Freesurfer

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30084 discussions

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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Problem Installing FS
by Millan, Carlos 01 Mar '16

01 Mar '16

Hi Zeke, I do have a file named license.txt in my FREESURFER_HOME directory as well as another one named LICENSE that comes with the FS installation. When I type: $> cd /Applications/freesurfer $> ls -l license.txt What happens is this: -rw-r--r--@ 1 carlosmillan staff 55 Feb 26 12:25 license.txt Does it mean I already have the license installed but I do not have administrator privileges and that’s why I’m not able to run FS? At this point I’m calling IT here at UM to see if that’s the problem, which is possible because it is not allowing me to use “sudo” either and the system says “sorry” after typing my password. Thanks, Carlos

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Corrupted head surface with mkheadsurf?
by Maheen Siddiqui 01 Mar '16

01 Mar '16

Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen

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Problem Installing Freesurfer
by Millan, Carlos 01 Mar '16

01 Mar '16

Dear Freesurfer Team, I am a researcher here at University of Miami and recently downloaded Freesurfer to do Cortical Thickness analysis. Unfortunately, I have followed the installation steps very carefully as indicated on your web page but I do not know if there is a security issue on this Mac or what is it? But when I am trying to test freesurfer I get a message that says "license not found". I have tried to install the license by copying and pasting the license text I received (license.txt) into the $FREESURFER_HOME directory but it did not work; so I tried to write the commands “cd /Applications/freesurfer” and then “pico license.txt”. In the next window I also pasted the license and then I saved the changes in pico, but that did not work either. Is there anything else I should do? I am attaching some screenshots from the terminal. Maybe those help you assessing the problem. Thank you, Carlos Millan Research Assistant Epilepsy Division – Neurology Department University of Miami [cid:D9BCD62E-EF2A-49DD-BC1F-A770010B9731]

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Seeking postdoctoral candidates for datascience positions
by Satrajit Ghosh 01 Mar '16

01 Mar '16

We are seeking two postdoctoral computational/data scientists with a PhD in computer science, electrical or biomedical engineering, neuroscience, statistics, or related fields to apply for positions in the McGovern Institute for Brain Research at Massachusetts Institute of Technology. The projects cover a broad array of neuroinformatics. - Datamining of gene-behavior-anatomy relationships - Architecting next generation dataflow systems - Reproducible research platforms and applications - Nonlinear image and other high-dimensional registration - Predictive analytics in mental health - Linked data platforms Working on these projects will involve collaboration partners within and across regional and international institutions. Candidates are expected to develop algorithms and prototype ideas, contribute to opensource tools, and perform software engineering, testing, and validation. Candidates will have the opportunity to mentor undergraduate and graduate students, and contribute to datascience at MIT. The ideal candidates will have strong computational skills, enjoy collaborating, and be able to adapt to and adopt a diverse set of technologies. A documented PhD in computer science, electrical or biomedical engineering, neuroscience, statistics, or related field is required before starting this position. Positions are available for one year, with a possibility of yearly extension depending on performance and funding. For inquiries please contact Satrajit Ghosh (satra(a)mit.edu)

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