Re: [Freesurfer] FreeSurfer relevance for studying structures other than the bra
Howdie Doug, We are interested in studying not the ventricles, per say, but the actual cells and components of the cells that comprise these ventricles. For example, cells from a heart, spleen, sperm, or cochlea. Since we are not using an MRI machine to obtain the images, is FreeSurfer of no use to us? (You said it handles only TI-weighted MRI data). Additionally, you mentioned in a previous correspondence that as our files traverse along the data stream in FreeSurfer, they will ultimately be converted into 8-bit format. However, since we need the files in 16-bit format, would this be a deal-breaker as well? Thanks. Greg _ http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_pcmag_0507 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Is converting to mgz conducive for 16-bit files?
Greetings, The data at this lab initially comes in a RAW data format. When converted to 16-bit TIFF files, the quantitative data is retained. I recognize that, in order for FreeSurfer to be of use, this data must be converted to mgz files. However, does the process of converting this information into the mgz format allow me to maintain quantitative data that is retained when converting to 16-bit TIFF files? Or does this process of converting to mgz files only ensure proper retention of data for 8-bit files? Thank you for your time and advice. Greg _ http://imagine-windowslive.com/hotmail/?locale=en-us&ocid=TXT_TAGHM_migration_HM_mini_pcmag_0507 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer relevance for studying structures other than the brain
Greetings, I am attempting to use FreeSurfer/Slicer to study data from a mass sprectrometer. To be of use, the segmentation capability of FreeSurfer/Slicer has to be based on quantitative data, not morphology. It appears as if FreeSurfer uses a generic mapping of the brain's structure as a starting point for the model it generates. However, for one seeking to study a structure other than the brain, this can be a concern. Can FreeSurfer/Slicer accommodate data whose source is not an MRI and or of the brain? This concern also stems from the file entitled "SlicerTraining06_vtkFreeSurferReaders.ppt" provided on a Slicer site that has about a dozen tutorials for Slicer 2.6 (this is one of them). On Slide #25, entitled 'Determining label numbers in an ASEG file', there is a list of the first 30 sections created and various parameters. The names of these sections seem to be predetermined (i.e., Left Cerebral-Exterior, Left Cerebral-White-Matter, Left Cerebral-Cortex, etc.). This seems to imply that FreeSurfer/Slicer know what to look for from the onset and thus the segementation is not based solely on quantitative data. Please let me know if these conclusions are warranted. If I am mistaken, please advise as to why. Thanks for your time and advice, Greg _ Need a brain boost? Recharge with a stimulating game. Play now! http://club.live.com/home.aspx?icid=club_hotmailtextlink1 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] 3D volume generation, ROI selection, subvolume analysis
Howdie Bruce, At this lab (NRIMS in Cambridge, MA; www.nrims.harvard.edu), the machine provides a stack of images that, when reassembled, can replicate the entity (i.e., nucleus) being studied. We have been able to read these images into Slicer as TIFF files as well as in the raw data format produced by the machine. After generating a 3D representation of the entity (presumably with FreeSurfer), we want to be able to segment areas of interest within this volume (comparable to focusing on the hypothalamus in the brain, but the boundaries may be user-defined and not anatomically-defined i.e. only part of the hypothalamus), and have the program automatically generate ROIs based on pixel count/size. The pixels contain quantitative information and thus their value cannot be tampered with. Papers that you have published (Whole Brain Segmentation (2002); Automatically Parcellating (2004); Sequence Independent Segmentation (2004); Cortical Surface-Based Analysis I . (1999)) attest to the feasibility of this endeavor to automatically generate ROIs. We already have the ability to manually draw ROIs with a separate program. But, analogous to the example of MR technicians you referred to in several of these papers, this process is time-consuming. Knowing that the method you devised is as if not more accurate than those trained to do so is reassuring, especially since those here who would manually draw ROIs are not as specialized in this practice like MR technicians. But the details of the actual process referred to in these papers can be left for another day. Before that time comes, more basic problems have to be solved. The online tutorial that incorporates Slicer and FreeSurfer (link on http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101) shows how volumes/surfaces are generated in FreeSurfer from the 3 orthogonal planes in Slicer. Since we have been able to read our images into Slicer, we are now seeking to take the next step of generating volumes and surfaces from the 3 planes in Slicer. However, there are several potential hindrances I foresee that could be deal-enders. I am hoping that you can either verify such a conclusion or provide a means of getting around these potential roadblocks. First is the issue of file format. To maintain the quantitative data contained in the images, we have to work with either the raw data format that is generated by the machine or with 16-bit TIFF files that have been converted from this raw data. Other formats risk losing or will flat out lose the information that has to be preserved. Slicer has been able to read the TIFF and raw data formats, but in a previous correspondence with a user on 07-27-06, you noted that FreeSurfer does not support TIFF files. 11 months later, is this still the case or has the program been modified to accept files in TIFF format? In your reply to this user, you said that FreeSurfer supports MRI volumes as input. The online demo for incorporating FreeSurfer referred to above has screen shots from Slicer. So if we can read our data as TIFF files into Slicer and save the collection of these TIFF files as a volume file, would FreeSurfer be content to read it as a volume file rather than as a collection of TIFF images? Second, it seems like the aseg file is crucial for the generation of 3D surfaces and volumes. Is this file provided by the MRI machine? (If so, we likely have been stopped in our tracks.) Or is there a way I can create an aseg file from the cross-sectional images I have? (My impression is that this aseg file provides the boundaries for the surfaces/volumes to be generated.) Thanks again. Greg _ Need a break? Find your escape route with Live Search Maps. http://maps.live.com/default.aspx?ss=Restaurants~Hotels~Amusement%20Park&cp=33.832922~-117.915659&style=r&lvl=13&tilt=-90&dir=0&alt=-1000&scene=1118863&encType=1&FORM=MGAC01 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] 3D volume generation, ROI selection, subvolume analysis
Good morning, We have been working on Slicer and have been able to read in our stack of images. I can view them at the desired cross-sections by moving the three planes at will. But now we would like to be able to generate a 3D volume (in this case a rectangular prism) that contains all of these images in the stack. Once this is assembled, we are interested in being able to have Slicer/Free Surfer select ROI's or do so ourselves and be able to analyze these subvolumes from within the prism itself. Before I delve to deeply into FreeSurfer, I just wanted to make sure that it was capable of providing these capabilities and that Slicer cannot do them on its own. Are there any resources that I could access to aid me that are not accessible through the main FreeSurfer site: http://surfer.nmr.mgh.hardvard.edu/fswiki ? Could you give me a few quick pointers to get me started? Thanks a lot. Greg _ Picture this share your photos and you could win big! http://www.GETREALPhotoContest.com?ocid=TXT_TAGHM&loc=us ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
