[Freesurfer] Announcement of HBM satellite conference on the DMN and other Intrinsic Networks

Dear FreeSurfer list, Just to let you know that soon it will be a conference on the Default Mode and other intrinsic networks in Barcelona. It is a satellite of the HBM conference. Please, take a look at the program (see links below) since many interesting people are comming to present their lates

[Freesurfer] Question about cortical surface area

Hi everyone, I had two questions: 1) I was wondering if it's ok to run a glm to compare cortical surface areas between two groups on a vertex-wide basis (just like a thickness analysis). Or is it better to extract the area of a label (as is the output of mri_anatomical_stats)? 2) The mri_ana

[Freesurfer] Group comparison -qdec clarification

Dear All, I want to perform group comparison of cortical thickness between my patient and control group. I read qdec tutorial regarding how to do this. I was little bit puzzled and not able to understand the following. Before creating qdec table of patient data, fsaverage was suggested to run,

Re: [Freesurfer] Question about cortical surface area

Hi Massieh, There were some posts related to this a while back. If I recall correctly, the vertex-wise area measure (and likewise the vertex-wise volume measure) is highly dependent on the local mesh triangulation, and thus is not really a meaningful variable from a biological perspective. So, yo

[Freesurfer] converting label to binary mask.mgh

Hello All, I have created a V1 label using Hinds and Fischl Method. Is a label a .mgh file as well ?? How do I convert this label to a binary mask mgh file ? Please let me know. Thanks much Rito ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

Re: [Freesurfer] converting label to binary mask.mgh

Try mri_label2vol doug Ritobrato Datta wrote: > Hello All, > > I have created a V1 label using Hinds and Fischl Method. Is a label a .mgh > file as well ?? > > How do I convert this label to a binary mask mgh file ? > > Please let me know. > > Thanks much > > Rito > > __

[Freesurfer] error while unzipping SuSE Itanium release

Hi there, I am getting the following error when unzipping the SuSE Itanium release: "tar: Archive contains obsolescent base-64 headers" Any help is appreciated. Thank you in advance, Regards, Amir -- Amir M. Tahmasebi, Ph.D. Medical Image Analysis Lab. Schoo

Re: [Freesurfer] error while unzipping SuSE Itanium release

Hi Amir 1. Try and check if the file you downloaded has the md5 checksum listed here -- http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/md5sum.txt For the Suse Itanium one, the string of characters you are looking for is "e064d9a8b08dc10ecc57d1b60f0094f" To find out the md5, use the co

[Freesurfer] ICV meaning...

Hi: Which is the meaning of the Intracaranial Volume (ICV) ?... it includes only the brain, or also the skull ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel

[Freesurfer] ICV meaning...

Hi: In aseg.stats file, appears "lh-cerebral-white-matter" and "Left-Cerebral-White-matter": which are the difference between both values?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las

Re: [Freesurfer] ICV meaning...

One is volume-based (Left-Cerebral-White-matter) and one is surface-based. Use the surfacse-based one. In the next version of FS, the volume-based one will no appear. doug Gonzalo Rojas wrote: > Hi: > >In aseg.stats file, appears "lh-cerebral-white-matter" and > "Left-Cerebral-White-matter

Re: [Freesurfer] ICV meaning...

it is everything inside the skull (including brain, csf, etc...) On Wed, 28 Apr 2010, Gonzalo Rojas wrote: > Hi: > > Which is the meaning of the Intracaranial Volume (ICV) ?... it > includes only the brain, or also the skull ?... > > Sincerely, > > > Gonzalo Rojas Costa > Laboratory for Advan

Re: [Freesurfer] ICV meaning...

note that this is an estimate based on the talairach registration. We do not actually measure the icv Bruce Fischl wrote: > it is everything inside the skull (including brain, csf, etc...) > On Wed, 28 > Apr 2010, Gonzalo Rojas wrote: > > >> Hi: >> >> Which is the meaning of the Intracarani

Re: [Freesurfer] error while unzipping SuSE Itanium release

Thanks a lot. It worked. Amir Krish Subramaniam wrote: > Hi Amir > > 1. Try and check if the file you downloaded has the md5 checksum > listed here -- > http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/md5sum.txt > > For the Suse Itanium one, the string of characters you are looking for

[Freesurfer] error running recon-all

Hi there, I am using the SuSE Itanium release and when running "recon-all", I am getting the following error: "mri_convert: cannot execute binary file" Any clue? Thanks in advance, Regards, Amir Amir M. Tahmasebi, Ph.D. Medical Image Analysis Lab. School of Computing, Queen's University, Ki

[Freesurfer] converting dicom files into mgz, looking forward to some help, thank you!

Dear Freesurfers: i failed every time i tried to transform my dicom GE structrual images into mgz format, because i am quite new for this software, so i'd like to ask some help from you. i will be very grateful if you can tell me what the reason is, or give me some suggestions on how to