using the most current version for hippocampal segmentation on the same > set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when > the develop version of fs 6 was installed, we began having an issue with the > fsaverage folder linking to the newest version, when we need it to link to > version 5.1 during processing. The label files that we need for processing > in version 5.1 are not accessible in the new version?s fsaverage > folder.?However, before we updated to fs 6.0 dev version on 28-Jan-2016, we > never had this issue. So, we are wondering if the newest develop version of > fs 6.0 does not allow?two versions of fs to be used in the same data.? > > Looking forward to hearing from you and thanks in advance. > > Best, > > ----- Fengji --- Fengji

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mri_label2vol projfrac missing voxels
by dgw 01 Mar '16

01 Mar '16

Hi, I am having trouble with the projfrac option in mri_label2vol (on the current dev freesurfer environment). When I use the following command: mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1 .01 I get many missed voxels from the gray matter (see the attached image, with the yellow representing the label overlaid on the ribbon.mgz). I have tried more extreme delta values and this doesn't help. (note scrolling to nearby slices indicates the neighboring voxels are included, so it isn't from the angle projecting oddly (that is why I took a slice from the middle of this large label)). Is there a better way to convert the annotation to a volume just in the gray matter, but including all of the relevant voxels? Is there a fundamental algorithmic difference between mris_volmask and mri_label2vol? If yes, why? Thanks, D

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running two versions of fs in the same dataset
by Fengji Geng 01 Mar '16

01 Mar '16

Dear fs developers, we are attempting to use the stable version of fs 5.1 for processing while also using the most current version for hippocampal segmentation on the same set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop version of fs 6 was installed, we began having an issue with the fsaverage folder linking to the newest version, when we need it to link to version 5.1 during processing. The label files that we need for processing in version 5.1 are not accessible in the new version’s fsaverage folder. However, before we updated to fs 6.0 dev version on 28-Jan-2016, we never had this issue. So, we are wondering if the newest develop version of fs 6.0 does not allow two versions of fs to be used in the same data. Looking forward to hearing from you and thanks in advance. Best, ----- Fengji

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Re: [Freesurfer] Entorhinal Cortex segmentation and volume
by Bruce Fischl 01 Mar '16

01 Mar '16

Hi Melina Sorry for the delay in responindg, can you tell us a bit more about the acquisition? They look very grainy and low contrast. Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: > Thank you both for your respond. > 1. I have attached you some pictures. Like douglas wrote it corresponds to > white matter in aseg, but is more often labelled as "none" than "cortex > unknown". So is this "normal" and can I trust those borders? Or would you > rather advise to control aseg and aparc segmentation to estimate the > entorhinal cortex segmentation? > > 2. You're right, Bruce, in freeview the exvivo label it just follows the > surface. So I'll try mri_label2vol. > > Cheers Melina > > Am 16.02.2015 um 16:33 schrieb Douglas Greve: >> On 2/16/15 9:31 AM, Bruce Fischl wrote: >>> Hi Melina >>> >>> 1. Can you send us a picture? I'm not sure given your description, >>> although the surfaces can be arbitrary in the hippocampus/amygdala and >>> should be ignored there. >> This corresponds to the "cortex unknown" label in aparc (and is >> probably labeled WM in the aseg). This is normal. >>> 2. You should be able to use mri_label2vol for this. Note that you can >>> load >>> the label itself directly into freeview if you want without needing to run >>> label2vol (but it will follow the white surface I believe and not fill the >>> ribbon) >>> >>> cheers >>> Bruce >>> >>> On Mon, 16 Feb 2015, Melina Lehnerer wrote: >>> >>>> Hi experts, >>>> I'm rather unexperienced with freesurfer so please excuse my basic >>>> requests. >>>> 1. I controlled the segmentation of the entorhinal cortex (EC) in over >>>> 50 subjects following the borders described in Fischl 2009 (Predicting >>>> the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg >>>> aparc-aseg.mgz. >>>> I noticed (esp. in the coronar slices and in approximately every mri) >>>> brain tissue between amygdala/ hippocampus/ temporalpole and the EC >>>> labelled as "none" or "ctx-?h-unknown". Has anything gone wrong with the >>>> segmentation? Or is a label (e.g. perirhinal cortex) not loaded? >>>> >>>> 2. Is there a possibility to visualize the EC volume in freeview or >>>> tkmedit from the exvivo.stats or exvivo.label file? I would like to >>>> compare it to the other EC volume because they have very different >>>> volumes. In the mail archive were similar questions about that but you >>>> haven't answered them yet. >>>> >>>> Many thanks in advance, >>>> Melina >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> 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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Very urgent matlab command line to transform vol to label.
by stdp82＠virgilio.it 01 Mar '16

01 Mar '16

Hi list,I have read on your mail list that I could use the command line reported below to covert vol to label.I'm confused on the matlab command line.Specifically, if I using an MRS voxel (in native space or MNI, as preferred) located bilaterally of 3.0x3.0x3.0 mm, which are lindex, lxyz, ovals? v = load_mgh('file_created_by_vol_2_surf.mgz'); ind = find(v > threshold); write_label(ind-1, [], v(ind), 'label_file_want_to_create'); Thanks,Stefano

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Fwd: View several Annot files in Tksurfer
by Faeze Vedaei 01 Mar '16

01 Mar '16

Hi Freesurfer Experts, In order to view specific annot files by tksurfer in Freesurfer, I used mris_label2annot command to create annot files based on Destrieux atlas. Now, I can import annot file in tksurfer, but just one file at the time. My aim is to view several annot files by their specific colors in tksurfer simultaneously. May you help me how can I do this? In advance, I'd appreciate your consideration. Regards, Faezeh Vedaei

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-qcache of v5.0 data with newer versions
by Daniel Ferreira 01 Mar '16

01 Mar '16

Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani

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Freesurfer March 2016